@article {pmid31228837, year = {2019}, author = {Dhaouefi, Z and Toledo-Cervantes, A and Ghedira, K and Chekir-Ghedira, L and Muñoz, R}, title = {Decolorization and phytotoxicity reduction in an innovative anaerobic/aerobic photobioreactor treating textile wastewater.}, journal = {Chemosphere}, volume = {234}, number = {}, pages = {356-364}, doi = {10.1016/j.chemosphere.2019.06.106}, pmid = {31228837}, issn = {1879-1298}, abstract = {The potential of a novel anaerobic/aerobic algal-bacterial photobioreactor for the treatment of synthetic textile wastewater (STWW) was here assessed. Algal-bacterial symbiosis supported total organic carbon, nitrogen and phosphorous removal efficiencies of 78 ± 2%, 47 ± 2% and 26 ± 2%, respectively, at a hydraulic retention time (HRT) of 8 days. A decrease in the HRT from 8 to 4 and 2 days resulted in a slight decrease in organic carbon and phosphate removal, but a sharp decrease in nitrogen removal. Moreover, an efficient decolorization of 99 ± 1% and 96 ± 3% for disperse orange-3 and of disperse blue-1, respectively, was recorded. The effective STWW treatment supported by the anaerobic/aerobic algal-bacterial photobioreactor was confirmed by the reduction in wastewater toxicity towards Raphanus sativus seed germination and growth. These results highlighted the potential of this innovative algal-bacterial photobioreactor configuration for the treatment of textile wastewater and water reuse.}, } @article {pmid31227910, year = {2019}, author = {Babadi, M and Zalaghi, R and Taghavi, M}, title = {A non-toxic polymer enhances sorghum-mycorrhiza symbiosis for bioremediation of Cd.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-019-00902-5}, pmid = {31227910}, issn = {1432-1890}, support = {96/3/02/16670//Shahid Chamran University of Ahvaz/ ; }, abstract = {In this study, the effect of a mycorrhizal symbiosis on the translocation of Cd from Cd-polluted soil to sorghum roots was investigated using rhizoboxes. A factorial experiment (two factors including fungus inoculation and Cd contamination) in a completely randomized design with three replicates was performed. In the rhizobox rhizosphere compartment, plants were cultivated in uncontaminated soil and mycorrhizal inoculation (inoculated with Claroideoglomus etunicatum or non-inoculated) was performed, and in the other compartment, the soil was contaminated with Cadmium (Cd) at one of three levels (0, 100 mg kg-1 using a non-toxic organic polymer (poly (N-vinyl succinate))-Cd, or 100 mg kg-1 using Cd-nitrate). Cd pollution resulted in a significant decrease in shoot dry weight (from 7.52 to 6.18 and 6.68 g pot-1, from control to polymer-Cd and nitrate-Cd respectively), root mycorrhizal colonization (from 32.33% to 8.16% and 8.33%), shoot phosphorus concentration (from 3.14 to 2.80 and 2.76 g kg-1), and soil carbohydrate (from 12.05 to 10.74 and 10.24 mg g-1), and also resulted in significant increases in soil glomalin (from 595.55 to 660.52 and 690.39 μg g-1). The use of mycorrhizal fungi increased the glomalin content of the soil and improved the studied parameters. The results revealed the key role of Claroideoglomus etunicatum in translocation of Cd in the rhizobox and also in precise control of Cd concentration of plant tissues (increase or decrease of them depending on Cd composition and Cd availability). Poly(N-vinyl succinate) increased Cd availability and Cd concentration of shoot tissue (5.19 mg kg-1) compared to nitrate-Cd (3.68 mg kg-1) and could be recommended for improving phytoremediation.}, } @article {pmid31227866, year = {2019}, author = {Mei, YZ and Zhu, YL and Huang, PW and Yang, Q and Dai, CC}, title = {Strategies for gene disruption and expression in filamentous fungi.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-09953-2}, pmid = {31227866}, issn = {1432-0614}, support = {2017YFD0800705//Key Technologies Research and Development Program/ ; Project No31570491//National Natural Science Foundation of China (CN)/ ; }, abstract = {Filamentous fungi can produce many valuable secondary metabolites; among these fungi, endophytic fungi play an ecological role in mutualistic symbiosis with plants, including promoting plant growth, disease resistance, and stress resistance. However, the biosynthesis of most secondary metabolites remains unclear, and knowledge of the interaction mechanisms between endophytes and plants is still limited, especially for some novel fungi, due to the lack of genetic manipulation tools for novel species. Herein, we review the newly discovered strategies of gene disruption, such as the CRISPR-Cas9 system, the site-specific recombination Cre/loxP system, and the I-SceI endonuclease-mediated system in filamentous fungi. Gene expression systems contain using integration of target genes into the genome, host-dependent expression cassette construction depending on the host, a host-independent, universal expression system independent of the host, and reporter-guided gene expression for filamentous fungi. Furthermore, the Newly CRISPRi, CRISPRa, and the selection markers were also discussed for gene disruption and gene expression were also discussed. These studies lay the foundation for the biosynthesis of secondary metabolites in these organisms and aid in understanding the ecological function of filamentous fungi.}, } @article {pmid30642248, year = {2019}, author = {Sibbald, SJ and Hopkins, JF and Filloramo, GV and Archibald, JM}, title = {Ubiquitin fusion proteins in algae: implications for cell biology and the spread of photosynthesis.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {38}, doi = {10.1186/s12864-018-5412-4}, pmid = {30642248}, issn = {1471-2164}, mesh = {Cercozoa/*genetics ; Cryptophyta/*genetics ; Evolution, Molecular ; *Gene Fusion ; Mutant Chimeric Proteins/*genetics ; Phylogeny ; Symbiosis ; Ubiquitins/*classification/*genetics ; }, abstract = {BACKGROUND: The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protein products can evolve new functions. The presence-absence of gene fusions can also be useful characters for inferring evolutionary relationships between organisms.

RESULTS: Here we show that the nuclear genomes of two unrelated single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans, possess an unexpected diversity of genes for ubiquitin fusion proteins, including novel arrangements in which ubiquitin occupies amino-terminal, carboxyl-terminal, and internal positions relative to its fusion partners. We explore the evolution of the ubiquitin multigene family in both genomes, and show that both algae possess a gene encoding an ubiquitin-nickel superoxide dismutase fusion protein (Ubiq-NiSOD) that is widely but patchily distributed across the eukaryotic tree of life - almost exclusively in phototrophs.

CONCLUSION: Our results suggest that ubiquitin fusion proteins are more common than currently appreciated; because of its small size, the ubiquitin coding region can go undetected when gene predictions are carried out in an automated fashion. The punctate distribution of the Ubiq-NiSOD fusion across the eukaryotic tree could serve as a beacon for the spread of plastids from eukaryote to eukaryote by secondary and/or tertiary endosymbiosis.}, } @article {pmid28904377, year = {2017}, author = {Rey, F and Costa, ED and Campos, AM and Cartaxana, P and Maciel, E and Domingues, P and Domingues, MRM and Calado, R and Cruz, S}, title = {Kleptoplasty does not promote major shifts in the lipidome of macroalgal chloroplasts sequestered by the sacoglossan sea slug Elysia viridis.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11502}, pmid = {28904377}, issn = {2045-2322}, mesh = {Animals ; Chloroplasts/*metabolism ; Chromatography, Liquid ; Gastropoda/*physiology ; Glycolipids/chemistry/metabolism ; *Lipid Metabolism ; Mass Spectrometry ; Molecular Structure ; Photosynthesis ; Seaweed/*metabolism ; *Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {Sacoglossan sea slugs, also known as crawling leaves due to their photosynthetic activity, are highly selective feeders that incorporate chloroplasts from specific macroalgae. These "stolen" plastids - kleptoplasts - are kept functional inside animal cells and likely provide an alternative source of energy to their host. The mechanisms supporting the retention and functionality of kleptoplasts remain unknown. A lipidomic mass spectrometry-based analysis was performed to study kleptoplasty of the sacoglossan sea slug Elysia viridis fed with Codium tomentosum. Total lipid extract of both organisms was fractionated. The fraction rich in glycolipids, exclusive lipids from chloroplasts, and the fraction rich in betaine lipids, characteristic of algae, were analysed using hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-LC-MS). This approach allowed the identification of 81 molecular species, namely galactolipids (8 in both organisms), sulfolipids (17 in C. tomentosum and 13 in E. viridis) and betaine lipids (51 in C. tomentosum and 41 in E. viridis). These lipid classes presented similar lipidomic profiles in C. tomentosum and E. viridis, indicating that the necessary mechanisms to perform photosynthesis are preserved during the process of endosymbiosis. The present study shows that there are no major shifts in the lipidome of C. tomentosum chloroplasts sequestered by E. viridis.}, } @article {pmid31219214, year = {2019}, author = {Muletz-Wolz, CR and Kurata, NP and Himschoot, EA and Wenker, ES and Quinn, EA and Hinde, K and Power, ML and Fleischer, RC}, title = {Diversity and temporal dynamics of primate milk microbiomes.}, journal = {American journal of primatology}, volume = {}, number = {}, pages = {e22994}, doi = {10.1002/ajp.22994}, pmid = {31219214}, issn = {1098-2345}, support = {//American Society of Primatologists/ ; //National Institutes of Health/ ; R24OD020347//Smithsonian Competitive Grant for Science/ ; //Directorate for Biological Sciences/ ; DDIG 0525025//NSF/ ; DDIG: 0746320//NSF/ ; RR000169/GF/NIH HHS/United States ; RR019970/GF/NIH HHS/United States ; DK77639//John Capitanio and the California National Primate Research Center/ ; }, abstract = {Milk is inhabited by a community of bacteria and is one of the first postnatal sources of microbial exposure for mammalian young. Bacteria in breast milk may enhance immune development, improve intestinal health, and stimulate the gut-brain axis for infants. Variation in milk microbiome structure (e.g., operational taxonomic unit [OTU] diversity, community composition) may lead to different infant developmental outcomes. Milk microbiome structure may depend on evolutionary processes acting at the host species level and ecological processes occurring over lactation time, among others. We quantified milk microbiomes using 16S rRNA high-throughput sequencing for nine primate species and for six primate mothers sampled over lactation. Our data set included humans (Homo sapiens, Philippines and USA) and eight nonhuman primate species living in captivity (bonobo [Pan paniscus], chimpanzee [Pan troglodytes], western lowland gorilla [Gorilla gorilla gorilla], Bornean orangutan [Pongo pygmaeus], Sumatran orangutan [Pongo abelii], rhesus macaque [Macaca mulatta], owl monkey [Aotus nancymaae]) and in the wild (mantled howler monkey [Alouatta palliata]). For a subset of the data, we paired microbiome data with nutrient and hormone assay results to quantify the effect of milk chemistry on milk microbiomes. We detected a core primate milk microbiome of seven bacterial OTUs indicating a robust relationship between these bacteria and primate species. Milk microbiomes differed among primate species with rhesus macaques, humans and mantled howler monkeys having notably distinct milk microbiomes. Gross energy in milk from protein and fat explained some of the variations in microbiome composition among species. Microbiome composition changed in a predictable manner for three primate mothers over lactation time, suggesting that different bacterial communities may be selected for as the infant ages. Our results contribute to understanding ecological and evolutionary relationships between bacteria and primate hosts, which can have applied benefits for humans and endangered primates in our care.}, } @article {pmid31218790, year = {2019}, author = {Khatabi, B and Gharechahi, J and Ghaffari, MR and Liu, D and Haynes, PA and McKay, MJ and Mirzaei, M and Salekdeh, GH}, title = {Plant-microbe symbiosis: What has proteomics taught us?.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e1800105}, doi = {10.1002/pmic.201800105}, pmid = {31218790}, issn = {1615-9861}, abstract = {Beneficial plant-microbes can have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications which play a critical role in mediating symbiotic plant-microbe interactions and have help to assess the underlying molecular aspects of the symbiotic relationship, including the developmental stages of legume-Rhizobium symbiosis and other non-legume based relationships. Functional proteomics and the study of protein interactions will help provide a better understanding of the protein-protein interaction networks associated with plant-microbe symbiosis and the during the developmental stages of the symbiotic process. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help to define the factors affecting the outcome of symbiosis. In this review, we provide an update on the current and potential applications of symbiosis based "omic" approaches to dissect different aspects of symbiotic plant interactions. We also discuss the application of proteomics, metaproteomics and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities. This article is protected by copyright. All rights reserved.}, } @article {pmid31218402, year = {2019}, author = {Motaharpoor, Z and Taheri, H and Nadian, H}, title = {Rhizophagus irregularis modulates cadmium uptake, metal transporter, and chelator gene expression in Medicago sativa.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-019-00900-7}, pmid = {31218402}, issn = {1432-1890}, abstract = {Arbuscular mycorrhizal fungi (AMF) are considered a potential biotechnological tool for mitigating heavy metal (HM) toxicity. A greenhouse experiment was conducted to evaluate the impacts of the AM fungus Rhizophagus irregularis on cadmium (Cd) uptake, mycorrhizal colonization, and some plant growth parameters of Medicago sativa (alfalfa) in Cd-polluted soils. In addition, expression of two metal chelators (MsPCS1 (phytochelatin synthase) and MsMT2 (metallothionein)) and two metal transporter genes (MsIRT1 and MsNramp1) was analyzed using quantitative real-time PCR (qRT-PCR). Cd addition had a significant negative effect on mycorrhizal colonization. However, AMF symbiosis promoted the accumulation of biomass under both stressed and unstressed conditions compared with non-mycorrhizal (NM) plants. Results also showed that inoculation with R. irregularis significantly reduced shoot Cd concentration in polluted soils. Transcripts abundance of MsPCS1, MsMT2, MsIRT1, and MsNRAMP1 genes were downregulated compared with NM plants indicating that metal sequestration within hyphal fungi probably made Cd concentration insufficient in root cells for induction of these genes. These results suggest that reduction of shoot Cd concentration in M. sativa colonized by R. irregularis could be a promising strategy for safe production of this plant in Cd-polluted soils.}, } @article {pmid31218384, year = {2019}, author = {Della Mónica, IF and Godeas, AM and Scervino, JM}, title = {In Vivo Modulation of Arbuscular Mycorrhizal Symbiosis and Soil Quality by Fungal P Solubilizers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01396-6}, pmid = {31218384}, issn = {1432-184X}, support = {PICT 2012 0285//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, abstract = {Phosphorus (P) is an essential nutrient with low bioavailability in soils for plant growth. The use of P solubilization fungi (PSF) has arisen as an eco-friendly strategy to increase this nutrient's bioavailability. The effect of PSF inoculation and its combination with P-transporting organisms (arbuscular mycorrhizal fungi, AMF) on plant growth has been previously studied. However, these studies did not evaluate the combined effect of PSF and AMF inoculation on plant growth, symbiosis, and soil quality. Therefore, the aim of this study is to assess the impact of PSF on the AMF-wheat symbiosis establishment and efficiency, considering the effect on plant growth and soil quality. We performed a greenhouse experiment with wheat under different treatments (+/-AMF: Rhizophagus irregularis; +/-PSF strains: Talaromyces flavus, T. helicus L7B, T. helicus N24, and T. diversus) and measured plant growth, AMF root colonization, symbiotic efficiency, and soil quality indicators. No interaction between PSF and R. irregularis was found in wheat growth, showcasing that their combination is not better than single inoculation. T. helicus strains did not interfere with the AMF-wheat symbiosis establishment, while T. diversus and T. flavus decreased it. The symbiotic efficiency was increased by T. flavus and T. helicus N24, and unchanged with T. helicus L7B and T. diversus inoculation. The soil quality indicators were higher with microbial co-inoculation, particularly the alkaline phosphatases parameter, showing the beneficial role of fungi in soil. This work highlights the importance of microbial interactions in the rhizosphere for crop sustainability and soil quality improvement, assessing the effects of PSF on AMF-wheat symbiosis.}, } @article {pmid31217550, year = {2019}, author = {Otani, S and Challinor, VL and Kreuzenbeck, NB and Kildgaard, S and Krath Christensen, S and Larsen, LLM and Aanen, DK and Rasmussen, SA and Beemelmanns, C and Poulsen, M}, title = {Disease-free monoculture farming by fungus-growing termites.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8819}, doi = {10.1038/s41598-019-45364-z}, pmid = {31217550}, issn = {2045-2322}, support = {DNRF57//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; CRC 1127 ChemBioSys//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; VKR10101//Villum Fonden (Villum Foundation)/ ; }, abstract = {Fungus-growing termites engage in an obligate mutualistic relationship with Termitomyces fungi, which they maintain in monocultures on specialised fungus comb structures, without apparent problems with infectious diseases. While other fungi have been reported in the symbiosis, detailed comb fungal community analyses have been lacking. Here we use culture-dependent and -independent methods to characterise fungus comb mycobiotas from three fungus-growing termite species (two genera). Internal Transcribed Spacer (ITS) gene analyses using 454 pyrosequencing and Illumina MiSeq showed that non-Termitomyces fungi were essentially absent in fungus combs, and that Termitomyces fungal crops are maintained in monocultures as heterokaryons with two or three abundant ITS variants in a single fungal strain. To explore whether the essential absence of other fungi within fungus combs is potentially due to the production of antifungal metabolites by Termitomyces or comb bacteria, we performed in vitro assays and found that both Termitomyces and chemical extracts of fungus comb material can inhibit potential fungal antagonists. Chemical analyses of fungus comb material point to a highly complex metabolome, including compounds with the potential to play roles in mediating these contaminant-free farming conditions in the termite symbiosis.}, } @article {pmid31217361, year = {2019}, author = {Shinohara, A and Nohara, M and Kondo, Y and Jogahara, T and Nagura-Kato, GA and Izawa, M and Koshimoto, C}, title = {Comparison of the gut microbiotas of laboratory and wild Asian house shrews (Suncus murinus) based on cloned 16S rRNA sequences.}, journal = {Experimental animals}, volume = {}, number = {}, pages = {}, doi = {10.1538/expanim.19-0021}, pmid = {31217361}, issn = {1881-7122}, abstract = {The Asian house shrew, Suncus murinus, is an insectivore (Eulipotyphla, Mammalia) and an important laboratory animal for life-science studies. The gastrointestinal tract of Suncus is simple: the length of the entire intestine is very short relative to body size, the large intestine is quite short, and there are no fermentative chambers such as the forestomach or cecum. These features imply that Suncus has a different nutritional physiology from those of humans and mice, but little is known about whether Suncus utilizes microbial fermentation in the large (LI) or small (SI) intestine. In addition, domestication may affect the gastrointestinal microbial diversity of Suncus. Therefore, we compared the gastrointestinal microbial diversity of Suncus between laboratory and wild Suncus and between the SI and LI (i.e., four groups: Lab-LI, Lab-SI, Wild-LI, and Wild-SI) using bacterial 16S rRNA gene library sequencing analyses with a sub-cloning method. We obtained 759 cloned sequences (176, 174, 195, and 214 from the Lab-LI, Lab-SI, Wild-LI, and Wild-SI samples, respectively), which revealed that the gastrointestinal microbiota of Suncus is rich in Firmicutes (mostly lactic acid bacteria), with few Bacteroidetes. We observed different bacterial communities according to intestinal region in laboratory Suncus, but not in wild Suncus. Furthermore, the gastrointestinal microbial diversity estimates were lower in laboratory Suncus than in wild Suncus. These results imply that Suncus uses lactic acid fermentation in the gut, and that the domestication process altered the gastrointestinal bacterial diversity.}, } @article {pmid30948550, year = {2019}, author = {Vizentin-Bugoni, J and Tarwater, CE and Foster, JT and Drake, DR and Gleditsch, JM and Hruska, AM and Kelley, JP and Sperry, JH}, title = {Structure, spatial dynamics, and stability of novel seed dispersal mutualistic networks in Hawai'i.}, journal = {Science (New York, N.Y.)}, volume = {364}, number = {6435}, pages = {78-82}, doi = {10.1126/science.aau8751}, pmid = {30948550}, issn = {1095-9203}, mesh = {Animals ; Hawaii ; Human Activities ; Humans ; *Introduced Species ; *Seed Dispersal ; *Symbiosis ; }, abstract = {Increasing rates of human-caused species invasions and extinctions may reshape communities and modify the structure, dynamics, and stability of species interactions. To investigate how such changes affect communities, we performed multiscale analyses of seed dispersal networks on O'ahu, Hawai'i. Networks consisted exclusively of novel interactions, were largely dominated by introduced species, and exhibited specialized and modular structure at local and regional scales, despite high interaction dissimilarity across communities. Furthermore, the structure and stability of the novel networks were similar to native-dominated communities worldwide. Our findings suggest that shared evolutionary history is not a necessary process for the emergence of complex network structure, and interaction patterns may be highly conserved, regardless of species identity and environment. Introduced species can quickly become well integrated into novel networks, making restoration of native ecosystems more challenging than previously thought.}, } @article {pmid30944036, year = {2019}, author = {Couradeau, E and Giraldo-Silva, A and De Martini, F and Garcia-Pichel, F}, title = {Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nitrogen-fixing cyanosphere.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {55}, doi = {10.1186/s40168-019-0661-2}, pmid = {30944036}, issn = {2049-2618}, mesh = {Cyanobacteria/*classification/genetics/isolation & purification ; DNA, Ribosomal/genetics ; Desert Climate ; *Nitrogen Fixation ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Biological soil crusts (biocrusts) are a key component of arid land ecosystems, where they render critical services such as soil surface stabilization and nutrient fertilization. The bundle-forming, filamentous, non-nitrogen-fixing cyanobacterium Microcoleus vaginatus is a pioneer primary producer, often the dominant member of the biocrust microbiome, and the main source of leaked organic carbon. We hypothesized that, by analogy to the rhizosphere of plant roots, M. vaginatus may shape the microbial populations of heterotrophs around it, forming a specialized cyanosphere.

RESULTS: By physically isolating bundles of M. vaginatus from biocrusts, we were able to study the composition of the microbial populations attached to it, in comparison to the bulk soil crust microbiome by means of high-throughput 16S rRNA sequencing. We did this in two M. vaginatus-dominated biocrust from distinct desert biomes. We found that a small, selected subset of OTUs was significantly enriched in close proximity to M. vaginatus. Furthermore, we also found that a majority of bacteria (corresponding to some two thirds of the reads) were significantly more abundant away from this cyanobacterium. Phylogenetic placements suggest that all typical members of the cyanosphere were copiotrophs and that many were diazotrophs (Additional file 1: Tables S2 and S3). Nitrogen fixation genes were in fact orders of magnitude more abundant in this cyanosphere than in the bulk biocrust soil as assessed by qPCR. By contrary, competition for light, CO2, and low organic carbon concentrations defined at least a part of the OTUs segregating from the cyanobacterium.

CONCLUSIONS: We showed that M. vaginatus acts as a significant spatial organizer of the biocrust microbiome. On the one hand, it possesses a compositionally differentiated cyanosphere that concentrates the nitrogen-fixing function. We propose that a mutualism based on C for N exchange between M. vaginatus and copiotrophic diazotrophs helps sustains this cyanosphere and that this consortium constitutes the true pioneer community enabling the colonization of nitrogen-poor soils. On the other hand, a large number of biocrust community members segregate away from the vicinity of M. vaginatus, potentially through competition for light or CO2, or because of a preference for oligotrophy.}, } @article {pmid30935407, year = {2019}, author = {Berglund, F and Österlund, T and Boulund, F and Marathe, NP and Larsson, DGJ and Kristiansson, E}, title = {Identification and reconstruction of novel antibiotic resistance genes from metagenomes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {52}, doi = {10.1186/s40168-019-0670-1}, pmid = {30935407}, issn = {2049-2618}, mesh = {Computational Biology/*methods ; *Drug Resistance, Microbial ; Environmental Microbiology ; Metagenomics ; Software ; Symbiosis ; }, abstract = {BACKGROUND: Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables cultivation-independent characterization of bacterial communities but the resulting data is noisy and highly fragmented, severely hampering the identification of previously undescribed ARGs. We have therefore developed fARGene, a method for identification and reconstruction of ARGs directly from shotgun metagenomic data.

RESULTS: fARGene uses optimized gene models and can therefore with high accuracy identify previously uncharacterized resistance genes, even if their sequence similarity to known ARGs is low. By performing the analysis directly on the metagenomic fragments, fARGene also circumvents the need for a high-quality assembly. To demonstrate the applicability of fARGene, we reconstructed β-lactamases from five billion metagenomic reads, resulting in 221 ARGs, of which 58 were previously not reported. Based on 38 ARGs reconstructed by fARGene, experimental verification showed that 81% provided a resistance phenotype in Escherichia coli. Compared to other methods for detecting ARGs in metagenomic data, fARGene has superior sensitivity and the ability to reconstruct previously unknown genes directly from the sequence reads.

CONCLUSIONS: We conclude that fARGene provides an efficient and reliable way to explore the unknown resistome in bacterial communities. The method is applicable to any type of ARGs and is freely available via GitHub under the MIT license.}, } @article {pmid29207272, year = {2017}, author = {Dale, C}, title = {Evolution: Weevils Get Tough on Symbiotic Tyrosine.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {R1282-R1284}, doi = {10.1016/j.cub.2017.10.031}, pmid = {29207272}, issn = {1879-0445}, mesh = {Animals ; Coleoptera/*genetics ; Genome, Bacterial ; Hardness ; Symbiosis/genetics ; Tyrosine/genetics ; Weevils/*genetics ; }, abstract = {Weevils, which represent one of the most diverse groups of terrestrial insects in nature, obtain a tough exoskeleton through the activity of an ancient bacterial symbiont with a tiny genome that serves as a factory for the production of tyrosine.}, } @article {pmid29207267, year = {2017}, author = {Petitjean, C and Williams, TA}, title = {Evolution: New Gene-Rich Mitochondria Found across the Eukaryotic Tree.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {R1270-R1271}, doi = {10.1016/j.cub.2017.10.028}, pmid = {29207267}, issn = {1879-0445}, mesh = {Eukaryota/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/genetics ; Symbiosis/genetics ; Trees/genetics ; }, abstract = {Mitochondria are the energy-generating organelles that power eukaryotic cells. Originally descended from endosymbiotic bacteria, their genomes have shrunk during evolution. New analyses suggest that large, gene-rich mitochondrial genomes are more common than previously thought, with interesting implications for eukaryotic genome evolution.}, } @article {pmid28950079, year = {2017}, author = {Archibald, JM}, title = {Evolution: Protein Import in a Nascent Photosynthetic Organelle.}, journal = {Current biology : CB}, volume = {27}, number = {18}, pages = {R1004-R1006}, doi = {10.1016/j.cub.2017.08.013}, pmid = {28950079}, issn = {1879-0445}, mesh = {*Amoeba ; Biological Evolution ; *Cercozoa ; Photosynthesis ; Plastids ; Symbiosis ; }, abstract = {An amoeba named Paulinella harbours 'chromatophores', cyanobacterium-derived photosynthetic bodies that evolved independent of plastids. Proteomics has shown that hundreds of nucleus-encoded proteins are targeted to the chromatophore, revealing the host cell's contributions to its recently established organelle.}, } @article {pmid31216282, year = {2019}, author = {Sieber, M and Pita, L and Weiland-Bräuer, N and Dirksen, P and Wang, J and Mortzfeld, B and Franzenburg, S and Schmitz, RA and Baines, JF and Fraune, S and Hentschel, U and Schulenburg, H and Bosch, TCG and Traulsen, A}, title = {Neutrality in the Metaorganism.}, journal = {PLoS biology}, volume = {17}, number = {6}, pages = {e3000298}, doi = {10.1371/journal.pbio.3000298}, pmid = {31216282}, issn = {1545-7885}, abstract = {Almost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, the metaorganism. Natural selection should favor hosts that shape the community composition of these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal hosts often pose selective environments, which only a subset of the environmentally available microbes are able to colonize. How these microbes assemble after colonization to form the complex microbiota is less clear. Neutral models are based on the assumption that the alternatives in microbiota community composition are selectively equivalent and thus entirely shaped by random population dynamics and dispersal. Here, we use the neutral model as a null hypothesis to assess microbiata composition in host organisms, which does not rely on invoking any adaptive processes underlying microbial community assembly. We show that the overall microbiota community structure from a wide range of host organisms, in particular including previously understudied invertebrates, is in many cases consistent with neutral expectations. Our approach allows to identify individual microbes that are deviating from the neutral expectation and are therefore interesting candidates for further study. Moreover, using simulated communities, we demonstrate that transient community states may play a role in the deviations from the neutral expectation. Our findings highlight that the consideration of neutral processes and temporal changes in community composition are critical for an in-depth understanding of microbiota-host interactions.}, } @article {pmid31216220, year = {2019}, author = {Plett, K and Raposo, AE and Anderson, IC and Piller, SC and Plett, JM}, title = {Protein arginine methyltransferase expression affects ectomycorrhizal symbiosis and the regulation of hormone signaling pathways.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-01-19-0007-R}, pmid = {31216220}, issn = {0894-0282}, abstract = {The genomes of all eukaryotic organisms, from small unicellular yeasts to humans, include members of the protein arginine methyltransferase (PRMT) family. These enzymes affect gene transcription, cellular signaling and function through the post-translational methylation of arginine residues. Mis-regulation of PRMTs results in serious developmental defects, disease or death, illustrating the importance of these enzymes to cellular processes. Plant genomes encode almost the full complement of PRMTs found in other higher organisms, plus an additional PRMT found uniquely in plants: PRMT10. Here we investigate the role of these highly conserved PRMTs in a process that is unique to perennial plants - the development of symbiosis with ectomycorrhizal fungi. We show that PRMT expression and arginine methylation is altered in the roots of the model tree Eucalyptus grandis by the presence of its ectomycorrhizal fungal symbiont Pisolithus albus. Further, using transgenic modifications, we demonstrate that E. grandis-encoded PRMT1 and PRMT10 have important, but opposing, effects in promoting this symbiosis. In particular, the plant specific EgPRMT10 has a potential role in the expression of plant hormone pathways during the colonization process and its over-expression reduces fungal colonization success.}, } @article {pmid31215669, year = {2019}, author = {Page, CE and Leggat, W and Heron, SF and Choukroun, SM and Lloyd, J and Ainsworth, TD}, title = {Seeking Resistance in Coral Reef Ecosystems: The Interplay of Biophysical Factors and Bleaching Resistance under a Changing Climate: The Interplay of a Reef's Biophysical Factors Can Mitigate the Coral Bleaching Response.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e1800226}, doi = {10.1002/bies.201800226}, pmid = {31215669}, issn = {1521-1878}, support = {NA14NES4320003//National Oceanic and Atmospheric Administration/ ; DP180103199//Australian Research Council/ ; NA14NES4320003//NOAA/ ; DP180103199//Australian Research Council Discovery Project/ ; }, abstract = {If we are to ensure the persistence of species in an increasingly warm world, of interest is the identification of drivers that affect the ability of an organism to resist thermal stress. Underpinning any organism's capacity for resistance is a complex interplay between biological and physical factors occurring over multiple scales. Tropical coral reefs are a unique system, in that their function is dependent upon the maintenance of a coral-algal symbiosis that is directly disrupted by increases in water temperature. A number of physical factors have been identified as affecting the biological responses of the coral organism under broadscale thermal anomalies. One such factor is water flow, which is capable of modulating both organismal metabolic functioning and thermal environments. Understanding the physiological and hydrodynamic drivers of organism response to thermal stress improves predictive capabilities and informs targeted management responses, thereby increasing the resilience of reefs into the future.}, } @article {pmid31215061, year = {2019}, author = {Law, SR}, title = {The genetic program at the root of the biological stock exchange.}, journal = {Physiologia plantarum}, volume = {166}, number = {3}, pages = {709-711}, doi = {10.1111/ppl.12980}, pmid = {31215061}, issn = {1399-3054}, abstract = {Beneath the gardens, farmlands and forest floors that surround us, a hidden world blooms in careful cooperation and intense competition. The mutualistic symbiosis of the thread-like hyphae of fungi and plant roots (collectively termed mycorrhizae from the Greek mýkēs - meaning 'fungus', and rhiza - for 'root') is present in the vast majority of plant species. As with most intimate relationships, this symbiosis functions on a principle of 'give and take'. As an autotroph, the plant is able to synthesize all the sugars it requires through photosynthesis; however, its immobility hinders its capacity to forage for nutrients vital for its growth and survival. With an expansive network of hyphae, the heterotrophic fungus is able to locate and remobilize water and nutrients, such as phosphorus (P) and nitrogen (N), and barter them for precious sugars with the plant. An article in this issue of Physiologia Plantarum (Zhao et al. 2019) describes alterations in the genetic programming that takes place in the plant root upon the establishment of this fascinating relationship, which has profound implications for plant productivity and soil management methods.}, } @article {pmid31214691, year = {2019}, author = {Phillips, AJ and Dornburg, A and Zapfe, KL and Anderson, FE and James, SW and Erséus, C and Moriarty Lemmon, E and Lemmon, AR and Williams, BW}, title = {Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz120}, pmid = {31214691}, issn = {1759-6653}, abstract = {Leeches (Hirudinida) comprise a charismatic, yet often maligned group of organisms. Despite their ecological, economic, and medical importance, a general consensus on the phylogenetic relationships of major hirudinidan lineages is lacking. This absence of a consistent, robust phylogeny of early-diverging lineages has hindered our understanding of the underlying processes that enabled evolutionary diversification of this clade. Here, we used an Anchored Hybrid Enrichment-based phylogenomic approach, capturing hundreds of loci to investigate phylogenetic relationships among major hirudinidan lineages and their closest living relatives. Our results suggest that a dramatic reinterpretation of early leech evolution is warranted. We recovered Branchiobdellida as sister to a clade that includes all major lineages of hirudinidans, but found Acanthobdella to be nested within Oceanobdelliformes. These results cast doubt on the utility of Acanthobdella as a 'missing link' used to explain the origin of blood-feeding in hirudineans. Further, our results support a deep divergence between predominantly marine and freshwater lineages, while not supporting the reciprocal monophyly of jawed and proboscis-bearing leeches. To sum up, our phylogenomic resolution of early-diverging leeches provides a necessary foundation for illuminating the evolution of host-symbiont associations and key adaptations that have allowed leeches to colonize a wide diversity of habitats worldwide.}, } @article {pmid31214211, year = {2019}, author = {Billault-Penneteau, B and Sandré, A and Folgmann, J and Parniske, M and Pawlowski, K}, title = {Dryas as a Model for Studying the Root Symbioses of the Rosaceae.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {661}, doi = {10.3389/fpls.2019.00661}, pmid = {31214211}, issn = {1664-462X}, abstract = {The nitrogen-fixing root nodule symbiosis is restricted to four plant orders: Fabales (legumes), Fagales, Cucurbitales and Rosales (Elaeagnaceae, Rhamnaceae, and Rosaceae). Interestingly all of the Rosaceae genera confirmed to contain nodulating species (i.e., Cercocarpus, Chamaebatia, Dryas, and Purshia) belong to a single subfamily, the Dryadoideae. The Dryas genus is particularly interesting from an evolutionary perspective because it contains closely related nodulating (Dryas drummondii) and non-nodulating species (Dryas octopetala). The close phylogenetic relationship between these two species makes Dryas an ideal model genus to study the genetic basis of nodulation by whole genome comparison and classical genetics. Therefore, we established methods for plant cultivation, transformation and DNA extraction for these species. We optimized seed surface sterilization and germination methods and tested growth protocols ranging from pots and Petri dishes to a hydroponic system. Transgenic hairy roots were obtained by adapting Agrobacterium rhizogenes-based transformation protocols for Dryas species. We compared several DNA extraction protocols for their suitability for subsequent molecular biological analysis. Using CTAB extraction, reproducible PCRs could be performed, but CsCl gradient purification was essential to obtain DNA in sufficient purity for high quality de novo genome sequencing of both Dryas species. Altogether, we established a basic toolkit for the culture, transient transformation and genetic analysis of Dryas sp.}, } @article {pmid31214134, year = {2019}, author = {Medrano, E and Merselis, DG and Bellantuono, AJ and Rodriguez-Lanetty, M}, title = {Proteomic Basis of Symbiosis: A Heterologous Partner Fails to Duplicate Homologous Colonization in a Novel Cnidarian- Symbiodiniaceae Mutualism.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1153}, doi = {10.3389/fmicb.2019.01153}, pmid = {31214134}, issn = {1664-302X}, abstract = {Reef corals and sea anemones form symbioses with unicellular symbiotic dinoflagellates. The molecular circumventions that underlie the successful intracellular colonization of hosts by symbionts are still largely unknown. We conducted proteomic analyses to determine molecular differences of Exaiptasia pallida anemones colonized by physiologically different symbiont species, in comparison with symbiont-free (aposymbiotic) anemones. We compared one homologous species, Symbiodinium linucheae, that is natively associated with the clonal Exaiptasia strain (CC7) to another heterologous species, Durusdinium trenchii, a thermally tolerant species that colonizes numerous coral species. This approach allowed the discovery of a core set of host genes that are differentially regulated as a function of symbiosis regardless of symbiont species. The findings revealed that symbiont colonization at higher densities requires circumvention of the host cellular immunological response, enhancement of ammonium regulation, and suppression of phagocytosis after a host cell in colonized. Furthermore, the heterologous symbionts failed to duplicate the same level of homologous colonization within the host, evidenced by substantially lower symbiont densities. This reduced colonization of D. trenchii correlated with its inability to circumvent key host systems including autophagy-suppressing modulators, cytoskeletal alteration, and isomerase activity. The larger capability of host molecular circumvention by homologous symbionts could be the result of a longer evolutionary history of host/symbiont interactions, which translates into a more finely tuned symbiosis. These findings are of great importance within the context of the response of reef corals to climate change since it has been suggested that coral may acclimatize to ocean warming by changing their dominant symbiont species.}, } @article {pmid31213566, year = {2019}, author = {Van Leuven, JT and Mao, M and Xing, DD and Bennett, GM and McCutcheon, JP}, title = {Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.01950-18}, pmid = {31213566}, issn = {2150-7511}, abstract = {Gene loss and genome reduction are defining characteristics of endosymbiotic bacteria. The most highly reduced endosymbiont genomes have lost numerous essential genes related to core cellular processes such as replication, transcription, and translation. Computational gene predictions performed for the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, "Candidatus Hodgkinia cicadicola" (Alphaproteobacteria) and "Ca Sulcia muelleri" (Bacteroidetes), have found only 26 and 16 tRNA genes and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original "Ca Hodgkinia cicadicola" genome annotation was missing several essential genes involved in tRNA processing, such as those encoding RNase P and CCA tRNA nucleotidyltransferase as well as several RNA editing enzymes required for tRNA maturation. How these cicada endosymbionts perform basic translation-related processes remains unknown. Here, by sequencing eukaryotic mRNAs and total small RNAs, we show that the limited tRNA set predicted by computational annotation of "Ca Sulcia muelleri" and "Ca Hodgkinia cicadicola" is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5' and 3' ends and seem to undergo nucleotide modification. Surprisingly, we found that most "Ca Hodgkinia cicadicola" and "Ca Sulcia muelleri" tRNAs exist as tRNA halves. We hypothesize that "Ca Sulcia muelleri" and "Ca Hodgkinia cicadicola" tRNAs function in bacterial translation but require host-encoded enzymes to do so.IMPORTANCE The smallest bacterial genomes, in the range of about 0.1 to 0.5 million base pairs, are commonly found in the nutritional endosymbionts of insects. These tiny genomes are missing genes that encode proteins and RNAs required for the translation of mRNAs, one of the most highly conserved and important cellular processes. In this study, we found that the bacterial endosymbionts of cicadas have genomes which encode incomplete tRNA sets and lack genes required for tRNA processing. Nevertheless, we found that endosymbiont tRNAs are correctly processed at their 5' and 3' ends and, surprisingly, that mostly exist as tRNA halves. We hypothesize that the cicada host must supply its symbionts with these missing tRNA processing activities.}, } @article {pmid31197001, year = {2019}, author = {Mascuch, S and Kubanek, J}, title = {A marine chemical defense partnership.}, journal = {Science (New York, N.Y.)}, volume = {364}, number = {6445}, pages = {1034-1035}, doi = {10.1126/science.aax8964}, pmid = {31197001}, issn = {1095-9203}, mesh = {*Ecosystem ; *Symbiosis ; }, } @article {pmid30675064, year = {2019}, author = {Tanoue, T and Morita, S and Plichta, DR and Skelly, AN and Suda, W and Sugiura, Y and Narushima, S and Vlamakis, H and Motoo, I and Sugita, K and Shiota, A and Takeshita, K and Yasuma-Mitobe, K and Riethmacher, D and Kaisho, T and Norman, JM and Mucida, D and Suematsu, M and Yaguchi, T and Bucci, V and Inoue, T and Kawakami, Y and Olle, B and Roberts, B and Hattori, M and Xavier, RJ and Atarashi, K and Honda, K}, title = {A defined commensal consortium elicits CD8 T cells and anti-cancer immunity.}, journal = {Nature}, volume = {565}, number = {7741}, pages = {600-605}, doi = {10.1038/s41586-019-0878-z}, pmid = {30675064}, issn = {1476-4687}, support = {DK43351/NH/NIH HHS/United States ; AT009708/NH/NIH HHS/United States ; }, mesh = {Adenocarcinoma/*immunology/pathology/*therapy ; Animals ; Antigens, CD/metabolism ; Bacteria/*classification/immunology/isolation & purification ; CD8-Positive T-Lymphocytes/cytology/*immunology ; Cell Line, Tumor ; Dendritic Cells/immunology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Healthy Volunteers ; Histocompatibility Antigens Class I/immunology ; Humans ; Integrin alpha Chains/metabolism ; Interferon-gamma/biosynthesis/immunology ; Listeria monocytogenes/immunology ; Listeriosis/immunology/microbiology/*prevention & control ; Male ; Mice ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; Symbiosis/*immunology ; Xenograft Model Antitumor Assays ; }, abstract = {There is a growing appreciation for the importance of the gut microbiota as a therapeutic target in various diseases. However, there are only a handful of known commensal strains that can potentially be used to manipulate host physiological functions. Here we isolate a consortium of 11 bacterial strains from healthy human donor faeces that is capable of robustly inducing interferon-γ-producing CD8 T cells in the intestine. These 11 strains act together to mediate the induction without causing inflammation in a manner that is dependent on CD103+ dendritic cells and major histocompatibility (MHC) class Ia molecules. Colonization of mice with the 11-strain mixture enhances both host resistance against Listeria monocytogenes infection and the therapeutic efficacy of immune checkpoint inhibitors in syngeneic tumour models. The 11 strains primarily represent rare, low-abundance components of the human microbiome, and thus have great potential as broadly effective biotherapeutics.}, } @article {pmid29924441, year = {2018}, author = {Barfield, SJ and Aglyamova, GV and Bay, LK and Matz, MV}, title = {Contrasting effects of Symbiodinium identity on coral host transcriptional profiles across latitudes.}, journal = {Molecular ecology}, volume = {27}, number = {15}, pages = {3103-3115}, doi = {10.1111/mec.14774}, pmid = {29924441}, issn = {1365-294X}, mesh = {Acclimatization ; Animals ; Anthozoa/*genetics ; Climate Change ; Coral Reefs ; Symbiosis/genetics/physiology ; }, abstract = {Reef-building corals can increase their resistance to heat-induced bleaching through adaptation and acclimatization and/or by associating with a more thermo-tolerant strain of algal symbiont (Symbiodinium sp.). Here, we show that these two adaptive pathways interact. We collected Acropora millepora corals from two contrasting thermal environments on the Great Barrier Reef: cooler, mid-latitude Orpheus Island, where all corals hosted a heat-sensitive clade C Symbiodinium, and warmer, low-latitude Wilkie Island, where corals hosted either a clade C or a more thermo-tolerant clade D. Corals were kept in a benign common garden to reveal differences in baseline gene expression, reflecting prior adaptation/long-term acclimatization. Model-based analysis identified gene expression differences between Wilkie and Orpheus corals that were negatively correlated with previously described transcriptome-wide signatures of heat stress, signifying generally elevated thermotolerance of Wilkie corals. Yet, model-free analyses of gene expression revealed that Wilkie corals hosting clade C were distinct from Wilkie corals hosting clade D, whereas Orpheus corals were more variable. Wilkie corals hosting clade C symbionts exhibited unique functional signatures, including downregulation of histone proteins and ion channels and upregulation of chaperones and RNA processing genes, putatively representing constitutive "frontloading" of stress response genes. Furthermore, clade C Symbiodinium exhibited constitutive expression differences between Wilkie and Orpheus, indicative of contrasting life history strategies. Our results demonstrate that hosting alternative Symbiodinium types is associated with different pathways of local adaptation for the coral host. These interactions could play a significant role in setting the direction of genetic adaptation to global warming in the two symbiotic partners.}, } @article {pmid28171752, year = {2017}, author = {de Vries, J and Archibald, JM}, title = {Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium?.}, journal = {Current biology : CB}, volume = {27}, number = {3}, pages = {R103-R105}, doi = {10.1016/j.cub.2016.12.006}, pmid = {28171752}, issn = {1879-0445}, mesh = {Biological Evolution ; *Cyanobacteria ; Fresh Water ; Phylogeny ; Plastids ; *Symbiosis ; }, abstract = {Photosynthetic eukaryotes are the product of an endosymbiotic event between a eukaryotic host and a cyanobacterium that became today's plastid. A new phylogenomic study suggests that the closest relative of plastids among extant cyanobacteria is the recently discovered freshwater-dwelling Gloeomargarita lithophora.}, } @article {pmid31212139, year = {2019}, author = {Müller, LM and Harrison, MJ}, title = {Phytohormones, miRNAs, and peptide signals integrate plant phosphorus status with arbuscular mycorrhizal symbiosis.}, journal = {Current opinion in plant biology}, volume = {50}, number = {}, pages = {132-139}, doi = {10.1016/j.pbi.2019.05.004}, pmid = {31212139}, issn = {1879-0356}, abstract = {Most land plant species engage in a beneficial interaction with arbuscular mycorrhizal fungi in order to increase mineral nutrient acquisition, in particular the major macronutrient phosphorus (P). Initiation, development, and maintenance of the symbiosis are largely under the control of the host plant and strongly influenced by the plants' P status. Recent advances reveal that phytohormones, microRNAs, and secreted peptides all regulate and integrate development of arbuscular mycorrhizal (AM) symbiosis with the P status of the plant. This occurs through a complex, multi-layered signaling network with crosstalk between phosphate (Pi) starvation signaling pathways and AM symbiosis signaling, and also via direct effects on the AM fungal symbiont. Multiple checkpoints allow the plant to fine-tune symbiosis based on its P status.}, } @article {pmid31211975, year = {2019}, author = {McCutcheon, JP and Lekberg, Y}, title = {Symbiosis: Fungi as Shrewd Trade Negotiators.}, journal = {Current biology : CB}, volume = {29}, number = {12}, pages = {R570-R572}, doi = {10.1016/j.cub.2019.05.002}, pmid = {31211975}, issn = {1879-0445}, abstract = {Symbiotic fungi associated with plant roots can shuttle a key nutrient through their hyphal network in response to resource inequality. This need-based transport optimizes trade conditions for carbon with plants.}, } @article {pmid31208116, year = {2019}, author = {Cui, C and Wang, H and Hong, L and Xu, Y and Zhao, Y and Zhou, C}, title = {MtBZR1 Plays an Important Role in Nodule Development in Medicago truncatula.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, doi = {10.3390/ijms20122941}, pmid = {31208116}, issn = {1422-0067}, support = {ZR2018ZC0334//Major Program of Shandong Province Natural Science Foundation/ ; 2015CB943500//Ministry of Science and Technology of the People's Republic of China/ ; 31671507//National Natural Science Foundation of China/ ; 31371235//National Natural Science Foundation of China/ ; }, abstract = {Brassinosteroid (BR) is an essential hormone in plant growth and development. The BR signaling pathway was extensively studied, in which BRASSINAZOLE RESISTANT 1 (BZR1) functions as a key regulator. Here, we carried out a functional study of the homolog of BZR1 in Medicago truncatula R108, whose expression was induced in nodules upon Sinorhizobium meliloti 1021 inoculation. We identified a loss-of-function mutant mtbzr1-1 and generated 35S:MtBZR1 transgenic lines for further analysis at the genetic level. Both the mutant and the overexpression lines of MtBZR1 showed no obvious phenotypic changes under normal growth conditions. After S. meliloti 1021 inoculation, however, the shoot and root dry mass was reduced in mtbzr1-1 compared with the wild type, caused by partially impaired nodule development. The transcriptomic analysis identified 1319 differentially expressed genes in mtbzr1-1 compared with wild type, many of which are involved in nodule development and secondary metabolite biosynthesis. Our results demonstrate the role of MtBZR1 in nodule development in M. truncatula, shedding light on the potential role of BR in legume-rhizobium symbiosis.}, } @article {pmid31207947, year = {2019}, author = {Dominguez, H and Loret, EP}, title = {Ulva lactuca, A Source of Troubles and Potential Riches.}, journal = {Marine drugs}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/md17060357}, pmid = {31207947}, issn = {1660-3397}, abstract = {Ulva lactuca is a green macro alga involved in devastating green tides observed worldwide. These green tides or blooms are a consequence of human activities. Ulva blooms occur mainly in shallow waters and the decomposition of this alga can produce dangerous vapors. Ulva lactuca is a species usually resembling lettuce, but genetic analyses demonstrated that other green algae with tubular phenotypes were U. lactuca clades although previously described as different species or even genera. The capacity for U. lactuca to adopt different phenotypes can be due to environment parameters, such as the degree of water salinity or symbiosis with bacteria. No efficient ways have been discovered to control these green tides, but the Mediterranean seas appear to be protected from blooms, which disappear rapidly in springtime. Ulva contains commercially valuable components, such as bioactive compounds, food or biofuel. The biomass due to this alga collected on beaches every year is beginning to be valorized to produce valuable compounds. This review describes different processes and strategies developed to extract these different valuable components.}, } @article {pmid31028027, year = {2019}, author = {Onchuru, TO and Kaltenpoth, M}, title = {Established Cotton Stainer Gut Bacterial Mutualists Evade Regulation by Host Antimicrobial Peptides.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {13}, pages = {}, doi = {10.1128/AEM.00738-19}, pmid = {31028027}, issn = {1098-5336}, abstract = {Symbioses with microorganisms are ubiquitous in nature and confer important ecological traits to animal hosts but also require control mechanisms to ensure homeostasis of the symbiotic interactions. In addition to protecting hosts against pathogens, animal immune systems recognize, respond to, and regulate mutualists. The gut bacterial symbionts of the cotton stainer bug, Dysdercus fasciatus, elicit an immune response characterized by the upregulation of c-type lysozyme and the antimicrobial peptide pyrrhocoricin in bugs with their native gut microbiota compared to that in dysbiotic insects. In this study, we investigated the impact of the elicited antimicrobial immune response on the established cotton stainer gut bacterial symbiont populations. To this end, we used RNA interference (RNAi) to knock down immunity-related genes hypothesized to regulate the symbionts, and we subsequently measured the effect of this silencing on host fitness and on the abundance of the major gut bacterial symbionts. Despite successful downregulation of target genes by both ingestion and injection of double-stranded RNA (dsRNA), the silencing of immunity-related genes had no effect on either host fitness or the qualitative and quantitative composition of established gut bacterial symbionts, indicating that the host immune responses are not actively involved in the regulation of the nutritional and defensive gut bacterial mutualists. These results suggest that close associations of bacterial symbionts with their hosts can result in the evolution of mechanisms ensuring that symbionts remain insensitive to host immunological responses, which may be important for the evolutionary stability of animal-microbe symbiotic associations.IMPORTANCE Animal immune systems are central for the protection of hosts against enemies by preventing or eliminating successful infections. However, in the presence of beneficial bacterial mutualists, the immune system must strike a balance of not killing the beneficial symbionts while at the same time preventing enemy attacks. Here, using the cotton stainer bug, we reveal that its long-term associated bacterial symbionts are insensitive to the host's immune effectors, suggesting adaptation to the host's defenses, thereby strengthening the stability of the symbiotic relationship. The ability of the symbionts to elicit host immune responses but remain insensitive themselves may be a mechanism by which the symbionts prime hosts to fight future pathogenic infections.}, } @article {pmid30830203, year = {2019}, author = {Marcionetti, A and Rossier, V and Roux, N and Salis, P and Laudet, V and Salamin, N}, title = {Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {869-882}, doi = {10.1093/gbe/evz042}, pmid = {30830203}, issn = {1759-6653}, mesh = {Animals ; *Biological Evolution ; Genome Components ; Perciformes/*genetics ; *Sea Anemones ; Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {Clownfishes are an iconic group of coral reef fishes, especially known for their mutualism with sea anemones. This mutualism is particularly interesting as it likely acted as the key innovation that triggered clownfish adaptive radiation. Indeed, after the acquisition of the mutualism, clownfishes diversified into multiple ecological niches linked with host and habitat use. However, despite the importance of this mutualism, the genetic mechanisms allowing clownfishes to interact with sea anemones are still unclear. Here, we used a comparative genomics and molecular evolutionary analyses to investigate the genetic basis of clownfish mutualism with sea anemones. We assembled and annotated the genome of nine clownfish species and one closely related outgroup. Orthologous genes inferred between these species and additional publicly available teleost genomes resulted in almost 16,000 genes that were tested for positively selected substitutions potentially involved in the adaptation of clownfishes to live in sea anemones. We identified 17 genes with a signal of positive selection at the origin of clownfish radiation. Two of them (Versican core protein and Protein O-GlcNAse) show particularly interesting functions associated with N-acetylated sugars, which are known to be involved in sea anemone discharge of toxins. This study provides the first insights into the genetic mechanisms of clownfish mutualism with sea anemones. Indeed, we identified the first candidate genes likely to be associated with clownfish protection form sea anemones, and thus the evolution of their mutualism. Additionally, the genomic resources acquired represent a valuable resource for further investigation of the genomic basis of clownfish adaptive radiation.}, } @article {pmid30715356, year = {2019}, author = {Pizarro, D and Dal Grande, F and Leavitt, SD and Dyer, PS and Schmitt, I and Crespo, A and Thorsten Lumbsch, H and Divakar, PK}, title = {Whole-Genome Sequence Data Uncover Widespread Heterothallism in the Largest Group of Lichen-Forming Fungi.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {721-730}, doi = {10.1093/gbe/evz027}, pmid = {30715356}, issn = {1759-6653}, mesh = {Genes, Mating Type, Fungal/*genetics ; *Genome, Fungal ; Lichens/*genetics ; *Reproduction, Asexual ; Symbiosis ; }, abstract = {Fungal reproduction is regulated by the mating-type (MAT1) locus, which typically comprises two idiomorphic genes. The presence of one or both allelic variants at the locus determines the reproductive strategy in fungi-homothallism versus heterothallism. It has been hypothesized that self-fertility via homothallism is widespread in lichen-forming fungi. To test this hypothesis, we characterized the MAT1 locus of 41 genomes of lichen-forming fungi representing a wide range of growth forms and reproductive strategies in the class Lecanoromycetes, the largest group of lichen-forming fungi. Our results show the complete lack of genetic homothallism suggesting that lichens evolved from a heterothallic ancestor. We argue that this may be related to the symbiotic lifestyle of these fungi, and may be a key innovation that has contributed to the accelerated diversification rates in this fungal group.}, } @article {pmid30715330, year = {2019}, author = {Irwin, NAT and Keeling, PJ}, title = {Extensive Reduction of the Nuclear Pore Complex in Nucleomorphs.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {678-687}, doi = {10.1093/gbe/evz029}, pmid = {30715330}, issn = {1759-6653}, mesh = {Cercozoa/*genetics ; Cryptophyta/*genetics ; *Nuclear Pore ; Nuclear Pore Complex Proteins/*genetics ; *Symbiosis ; }, abstract = {The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expression. Accordingly, the NPC constitutes a highly integrated nuclear component that is ubiquitous and conserved among eukaryotes. Potential exceptions to this are nucleomorphs: Highly reduced, relict nuclei that were derived from green and red algae following their endosymbiotic integration into two lineages, the chlorarachniophytes and the cryptophyceans. A previous investigation failed to identify NPC genes in nucleomorph genomes suggesting that these genes have either been relocated to the host nucleus or lost. Here, we sought to investigate the composition of the NPC in nucleomorphs by using genomic and transcriptomic data to identify and phylogenetically classify NPC proteins in nucleomorph-containing algae. Although we found NPC proteins in all examined lineages, most of those found in chlorarachniophytes and cryptophyceans were single copy, host-related proteins that lacked signal peptides. Two exceptions were Nup98 and Rae1, which had clear nucleomorph-derived homologs. However, these proteins alone are likely insufficient to structure a canonical NPC and previous reports revealed that Nup98 and Rae1 have other nuclear functions. Ultimately, these data indicate that nucleomorphs represent eukaryotic nuclei without a canonical NPC, raising fundamental questions about their structure and function.}, } @article {pmid30311871, year = {2018}, author = {Taylor, MJ and Bordenstein, SR and Slatko, B}, title = {Microbe Profile: Wolbachia: a sex selector, a viral protector and a target to treat filarial nematodes.}, journal = {Microbiology (Reading, England)}, volume = {164}, number = {11}, pages = {1345-1347}, doi = {10.1099/mic.0.000724}, pmid = {30311871}, issn = {1465-2080}, support = {R01 AI132581/AI/NIAID NIH HHS/United States ; R21 AI133522/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Arthropods/*microbiology ; Filarioidea/*microbiology ; Genome, Bacterial/genetics ; Host Specificity/*physiology ; Humans ; Symbiosis/physiology ; Wolbachia/*genetics/*physiology ; }, abstract = {Wolbachia is the most widespread genus of endosymbiotic bacteria in the animal world, infecting a diverse range of arthropods and nematodes. A broad spectrum of associations from parasitism to mutualism occur, with a tendency to drive reproductive manipulation or influence host fecundity to spread infection through host populations. These varied effects of Wolbachia are exploited for public health benefits. Notably, the protection of insect hosts from viruses is being tested as a potential control strategy for human arboviruses, and the mutualistic relationship with filarial nematodes makes Wolbachia a target for antibiotic therapy of human and veterinary nematode diseases.}, } @article {pmid31204904, year = {2019}, author = {Zou, H and Zhang, NN and Pan, Q and Zhang, JH and Chen, J and Wei, GH}, title = {Hydrogen Sulfide Promotes Nodulation and Nitrogen Fixation in Soybean-Rhizobia Symbiotic System.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI01190003R}, doi = {10.1094/MPMI-01-19-0003-R}, pmid = {31204904}, issn = {0894-0282}, abstract = {The rhizobium-legume symbiotic system is crucial for nitrogen cycle balance in agriculture. Hydrogen sulfide (H2S), a gaseous signaling molecule, may regulate various physiological processes in plants. However, whether H2S has regulatory effect in this symbiotic system remains unknown. Herein, we investigated the possible role of H2S in the symbiosis between soybean (Glycine max) and rhizobium (Sinorhizobium fredii). Our results demonstrated that an exogenous H2S donor (sodium hydrosulfide [NaHS]) treatment promoted soybean growth, nodulation, and nitrogenase (Nase) activity. Western blotting analysis revealed that the abundance of Nase component nifH was increased by NaHS treatment in nodules. Quantitative real-time polymerase chain reaction data showed that NaHS treatment upregulated the expressions of symbiosis-related genes nodA, nodC, and nodD of S. fredii. In addition, expression of soybean nodulation marker genes, including early nodulin 40 (GmENOD40), ERF required for nodulation (GmERN), nodulation signaling pathway 2b (GmNSP2b), and nodulation inception genes (GmNIN1a, GmNIN2a, and GmNIN2b), were upregulated. Moreover, the expressions of glutamate synthase (GmGOGAT), asparagine synthase (GmAS), nitrite reductase (GmNiR), ammonia transporter (GmSAT1), leghemoglobin (GmLb), and nifH involved in nitrogen metabolism were upregulated in NaHS-treated soybean roots and nodules. Together, our results suggested that H2S may act as a positive signaling molecule in the soybean-rhizobia symbiotic system and enhance the system's nitrogen fixation ability.}, } @article {pmid31203796, year = {2019}, author = {Ravindran, S and Tambe, AJ and Suthar, JK and Chahar, DS and Fernandes, JM and Desai, V}, title = {Nanomedicine: Bioavailability, Biotransformation and Biokinetics.}, journal = {Current drug metabolism}, volume = {}, number = {}, pages = {}, doi = {10.2174/1389200220666190614150708}, pmid = {31203796}, issn = {1875-5453}, abstract = {BACKGROUND: Nanomedicine is increasingly used to treat various ailments. Biocompatibility of nanomedicine is primarily governed by its properties such as bioavailability, biotransformation, and biokinetics. One of the major advantages of nanomedicine is the enhanced bioavailability of drugs. Biotransformation of nanomedicine is important to understand the pharmacological effects of nanomedicine. Biokinetics includes both pharmacokinetics and toxicokinetics of nanomedicine. Physicochemical parameters of nanomaterials have extensive influence on bioavailability, biotransformation, and biokinetics of nanomedicine.

METHOD: We carried out a structured peer-reviewed research literature survey and analysis using bibliographic databases.

RESULTS: Seventy-nine papers were included in the review. Papers dealing with bioavailability, biotransformation, and biokinetics of nanomedicine are found and reviewed. Bioavailability and biotransformation along with biokinetics are three major factors that determine the biological fate of nanomedicine. Extensive research work has been done for drugs of micron size but studies on nanomedicine are scarce. Therefore, more emphasis in this review is given on bioavailability and biotransformation of nanomedicine along with biokinetics.

CONCLUSION: Bioavailability results based on various nanomedicine are summarized in the present work. Biotransformation of nanodrugs, as well as nanoformulations, is also the focus of this article. Both in vitro and in vivo biotransformation studies on nanodrugs and its excipients are necessary to know the effect of metabolites formed. Biokinetics of nanomedicine is captured in details that are complementary to bioavailability and biotransformation. Nanomedicine has the potential to be developed as a personalized medicine once its physicochemical properties and its effect on biological system is well understood.}, } @article {pmid30516980, year = {2018}, author = {Bell, TJ and Draper, SL and Centanni, M and Carnachan, SM and Tannock, GW and Sims, IM}, title = {Characterization of Polysaccharides from Feijoa Fruits (Acca sellowiana Berg.) and Their Utilization as Growth Substrates by Gut Commensal Bacteroides Species.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {50}, pages = {13277-13284}, doi = {10.1021/acs.jafc.8b05080}, pmid = {30516980}, issn = {1520-5118}, mesh = {Bacteroides/*growth & development/metabolism ; Feijoa/*chemistry/metabolism ; Fruit/chemistry/metabolism ; Gastrointestinal Microbiome/*drug effects ; Humans ; Plant Extracts/*chemistry/metabolism ; Symbiosis ; }, abstract = {Polysaccharides from feijoa fruit were extracted and analyzed; the composition of these polysaccharides conforms to those typically found in the primary cell walls of eudicotyledons. The two major polysaccharide extracts consisted of mainly pectic polysaccharides and hemicellulosic polysaccharides [xyloglucan (77%) and arabinoxylan (16%)]. A collection of commensal Bacteroides species was screened for growth in culture using these polysaccharide preparations and placed into five categories based on their preference for each substrate. Most of the species tested could utilize the pectic polysaccharides, but growth on the hemicellulose was more limited. Constituent sugar and glycosyl linkage analysis showed that species that grew on the hemicellulose fraction showed differences in their preference for the two polysaccharides in this preparation. Our data demonstrate that the members of the genus Bacteroides show differential hydrolysis of pectic polysaccharides, xyloglucan, and arabinoxylan, which might influence the structure and metabolic activities of the microbiota in the human gut.}, } @article {pmid30358445, year = {2018}, author = {Sigwart, JD and Chen, C}, title = {Comparative Oxygen Consumption of Gastropod Holobionts from Deep-Sea Hydrothermal Vents in the Indian Ocean.}, journal = {The Biological bulletin}, volume = {235}, number = {2}, pages = {102-112}, doi = {10.1086/699326}, pmid = {30358445}, issn = {1939-8697}, mesh = {Animals ; Gastropoda/*metabolism ; *Hydrothermal Vents ; Indian Ocean ; Oxygen Consumption/*physiology ; Symbiosis/*physiology ; Temperature ; }, abstract = {Physiological traits are the foundation of an organism's success in a dynamic environment, yet basic measurements are unavailable for many taxa and even ecosystems. We measured routine metabolism in two hydrothermal vent gastropods, Alviniconcha marisindica (n = 40) and the scaly-foot gastropod Chrysomallon squamiferum (n = 18), from Kairei and Edmond vent fields on the Central Indian Ridge (23-25°S, about 3000 meter depth). No previous studies have measured metabolism in any Indian Ocean vent animals. After recovering healthy animals to the surface, we performed shipboard closed-chamber respirometry experiments to compare oxygen uptake at different temperatures (10, 16, and 25 °C) at surface pressure (1 atm). The physiology of these species is driven by the demands of their chemoautotrophic symbionts. Chrysomallon has very enlarged respiratory and circulatory systems, and endosymbionts are housed in its trophosome-like internal esophageal gland. By contrast, Alviniconcha has chemoautotrophic bacteria within the gill and less extensive associated anatomical adaptations. Thus, we predicted that routine oxygen consumption of Chrysomallon might be higher than that of Alviniconcha. However, oxygen consumption of Chrysomallon was not higher than that of Alviniconcha, and, further, Chrysomallon maintained a steady metabolic demand in two widely separated experimental temperatures, while Alviniconcha did not. We interpret that these findings indicate that (1) the "trophosome" does not fundamentally increase oxygen requirement compared to other gastropod holobionts, and (2) cold temperatures (10 °C) induce a stress response in Alviniconcha, resulting in aberrantly high uptake. While these two large gastropod species co-occur, differences in oxygen consumption may reflect the separate niches they occupy in the vent ecosystem.}, } @article {pmid30053110, year = {2018}, author = {Burke, GR and Simmonds, TJ and Sharanowski, BJ and Geib, SM}, title = {Rapid Viral Symbiogenesis via Changes in Parasitoid Wasp Genome Architecture.}, journal = {Molecular biology and evolution}, volume = {35}, number = {10}, pages = {2463-2474}, doi = {10.1093/molbev/msy148}, pmid = {30053110}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Animals ; Baculoviridae/*genetics ; *Biological Evolution ; Gene Expression Regulation, Viral ; *Genome, Insect ; Host-Parasite Interactions/*genetics ; Symbiosis ; Wasps/genetics/*virology ; }, abstract = {Viral genome integration provides a complex route to biological innovation that has rarely but repeatedly occurred in one of the most diverse lineages of organisms on the planet, parasitoid wasps. We describe a novel endogenous virus in braconid wasps derived from pathogenic alphanudiviruses. Limited to a subset of the genus Fopius, this recent acquisition allows an unprecedented opportunity to examine early endogenization events. Massive amounts of virus-like particles (VLPs) are produced in wasp ovaries. Unlike most endogenous viruses of parasitoid wasps, the VLPs do not contain DNA, translating to major differences in parasitism-promoting strategies. Rapid changes include genomic rearrangement, loss of DNA processing proteins, and wasp control of viral gene expression. These events precede the full development of tissue-specific viral gene expression observed in older associations. These data indicate that viral endogenization can rapidly result in functional and evolutionary changes associated with genomic novelty and adaptation in parasitoids.}, } @article {pmid29900626, year = {2018}, author = {van Oppen, MJH and Bongaerts, P and Frade, P and Peplow, LM and Boyd, SE and Nim, HT and Bay, LK}, title = {Adaptation to reef habitats through selection on the coral animal and its associated microbiome.}, journal = {Molecular ecology}, volume = {27}, number = {14}, pages = {2956-2971}, doi = {10.1111/mec.14763}, pmid = {29900626}, issn = {1365-294X}, mesh = {Acclimatization ; Adaptation, Physiological/genetics ; Animals ; Anthozoa/*genetics/growth & development/microbiology ; *Coral Reefs ; Dinoflagellida/*genetics/growth & development ; Ecosystem ; Gene Flow ; Genetics, Population ; Genome/genetics ; Microbiota/genetics ; Photosynthesis/genetics ; Symbiosis/*genetics ; }, abstract = {Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction site-associated sequencing) and characterized both the dinoflagellate photosymbiont- and tissue-associated prokaryote microbiomes (using metabarcoding) of a reef flat and slope population of the reef-building coral, Pocillopora damicornis, at two locations on Heron Island in the southern Great Barrier Reef. Reef flat and slope populations were separated by <100 m horizontally and ~5 m vertically, and the two study locations were separated by ~1 km. For the coral host, genetic divergence between habitats was much greater than between locations, suggesting limited gene flow between the flat and slope populations. Consistent with environmental selection, outlier loci primarily belonged to the conserved, minimal cellular stress response, likely reflecting adaptation to the different temperature and irradiance regimes on the reef flat and slope. The prokaryote community differed across both habitat and, to a lesser extent, location, whereas the dinoflagellate photosymbionts differed by habitat but not location. The observed intraspecific diversity associated with divergent habitats supports that environmental adaptation involves multiple members of the coral holobiont. Adaptive alleles or microbial associations present in coral populations from the environmentally variable reef flat may provide a source of adaptive variation for assisted evolution approaches, through assisted gene flow, artificial cross-breeding or probiotic inoculations, with the aim to increase climate resilience in the slope populations.}, } @article {pmid29746094, year = {2018}, author = {Zúñiga, A and Fuente, F and Federici, F and Lionne, C and Bônnet, J and de Lorenzo, V and González, B}, title = {An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth.}, journal = {ACS synthetic biology}, volume = {7}, number = {6}, pages = {1519-1527}, doi = {10.1021/acssynbio.8b00002}, pmid = {29746094}, issn = {2161-5063}, mesh = {4-Butyrolactone/analogs & derivatives/metabolism ; Arabidopsis/*growth & development/*microbiology ; Cupriavidus/genetics/*metabolism ; Feedback, Physiological ; Gene Expression Regulation, Bacterial ; Indoleacetic Acids/*metabolism ; Metabolic Engineering/*methods ; Microorganisms, Genetically-Modified ; Plant Roots/microbiology ; Plasmids/genetics ; Quorum Sensing ; Symbiosis ; }, abstract = {The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium Cupriavidus pinatubonensis JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated Arabidopsis thaliana. These results not only demonstrated the value of the designed genetic module, but also validated C. pinatubonensis JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations.}, } @article {pmid29588346, year = {2018}, author = {Chen, Y and Chaudhary, N and Yang, N and Granato, A and Turner, JA and Howard, SL and Devereaux, C and Zuo, T and Shrestha, A and Goel, RR and Neuberg, D and Wesemann, DR}, title = {Microbial symbionts regulate the primary Ig repertoire.}, journal = {The Journal of experimental medicine}, volume = {215}, number = {5}, pages = {1397-1415}, pmid = {29588346}, issn = {1540-9538}, support = {P40 OD010995/OD/NIH HHS/United States ; R01 AI113217/AI/NIAID NIH HHS/United States ; R01 AI121394/AI/NIAID NIH HHS/United States ; T32 AI007306/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; B-Lymphocytes/immunology ; Bacteria/*metabolism ; Clone Cells ; Germ-Free Life ; Immunity, Mucosal ; Immunoglobulin Heavy Chains/metabolism ; Immunoglobulin Variable Region/metabolism ; Immunoglobulins/*metabolism ; Intestine, Small/microbiology ; Mice, Inbred C57BL ; Receptors, Antigen, B-Cell/metabolism ; Spleen/cytology ; *Symbiosis ; T-Lymphocytes/cytology ; }, abstract = {The ability of immunoglobulin (Ig) to recognize pathogens is critical for optimal immune fitness. Early events that shape preimmune Ig repertoires, expressed on IgM+ IgD+ B cells as B cell receptors (BCRs), are poorly defined. Here, we studied germ-free mice and conventionalized littermates to explore the hypothesis that symbiotic microbes help shape the preimmune Ig repertoire. Ig-binding assays showed that exposure to conventional microbial symbionts enriched frequencies of antibacterial IgM+ IgD+ B cells in intestine and spleen. This enrichment affected follicular B cells, involving a diverse set of Ig-variable region gene segments, and was T cell-independent. Functionally, enrichment of microbe reactivity primed basal levels of small intestinal T cell-independent, symbiont-reactive IgA and enhanced systemic IgG responses to bacterial immunization. These results demonstrate that microbial symbionts influence host immunity by enriching frequencies of antibacterial specificities within preimmune B cell repertoires and that this may have consequences for mucosal and systemic immunity.}, } @article {pmid29431439, year = {2018}, author = {Miller, JH and Field, JJ and Kanakkanthara, A and Owen, JG and Singh, AJ and Northcote, PT}, title = {Marine Invertebrate Natural Products that Target Microtubules.}, journal = {Journal of natural products}, volume = {81}, number = {3}, pages = {691-702}, doi = {10.1021/acs.jnatprod.7b00964}, pmid = {29431439}, issn = {1520-6025}, mesh = {Animals ; Aquatic Organisms/*chemistry ; Bacteria/drug effects ; Biological Products/*chemistry ; Humans ; Invertebrates/*chemistry ; Microtubules/*metabolism ; Symbiosis/drug effects ; }, abstract = {Marine natural products as secondary metabolites are a potential major source of new drugs for treating disease. In some cases, cytotoxic marine metabolites target the microtubules of the eukaryote cytoskeleton for reasons that will be discussed. This review covers the microtubule-targeting agents reported from sponges, corals, tunicates, and molluscs and the evidence that many of these secondary metabolites are produced by bacterial symbionts. The review finishes by discussing the directions for future development and production of clinically relevant amounts of these natural products and their analogues through aquaculture, chemical synthesis, and biosynthesis by bacterial symbionts.}, } @article {pmid31200330, year = {2019}, author = {Jiang, J and Lu, Y}, title = {Metabolite profiling of Breviolum minutum in response to acidification.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {213}, number = {}, pages = {105215}, doi = {10.1016/j.aquatox.2019.05.017}, pmid = {31200330}, issn = {1879-1514}, abstract = {Coral reefs are in significant decline globally due to climate change and environmental pollution. The ocean is becoming more acidic due to rising atmospheric pCO2, and ocean acidification is considered a major threat to coral reefs. However, little is known about the exact mechanism by which acidification impacts coral symbiosis. As an important component of the symbiotic association, to explore the responses of symbionts could greatly enhance our understanding of this issue. The present work aimed to identify metabolomic changes of Breviolum minutum in acidification (low pH) condition, and investigate the underlying mechanisms responsible. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied to determine metabolite profiles after exposure to ambient and acidic conditions. We analysed the resulting metabolite data, and acidification appeared to have little effect on photosynthetic parameters, but it inhibited growth. Marked alterations in metabolite pools were observed in response to acidification that may be important in acclimation to climate change. Acidification may affect the biosynthesis of amino acids and proteins, and thereby inhibit the growth of B. minutum. Metabolites identified using this approach provide targets for future analyses aimed at understanding the responses of Symbiodiniaceae to environmental disturbance.}, } @article {pmid31197972, year = {2019}, author = {Rader, B and McAnulty, SJ and Nyholm, SV}, title = {Persistent symbiont colonization leads to a maturation of hemocyte response in the Euprymna scolopes/Vibrio fischeri symbiosis.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e858}, doi = {10.1002/mbo3.858}, pmid = {31197972}, issn = {2045-8827}, support = {1R15GM119100/GF/NIH HHS/United States ; IOS-0958006//NSF/ ; IOS-155794//NSF/ ; }, abstract = {The binary association between the squid, Euprymna scolopes, and its symbiont, Vibrio fischeri, serves as a model system to study interactions between beneficial bacteria and the innate immune system. Previous research demonstrated that binding of the squid's immune cells, hemocytes, to V. fischeri is altered if the symbiont is removed from the light organ, suggesting that host colonization alters hemocyte recognition of V. fischeri. To investigate the influence of symbiosis on immune maturation during development, we characterized hemocyte binding and phagocytosis of V. fischeri and nonsymbiotic Vibrio harveyi from symbiotic (sym) and aposymbiotic (apo) juveniles, and wild-caught and laboratory-raised sym and apo adults. Our results demonstrate that while light organ colonization by V. fischeri did not alter juvenile hemocyte response, these cells bound a similar number of V. fischeri and V. harveyi yet phagocytosed only V. harveyi. Our results also indicate that long-term colonization altered the adult hemocyte response to V. fischeri but not V. harveyi. All hemocytes from adult squid, regardless of apo or sym state, both bound and phagocytosed a similar number of V. harveyi while hemocytes from both wild-caught and sym-raised adults bound significantly fewer V. fischeri, although more V. fischeri were phagocytosed by hemocytes from wild-caught animals. In contrast, hemocytes from apo-raised squid bound similar numbers of both V. fischeri and V. harveyi, although more V. harveyi cells were engulfed, suggesting that blood cells from apo-raised adults behaved similarly to juvenile hosts. Taken together, these data suggest that persistent colonization by the light organ symbiont is required for hemocytes to differentially bind and phagocytose V. fischeri. The cellular immune system of E. scolopes likely possesses multiple mechanisms at different developmental stages to promote a specific and life-long interaction with the symbiont.}, } @article {pmid31197351, year = {2019}, author = {Martínez-Medina, A and Pescador-Azofra, L and Terrón-Camero, L and Pozo, MJ and Romero-Puertas, MC}, title = {Nitric oxide shape plant-fungi interactions.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erz289}, pmid = {31197351}, issn = {1460-2431}, abstract = {In their complex environments, plants continuously interact with fungi. While many of those interactions are detrimental for plants and challenge plant capability for growth and survival, others are beneficial improving plant growth and stress tolerance. Accordingly, plants have evolved sophisticated mechanisms to restrict pathogenic interactions while promoting mutualistic relationships. Several studies demonstrated the importance of nitric oxide (NO) in the regulation of plant defence mounted against fungal pathogens. NO triggers a reprograming of defence related gene expression, the production of secondary metabolites with antimicrobial properties and the hypersensitive response. More recent evidences have further shown the regulation of NO during the establishment of plant-fungus mutualistic associations from early steps of the interaction. Indeed NO has been recently shown to be produced by the plant after the recognition of root fungal symbionts, and to be required for the optimal control of the mycorrhizal symbiosis. Although studies dealing with NO function in plant-fungus mutualistic associations are still scarce, experimental data support a different regulation patterns and functions for NO in plant interactions with pathogenic and mutualistic fungi. Here we review recent evidences about NO function in plant-fungus interactions, trying to identify common and differential patterns related to the fungus life-style and their impact on plant health.}, } @article {pmid31197117, year = {2019}, author = {Lipa, P and Vinardell, JM and Janczarek, M}, title = {Transcriptomic Studies Reveal that the Rhizobium leguminosarum Serine/Threonine Protein Phosphatase PssZ has a Role in the Synthesis of Cell-Surface Components, Nutrient Utilization, and Other Cellular Processes.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, doi = {10.3390/ijms20122905}, pmid = {31197117}, issn = {1422-0067}, abstract = {Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing symbiotic associations with clover plants (Trifolium spp.). Surface polysaccharides, transport systems, and extracellular components synthesized by this bacterium are required for both the adaptation to changing environmental conditions and successful infection of host plant roots. The pssZ gene located in the Pss-I region, which is involved in the synthesis of extracellular polysaccharide, encodes a protein belonging to the group of serine/threonine protein phosphatases. In this study, a comparative transcriptomic analysis of R. leguminosarum bv. trifolii wild-type strain Rt24.2 and its derivative Rt297 carrying a pssZ mutation was performed. RNA-Seq data identified a large number of genes differentially expressed in these two backgrounds. Transcriptome profiling of the pssZ mutant revealed a role of the PssZ protein in several cellular processes, including cell signalling, transcription regulation, synthesis of cell-surface polysaccharides and components, and bacterial metabolism. In addition, we show that inactivation of pssZ affects the rhizobial ability to grow in the presence of different sugars and at various temperatures, as well as the production of different surface polysaccharides. In conclusion, our results identified a set of genes whose expression was affected by PssZ and confirmed the important role of this protein in the rhizobial regulatory network.}, } @article {pmid31196985, year = {2019}, author = {Zan, J and Li, Z and Tianero, MD and Davis, J and Hill, RT and Donia, MS}, title = {A microbial factory for defensive kahalalides in a tripartite marine symbiosis.}, journal = {Science (New York, N.Y.)}, volume = {364}, number = {6445}, pages = {}, doi = {10.1126/science.aaw6732}, pmid = {31196985}, issn = {1095-9203}, support = {DP2 AI124441/AI/NIAID NIH HHS/United States ; }, abstract = {Chemical defense against predators is widespread in natural ecosystems. Occasionally, taxonomically distant organisms share the same defense chemical. Here, we describe an unusual tripartite marine symbiosis, in which an intracellular bacterial symbiont ("Candidatus Endobryopsis kahalalidefaciens") uses a diverse array of biosynthetic enzymes to convert simple substrates into a library of complex molecules (the kahalalides) for chemical defense of the host, the alga Bryopsis sp., against predation. The kahalalides are subsequently hijacked by a third partner, the herbivorous mollusk Elysia rufescens, and employed similarly for defense. "Ca E. kahalalidefaciens" has lost many essential traits for free living and acts as a factory for kahalalide production. This interaction between a bacterium, an alga, and an animal highlights the importance of chemical defense in the evolution of complex symbioses.}, } @article {pmid31195965, year = {2019}, author = {Dreyer, J and Rautenbach, M and Booysen, E and van Staden, AD and Deane, SM and Dicks, LMT}, title = {Xenorhabdus khoisanae SB10 produces Lys-rich PAX lipopeptides and a Xenocoumacin in its antimicrobial complex.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {132}, doi = {10.1186/s12866-019-1503-x}, pmid = {31195965}, issn = {1471-2180}, support = {not applicable//National Research Foundation/ ; not applicable//BIOPEP Peptide fund/ ; }, abstract = {BACKGROUND: Xenorhabdus spp. live in close symbiosis with nematodes of the Steinernema genus. Steinernema nematodes infect an insect larva and release their symbionts into the haemocoel of the insect. Once released into the haemocoel, the bacteria produce bioactive compounds to create a semi-exclusive environment by inhibiting the growth of bacteria, yeasts and molds. The antimicrobial compounds thus far identified are xenocoumacins, xenortides, xenorhabdins, indole derivatives, xenoamicins, bicornutin and a number of antimicrobial peptides. The latter may be linear peptides such as the bacteriocins xenocin and xenorhabdicin, rhabdopeptides and cabanillasin, or cyclic, such as PAX lipopeptides, taxlllaids, xenobactin and szentiamide. Thus far, production of antimicrobial compounds have been reported for Xenorhabdus nematophila, Xenorhabdus budapestensis, Xenorhabdus cabanillasii, Xenorhabdus kozodoii, Xenorhabdus szentirmaii, Xenorhabdus doucetiae, Xenorhabdus mauleonii, Xenorhabdus indica and Xenorhabdus bovienii. Here we describe, for the first time, PAX lipopeptides and xenocoumacin 2 produced by Xenorhabdus khoisanae. These compounds were identified using ultraperformance liquid chromatography, linked to high resolution electrospray ionisation mass spectrometry and tandem mass spectrometry.

RESULTS: Cell-free supernatants of X. khoisanae SB10 were heat stable and active against Bacillus subtilis subsp. subtilis, Escherichia coli and Candida albicans. Five lysine-rich lipopeptides from the PAX group were identified in HPLC fractions, with PAX1' and PAX7 present in the highest concentrations. Three novel PAX7 peptides with putative enoyl modifications and two linear analogues of PAX1' were also detected. A small antibiotic compound, yellow in colour and λmax of 314 nm, was recovered from the HPLC fractions and identified as xenocoumacin 2. The PAX lipopeptides and xenocoumacin 2 correlated with the genes and gene clusters in the genome of X. khoisanae SB10.

CONCLUSION: With UPLC-MS and MSe analyses of compounds in the antimicrobial complex of X. khoisanae SB10, a number of PAX peptides and a xenocoumacin were identified. The combination of pure PAX1' peptide with xenocoumacin 2 resulted in high antimicrobial activity. Many of the fractions did, however, contain labile compounds and some fractions were difficult to resolve. It is thus possible that strain SB10 may produce more antimicrobial compounds than reported here, as suggested by the APE Ec biosynthetic complex. Further research is required to develop these broad-spectrum antimicrobial compounds into drugs that may be used in the fight against microbial infections.}, } @article {pmid31195952, year = {2019}, author = {Ikram, M and Ali, N and Jan, G and Guljan, F and Khan, N}, title = {Endophytic fungal diversity and their interaction with plants for agriculture sustainability under stressful condition.}, journal = {Recent patents on food, nutrition & agriculture}, volume = {}, number = {}, pages = {}, doi = {10.2174/2212798410666190612130139}, pmid = {31195952}, issn = {1876-1429}, abstract = {Endophytic fungi or endophytes as fascinating group of organism that colonize widely the healthy internal tissues of living plants, and do not cause any symptoms of disease in the host cells. Several decades of study and research have rustled the co-existing endophytes with their host plants, which can significantly influence the formation of metabolic products in plants, its ability to produce new interesting bioactive compound, which are of pharmaceutical, industrial and agricultural importance. The analytical results indicate that the endophytic fungi can confer profound impacts on plant communities by enhancing their growth, increasing their fitness, strengthening their tolerances to abiotic and biotic stresses, enhance defense mechanism and promoting their accumulation of secondary metabolites that provide immunity to the victims. This review focused on the biodiversity and biological roles of endophytic fungi in association with their host plants through reviewing of published research data obtained from the last 30 years.}, } @article {pmid31195052, year = {2019}, author = {Lee, J and Kim, CH and Jang, HA and Kim, JK and Kotaki, T and Shinoda, T and Shinada, T and Yoo, JW and Lee, BL}, title = {Burkholderia gut symbiont modulates titer of specific juvenile hormone in the bean bug Riptortus pedestris.}, journal = {Developmental and comparative immunology}, volume = {}, number = {}, pages = {103399}, doi = {10.1016/j.dci.2019.103399}, pmid = {31195052}, issn = {1879-0089}, abstract = {Recent studies have provided molecular evidence that gut symbiotic bacteria modulate host insect development, fitness and reproduction. However, the molecular mechanisms through which gut symbionts regulate these aspects of host physiology remain elusive. To address these questions, we prepared two different Riptortus-Burkholderia insect models, Burkholderia gut symbiont-colonized (Sym) Riptortus pedestris insects and gut symbiont-noncolonized (Apo) insects. Upon LC-MS analyses, juvenile hormone III skipped bisepoxide (JHSB3) was newly identified from Riptortus Apo- and Sym-female and male adults' insect hemolymph and JHSB3 titer in the Apo- and Sym-female insects were measured because JH is important for regulating reproduction in adult insects. The JHSB3 titer in the Sym-females were consistently higher compared to those of Apo-females. Since previous studies reported that Riptortus hexamerin-α and vitellogenin proteins were upregulated by the topical abdominal application of a JH-analog, chemically synthesized JHSB3 was administered to Apo-females. As expected, the hexamerin-α and vitellogenin proteins were dramatically increased in the hemolymph of JHSB3-treated Apo-females, resulting in increased egg production compared to that in Sym-females. Taken together, these results demonstrate that colonization of Burkholderia gut symbiont in the host insect stimulates biosynthesis of the heteroptera-specific JHSB3, leading to larger number of eggs produced and enhanced fitness in Riptortus host insects.}, } @article {pmid31194818, year = {2019}, author = {Jung, M and Lee, DH}, title = {Abundance and diversity of gut-symbiotic bacteria, the genus Burkholderia in overwintering Riptortus pedestris (Hemiptera: Alydidae) populations and soil in South Korea.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0218240}, doi = {10.1371/journal.pone.0218240}, pmid = {31194818}, issn = {1932-6203}, abstract = {Riptortus pedestris is a major agricultural pest on leguminous plants in South Korea and Japan. Recent studies have revealed that R. pedestris can form beneficial symbiosis with bacteria belonging to genus Burkholderia acquired from soil newly for every generation. Although their physiological interactions are relatively well-understood, infection rate and abundance of the Burkholderia in overwintering natural populations of R. pedestris remain unknown. Therefore, the objective of this study was to characterize Burkholderia infection ratio and clade composition of overwintering R. pedestris populations as well as prevalence and diversity of the genus Burkholderia in soil by conducting a two-year field survey. From the field survey, we found 29 overwintering R. pedestris adults in forested areas nearby soybean fields. Diagnostic PCR analysis revealed that overall infection rate of the symbiotic Burkholderia was 93.1% from overwintering adults. Among the Burkholderia-infected R. pedestris, 70.4% of individuals harbored unclassified Burkholderia clades whereas 22.2% and 7.4% of R. pedestris harbor stinkbug-associated beneficial and environmental (SBE) group and Burkholderia cepacia and complex (BCC), respectively. All R. pedestris were infected with a single clade of Burkholderia. In soil, 56.2% of soil samples were Burkholderia positive, and unlike R. pedestris, multiple Burkholderia clades were detected from 62.2% of those samples. Clade composition of the genus Burkholderia in the samples with the bacteria was 91.1%, 60.0%, 31.1% and 8.8% for plant-associated beneficial and environment (PBE), BCC, SBE and unclassified clade, respectively.}, } @article {pmid31192354, year = {2019}, author = {Liu, Z and Chen, W and Jiao, S and Wang, X and Fan, M and Wang, E and Wei, G}, title = {New insight into the evolution of symbiotic genes in black locust-associated rhizobia.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz116}, pmid = {31192354}, issn = {1759-6653}, abstract = {Nitrogen fixation in legumes occurs via symbiosis with rhizobia. This process involves packages of symbiotic genes on mobile genetic elements that are readily transferred within or between rhizobial species, furnishing the recipient with the ability to interact with plant hosts. However, it remains elusive whether plant host migration has played a role in shaping the current distribution of genetic variation in symbiotic genes. Herein, we examined the genetic structure and phylogeographic pattern of symbiotic genes in 286 symbiotic strains of Mesorhizobium nodulating black locust (Robinia pseudoacacia), a cross-continental invasive legume species that is native to North America. We conducted detailed phylogeographic analysis and approximate Bayesian computation to unravel the complex demographic history of five key symbiotic genes. The sequencing results indicate an origin of symbiotic genes in Germany rather than North America. Our findings provide strong evidence of prehistoric lineage splitting and spatial expansion events resulting in multiple radiations of descendent clones from founding sequence types worldwide. Estimates of the timescale of divergence in North American and Chinese subclades suggest that black locust-specific symbiotic genes have been present in these continent many thousands of years before recent migration of plant host. Although numerous crop plants, including legumes, have found their centers of origin as centers of evolution and diversity, the number of legume-specific symbiotic genes with a known geographic origin is limited. This work sheds light on the coevolution of legumes and rhizobia.}, } @article {pmid31191571, year = {2019}, author = {Defrenne, CE and Philpott, TJ and Guichon, SHA and Roach, WJ and Pickles, BJ and Simard, SW}, title = {Shifts in Ectomycorrhizal Fungal Communities and Exploration Types Relate to the Environment and Fine-Root Traits Across Interior Douglas-Fir Forests of Western Canada.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {643}, doi = {10.3389/fpls.2019.00643}, pmid = {31191571}, issn = {1664-462X}, abstract = {Large-scale studies that examine the responses of ectomycorrhizal fungi across biogeographic gradients are necessary to assess their role in mediating current and predicted future alterations in forest ecosystem processes. We assessed the extent of environmental filtering on interior Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) ectomycorrhizal fungal communities across regional gradients in precipitation, temperature, and soil fertility in interior Douglas-fir dominated forests of western Canada. We also examined relationships between fine-root traits and mycorrhizal fungal exploration types by combining root and fungal trait measurements with next-generation sequencing. Temperature, precipitation, and soil C:N ratio affected fungal community dissimilarity and exploration type abundance but had no effect on α-diversity. Fungi with rhizomorphs (e.g., Piloderma sp.) or proteolytic abilities (e.g., Cortinarius sp.) dominated communities in warmer and less fertile environments. Ascomycetes (e.g., Cenococcum geophilum) or shorter distance explorers, which potentially cost the plant less C, were favored in colder/drier climates where soils were richer in total nitrogen. Environmental filtering of ectomycorrhizal fungal communities is potentially related to co-evolutionary history between Douglas-fir populations and fungal symbionts, suggesting success of interior Douglas-fir as climate changes may be dependent on maintaining strong associations with local communities of mycorrhizal fungi. No evidence for a link between root and fungal resource foraging strategies was found at the regional scale. This lack of evidence further supports the need for a mycorrhizal symbiosis framework that is independent of root trait frameworks, to aid in understanding belowground plant uptake strategies across environments.}, } @article {pmid31191510, year = {2019}, author = {Habineza, P and Muhammad, A and Ji, T and Xiao, R and Yin, X and Hou, Y and Shi, Z}, title = {The Promoting Effect of Gut Microbiota on Growth and Development of Red Palm Weevil, Rhynchophorus ferrugineus (Olivier) (Coleoptera: Dryophthoridae) by Modulating Its Nutritional Metabolism.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1212}, doi = {10.3389/fmicb.2019.01212}, pmid = {31191510}, issn = {1664-302X}, abstract = {Red palm weevil (RPW), Rhynchophorus ferrugineus Olivier, is a destructive pest for palm trees worldwide. Recent studies have shown that RPW gut is colonized by microbes and alterations in gut microbiota can significantly modify its hemolymph nutrition content. However, the exact effects of gut microbiota on RPW phenotype and the underlying mechanisms remain elusive. Here germ-free (GF) RPW larvae were generated from dechorionated eggs which were reared on sterilized artificial food under axenic conditions. Compared with controls, the larval development of GF RPW individuals was markedly depressed and their body mass was reduced as well. Furthermore, the content of hemolymph protein, glucose and triglyceride were dropped significantly in GF RPW larvae. Interestingly, introducing gut microbiota into GF individuals could significantly increase the levels of the three nutrition indices. Additionally, it has also been demonstrated that RPW larvae monoassociated with Lactococcus lactis exhibited the same level of protein content with the CR (conventionally reared) insects while feeding Enterobacter cloacae to GF larvae increased their hemolymph triglyceride and glucose content markedly. Consequently, our findings suggest that gut microbiota profoundly affect the development of this pest by regulating its nutrition metabolism and different gut bacterial species show distinct impact on host physiology. Taken together, the establishment of GF and gnotobiotic RPW larvae will advance the elucidation of molecular mechanisms behind the interactions between RPW and its gut microbiota.}, } @article {pmid31190278, year = {2019}, author = {Lee, SJ and Morse, D and Hijri, M}, title = {Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-019-00903-4}, pmid = {31190278}, issn = {1432-1890}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.}, } @article {pmid30999960, year = {2019}, author = {Sabūnas, V and Radzijevskaja, J and Sakalauskas, P and Petkevičius, S and Karvelienė, B and Žiliukienė, J and Lipatova, I and Paulauskas, A}, title = {Dirofilaria repens in dogs and humans in Lithuania.}, journal = {Parasites & vectors}, volume = {12}, number = {1}, pages = {177}, doi = {10.1186/s13071-019-3406-y}, pmid = {30999960}, issn = {1756-3305}, support = {VP1-3.1-ŠMM-01-V-02-003//Lietuvos Mokslo Taryba (LT)/ ; }, mesh = {Adult ; Aged ; Animals ; Child ; *Dirofilaria repens/microbiology ; Dirofilariasis/epidemiology/*parasitology ; Dog Diseases/epidemiology/*parasitology ; Dogs ; Eye Diseases/parasitology ; Female ; Humans ; Lithuania/epidemiology ; Male ; Middle Aged ; Phylogeny ; Polymerase Chain Reaction ; Prevalence ; Symbiosis ; Wolbachia/isolation & purification ; }, abstract = {BACKGROUND: In Lithuania, the first case of canine subcutaneous dirofilariosis was recorded in 2010. Since then, an increasing number of cases of canine dirofilariosis have been documented in different veterinary clinics throughout the country. Human dirofilariosis was diagnosed in Lithuania for the first time in September 2011. However, to the authors' knowledge, there are no published data on the presence and prevalence of autochthonous dirofilariosis in dogs and humans in the country. The present study provides information about the predominant species and prevalence of Dirofilaria in dogs and describes the cases of human dirofilariosis in Lithuania. It also outlines PCR detection of the bacterial endosymbiont Wolbachia that contributes to the inflammatory features of filarioid infection.

RESULTS: A total of 2280 blood samples and six adult worms from pet and shelter dogs were collected in the central and eastern regions of Lithuania in 2013-2015. Based on their morphological appearance, morphometric measurements and molecular analysis, all the adult nematodes were identified as Dirofilaria repens. The diagnosis of microfilariae in blood samples was based on blood smear analysis and Knott's test. The PCR and sequence analysis of the ribosomal DNA ITS2 region and cox1 gene confirmed the presence of D. repens. Overall, 61 (2.7%) of the 2280 blood samples were found to be positive for the presence of D. repens. The infection rate of D. repens was significantly higher in shelter dogs (19.0%; 19/100) than in pet dogs (1.9%; 42/2180) (χ2 = 100.039, df = 1, P < 0.0001). Forty-nine DNA samples of D. repens-infected dogs were tested for the presence of the bacterial endosymbiont Wolbachia and, of these, 40 samples (81.6%) were found to be positive. Three ocular and six subcutaneous cases of human dirofilariosis were diagnosed in Lithuania in the period 2011-2018.

CONCLUSIONS: To the authors' knowledge, this is the first report of autochthonous D. repens infection in dogs and humans in Lithuania. The present data demonstrate that D. repens is the main etiological agent of dirofilariosis in Lithuania. The DNA of the filarioid endosymbiotic bacterium Wolbachia was detected in the vast majority of dogs infected with D. repens.}, } @article {pmid30806054, year = {2019}, author = {Du, J and Jiang, S and Wei, J and Shen, Y and Ni, J}, title = {[Co-expression of lignocellulase from termite and their endosymbionts].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {35}, number = {2}, pages = {244-253}, doi = {10.13345/j.cjb.180235}, pmid = {30806054}, issn = {1000-3061}, mesh = {Animals ; Cellulase ; Cellulose ; Hydrolysis ; *Isoptera ; Lignin ; Symbiosis ; beta-Glucosidase ; }, abstract = {Natural lignocellulosic materials contain cellulose, hemicellulose, and lignin. Cellulose hydrolysis to glucose requires a series of lignocellulases. Recently, the research on the synergistic effect of lignocellulases has become a new research focus. Here, four lignocellulase genes encoding β-glucosidase, endo-1,4-β-glucanase, xylanase and laccase from termite and their endosymbionts were cloned into pETDuet-1 and pRSFDuet-1 and expressed in Escherichia coli. After SDS-PAGE analysis, the corresponding protein bands consistent with the theoretical values were observed and all the proteins showed enzyme activities. We used phosphoric acid swollen cellulose (PASC) as substrate to measure the synergistic effect of crude extracts of co-expressing enzymes and the mixture of single enzyme. The co-expressed enzymes increased the degradation efficiency of PASC by 44% compared with the single enzyme mixture; while the degradation rate increased by 34% and 20%, respectively when using filter paper and corn cob pretreated with phosphoric acid as substrates. The degradation efficiency of the co-expressed enzymes was higher than the total efficiency of the single enzyme mixture.}, } @article {pmid30708172, year = {2019}, author = {Shaikevich, E and Bogacheva, A and Rakova, V and Ganushkina, L and Ilinsky, Y}, title = {Wolbachia symbionts in mosquitoes: Intra- and intersupergroup recombinations, horizontal transmission and evolution.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {24-34}, doi = {10.1016/j.ympev.2019.01.020}, pmid = {30708172}, issn = {1095-9513}, mesh = {Aedes/microbiology ; Alleles ; Animals ; Anopheles/genetics ; *Biological Evolution ; Culicidae/*microbiology ; Databases, Genetic ; *Gene Transfer, Horizontal ; Haplotypes/genetics ; Humans ; Mosquito Vectors/microbiology ; Multilocus Sequence Typing ; Phylogeny ; *Recombination, Genetic ; Species Specificity ; *Symbiosis ; Wolbachia/*genetics ; }, abstract = {Many mosquitoes harbour Wolbachia symbionts that could affect the biology of their host in different ways. Evolutionary relationships of mosquitoes' Wolbachia infection, geographical distribution and symbiont prevalence in many mosquito species are not yet clear. Here, we present the results of Wolbachia screening of 17 mosquito species of four genera-Aedes, Anopheles, Coquillettidia and Culex collected from five regions of Eastern Europe and the Caucasus in 2012-2016. Based on multilocus sequence typing (MLST) data previously published and generated in this study, we try to reveal genetic links between mosquitoes' and other hosts' Wolbachia. The Wolbachia symbionts are found in Culex pipiens, Aedes albopictus and Coquillettidia richiardii and for the first time in Aedes cinereus and Aedes cantans, which are important vectors of human pathogens. Phylogenetic analysis demonstrated multiple origins of infection in mosquitoes although the one-allele-criterion approach revealed links among B-supergroup mosquito Wolbachia with allele content of lepidopteran hosts. The MLST gene content of strain wAlbA from the A-supergroup is linked with different ant species. Several cases of intersupergroup recombinations were found. One of them occurred in the wAlbaB strain of Aedes albopictus, which contains the coxA allele of the A-supergroup, whereas other loci, including wsp, belong to supergroup B. Other cases are revealed for non-mosquito symbionts and they exemplified genetic exchanges of A, B and F supergroups. We conclude that modern Wolbachia diversity in mosquitoes and in many other insect taxa is a recent product of strain recombination and symbiont transfers.}, } @article {pmid30665024, year = {2019}, author = {Kitamoto, M and Tokuda, G and Watanabe, H and Arioka, M}, title = {Characterization of CBM36-containing GH11 endoxylanase NtSymX11 from the hindgut metagenome of higher termite Nasutitermes takasagoensis displaying prominent catalytic activity.}, journal = {Carbohydrate research}, volume = {474}, number = {}, pages = {1-7}, doi = {10.1016/j.carres.2019.01.003}, pmid = {30665024}, issn = {1873-426X}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*chemistry/enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Calcium/chemistry ; Cloning, Molecular ; Endo-1,4-beta Xylanases/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genetic Vectors/chemistry/metabolism ; Glucuronates/chemistry/*metabolism ; Hydrogen-Ion Concentration ; Intestines/microbiology ; Isoptera/*microbiology ; Kinetics ; Metagenome ; Oligosaccharides/chemistry/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Symbiosis/physiology ; Temperature ; Xylans/chemistry/*metabolism ; }, abstract = {Symbionts in the gut of termites are expected to be large sources of enzymes involved in lignocellulose degradation, but their biotechnological potential has not been fully explored. In this study, we expressed, purified, and biochemically characterized a glycoside hydrolase family 11 xylanase, NtSymX11, from a symbiotic bacterium of the higher termite, Nasutitermes takasagoensis. NtSymX11 is a multimodular enzyme consisting of a catalytic domain and two tandem carbohydrate-binding modules (CBM36). The pH and temperature optima of NtSymX11 were pH 6.0 and 40 °C, respectively. By comparing the properties of full-length and truncated variants of NtSymX11, it was shown that CBM36 decreases the enzyme stability at acidic pH and high temperature. The main products from xylohexaose and various xylan substrates were X1-X3 xylooligosaccharides. Analysis of kinetic parameters indicated that NtSymX11 displays an outstanding catalytic performance when compared to other reported xylanases, and CBM36 enhances the activity by increasing the affinity to the substrate. Addition of Ca2+ boosted the activity of full-length enzyme, but not the truncated variant lacking the CBM, against the insoluble substrate, suggesting that CBM36 plays a role in the Ca2+-dependent increase of catalytic efficiency.}, } @article {pmid30344303, year = {2018}, author = {Jankauskaitė, L and Misevičienė, V and Vaidelienė, L and Kėvalas, R}, title = {Lower Airway Virology in Health and Disease-From Invaders to Symbionts.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {54}, number = {5}, pages = {}, pmid = {30344303}, issn = {1648-9144}, mesh = {Adaptive Immunity ; Asthma/immunology/virology ; Bacteria/virology ; Bacteriophages/genetics ; Chronic Disease ; Humans ; Immunity, Innate ; Lung/*virology ; Lung Diseases/*virology ; *Microbiota ; Symbiosis ; Virus Diseases/immunology/*virology ; Viruses/*pathogenicity ; }, abstract = {Studies of human airway virome are relatively recent and still very limited. Culture-independent microbial techniques showed growing evidence of numerous viral communities in the respiratory microbial ecosystem. The significance of different acute respiratory viruses is already known in the pathogenesis of chronic conditions, such as asthma, cystic fibrosis (CF), or chronic obstructive lung disease (COPD), and their exacerbations. Viral pathogens, such as influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, or rhinovirus, have been associated with impaired immune response, acute exacerbations, and decrease in lung function in chronic lung diseases. However, more data have attributed a role to Herpes family viruses or the newly identified Anelloviridae family of viruses in chronic diseases, such as asthma, idiopathic pulmonary fibrosis (IPF), or CF. Impaired antiviral immunity, bacterial colonization, or used medication, such as glucocorticoids or antibiotics, contribute to the imbalance of airway microbiome and may shape the local viral ecosystem. A specific part of virome, bacteriophages, frames lung microbial communities through direct contact with its host, the specific bacteria known as Pseudomonas aeruginosa or their biofilm formation. Moreover, antibiotic resistance is induced through phages via horizontal transfer and leads to more severe exacerbations of chronic airway conditions. Morbidity and mortality of asthma, COPD, CF, and IPF remains high, despite an increased understanding and knowledge about the impact of respiratory virome in the pathogenesis of these conditions. Thus, more studies focus on new prophylactic methods or therapeutic agents directed toward viral⁻host interaction, microbial metabolic function, or lung microbial composition rearrangement.}, } @article {pmid30343053, year = {2018}, author = {Li, J and Han, M and Yu, J}, title = {Simple paratransgenic mosquitoes models and their dynamics.}, journal = {Mathematical biosciences}, volume = {306}, number = {}, pages = {20-31}, doi = {10.1016/j.mbs.2018.10.005}, pmid = {30343053}, issn = {1879-3134}, mesh = {Animals ; Animals, Genetically Modified ; Bacteria/*genetics/pathogenicity ; Disease Transmission, Infectious ; Female ; Host Microbial Interactions ; Host-Parasite Interactions ; Humans ; Malaria/prevention & control/transmission ; Male ; Mathematical Concepts ; *Models, Biological ; Mosquito Vectors/growth & development/*microbiology/*parasitology ; Plasmodium/microbiology/pathogenicity ; Symbiosis ; }, abstract = {To study the interactive dynamics of wild mosquitoes and mosquitoes carrying genetically-modified bacteria, we formulate continuous-time homogeneous and stage-structured models in this study. With appropriate transformations, complete results of the existence and stability of all boundary and positive equilibria for the homogeneous model are established and complete results of the existence and local stability of all boundary and positive equilibria for the stage-structured model are obtained as well. The outcomes from the homogeneous and the stage-structured models are similar. Based on the homogeneous model, we particularly investigate how the horizontal transmission of the transgenic bacteria, via the uptake rate of the transgenic bacteria, affects the interactive dynamics.}, } @article {pmid30045944, year = {2018}, author = {Macpherson, AJ and Ganal-Vonarburg, SC}, title = {IgA-about the unexpected.}, journal = {The Journal of experimental medicine}, volume = {215}, number = {8}, pages = {1965-1966}, pmid = {30045944}, issn = {1540-9538}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Immunoglobulin A ; Symbiosis ; }, abstract = {In this issue of JEM, Nakajima et al. (https://doi.org/10.1084/jem.20180427) demonstrate that glycan-dependent, epitope-independent IgA coating of intestinal bacteria alters bacterial gene expression and metabolism. This conferred coated bacteria with fitness within the mucus niche and contributed to intestinal homeostasis through cross-phylum interactions.}, } @article {pmid30013237, year = {2018}, author = {Boldock, E and Surewaard, BGJ and Shamarina, D and Na, M and Fei, Y and Ali, A and Williams, A and Pollitt, EJG and Szkuta, P and Morris, P and Prajsnar, TK and McCoy, KD and Jin, T and Dockrell, DH and van Strijp, JAG and Kubes, P and Renshaw, SA and Foster, SJ}, title = {Human skin commensals augment Staphylococcus aureus pathogenesis.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {881-890}, pmid = {30013237}, issn = {2058-5276}, support = {//Wellcome Trust/United Kingdom ; MR/K015753/1//Medical Research Council/United Kingdom ; MR/M004864/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*metabolism ; Disease Models, Animal ; Humans ; Inflammasomes/metabolism ; Kupffer Cells/cytology/immunology ; Macrophages/metabolism ; Mice ; Microbiota ; Peptidoglycan/metabolism/*pharmacology ; Reactive Oxygen Species/metabolism ; Sepsis/immunology/*microbiology ; Skin/*microbiology ; Staphylococcal Infections/immunology/*microbiology ; Staphylococcus aureus/growth & development/*pathogenicity ; Symbiosis ; Virulence ; }, abstract = {All bacterial infections occur within a polymicrobial environment, from which a pathogen population emerges to establish disease within a host. Emphasis has been placed on prevention of pathogen dominance by competing microflora acting as probiotics1. Here we show that the virulence of the human pathogen Staphylococcus aureus is augmented by native, polymicrobial, commensal skin flora and individual species acting as 'proinfectious agents'. The outcome is pathogen proliferation, but not commensal. Pathogenesis augmentation can be mediated by particulate cell wall peptidoglycan, reducing the S. aureus infectious dose by over 1,000-fold. This phenomenon occurs using a range of S. aureus strains and infection models and is not mediated by established receptor-mediated pathways including Nod1, Nod2, Myd88 and the NLPR3 inflammasome. During mouse sepsis, augmentation depends on liver-resident macrophages (Kupffer cells) that capture and internalize both the pathogen and the proinfectious agent, leading to reduced production of reactive oxygen species, pathogen survival and subsequent multiple liver abscess formation. The augmented infection model more closely resembles the natural situation and establishes the role of resident environmental microflora in the initiation of disease by an invading pathogen. As the human microflora is ubiquitous2, its role in increasing susceptibility to infection by S. aureus highlights potential strategies for disease prevention.}, } @article {pmid29922600, year = {2018}, author = {Fourie, R and Kuloyo, OO and Mochochoko, BM and Albertyn, J and Pohl, CH}, title = {Iron at the Centre of Candida albicans Interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {185}, pmid = {29922600}, issn = {2235-2988}, mesh = {Candida albicans/*metabolism/pathogenicity ; Candidiasis ; Gastrointestinal Tract ; Gene Expression Regulation, Fungal ; Homeostasis ; Host-Pathogen Interactions/*physiology ; Humans ; Immunity ; Iron/*metabolism ; Microbial Interactions/*physiology ; Symbiosis ; Virulence ; }, abstract = {Iron is an absolute requirement for both the host and most pathogens alike and is needed for normal cellular growth. The acquisition of iron by biological systems is regulated to circumvent toxicity of iron overload, as well as the growth deficits imposed by iron deficiency. In addition, hosts, such as humans, need to limit the availability of iron to pathogens. However, opportunistic pathogens such as Candida albicans are able to adapt to extremes of iron availability, such as the iron replete environment of the gastrointestinal tract and iron deficiency during systemic infection. C. albicans has developed a complex and effective regulatory circuit for iron acquisition and storage to circumvent iron limitation within the human host. As C. albicans can form complex interactions with both commensal and pathogenic co-inhabitants, it can be speculated that iron may play an important role in these interactions. In this review, we highlight host iron regulation as well as regulation of iron homeostasis in C. albicans. In addition, the review argues for the need for further research into the role of iron in polymicrobial interactions. Lastly, the role of iron in treatment of C. albicans infection is discussed.}, } @article {pmid29792944, year = {2018}, author = {Stouthamer, CM and Kelly, S and Hunter, MS}, title = {Enrichment of low-density symbiont DNA from minute insects.}, journal = {Journal of microbiological methods}, volume = {151}, number = {}, pages = {16-19}, doi = {10.1016/j.mimet.2018.05.013}, pmid = {29792944}, issn = {1872-8359}, mesh = {Animals ; Arthropods/genetics/microbiology ; Bacteria/*genetics ; DNA, Bacterial/*isolation & purification ; Host Microbial Interactions/*genetics ; Insecta/genetics/*microbiology ; Molecular Biology/*methods ; Sequence Analysis, DNA ; *Symbiosis ; Wasps/genetics/microbiology ; Wolbachia/genetics ; }, abstract = {Symbioses between bacteria and insects are often associated with changes in important biological traits that can significantly affect host fitness. To a large extent, studies of these interactions have been based on physiological changes or induced phenotypes in the host, and the genetic mechanisms by which symbionts interact with their hosts have only recently become better understood. Learning about symbionts has been challenging in part due to difficulties such as obtaining enough high quality genomic material for high throughput sequencing technology, especially for symbionts present in low titers, and in small or difficult to rear non-model hosts. Here we introduce a new method that substantially increases the yield of bacterial DNA in minute arthropod hosts, and requires less starting material relative to previous published methods.}, } @article {pmid29725101, year = {2018}, author = {Toju, H and Peay, KG and Yamamichi, M and Narisawa, K and Hiruma, K and Naito, K and Fukuda, S and Ushio, M and Nakaoka, S and Onoda, Y and Yoshida, K and Schlaeppi, K and Bai, Y and Sugiura, R and Ichihashi, Y and Minamisawa, K and Kiers, ET}, title = {Core microbiomes for sustainable agroecosystems.}, journal = {Nature plants}, volume = {4}, number = {5}, pages = {247-257}, doi = {10.1038/s41477-018-0139-4}, pmid = {29725101}, issn = {2055-0278}, mesh = {*Agriculture/methods ; *Ecosystem ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.}, } @article {pmid29659974, year = {2018}, author = {Chan, CX and Vaysberg, P and Price, DC and Pelletreau, KN and Rumpho, ME and Bhattacharya, D}, title = {Active Host Response to Algal Symbionts in the Sea Slug Elysia chlorotica.}, journal = {Molecular biology and evolution}, volume = {35}, number = {7}, pages = {1706-1711}, doi = {10.1093/molbev/msy061}, pmid = {29659974}, issn = {1537-1719}, mesh = {Animals ; Down-Regulation ; Mollusca/*metabolism/*microbiology ; Stramenopiles/*physiology ; *Symbiosis ; Up-Regulation ; }, abstract = {Sacoglossan sea slugs offer fascinating systems to study the onset and persistence of algal-plastid symbioses. Elysia chlorotica is particularly noteworthy because it can survive for months, relying solely on energy produced by ingested plastids of the stramenopile alga Vaucheria litorea that are sequestered in cells lining its digestive diverticula. How this animal can maintain the actively photosynthesizing organelles without replenishment of proteins from the lost algal nucleus remains unknown. Here, we used RNA-Seq analysis to test the idea that plastid sequestration leaves a significant signature on host gene expression during E. chlorotica development. Our results support this hypothesis and show that upon exposure to and ingestion of V. litorea plastids, genes involved in microbe-associated molecular patterns and oxidative stress-response mechanisms are significantly up-regulated. Interestingly, our results with E. chlorotica mirror those found with corals that maintain dinoflagellates as intact cells in symbiosomes, suggesting parallels between these animal-algal symbiotic interactions.}, } @article {pmid29659942, year = {2018}, author = {Vdacný, P}, title = {Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial-Placental Split.}, journal = {Molecular biology and evolution}, volume = {35}, number = {7}, pages = {1757-1769}, pmid = {29659942}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Ciliophora/*genetics ; Gastrointestinal Tract/*parasitology ; Marsupialia/*parasitology ; RNA, Ribosomal, 18S/genetics ; Symbiosis ; }, abstract = {Trichostome ciliates are among the most conspicuous protists in the gastrointestinal tract of a large variety of vertebrates. However, little is still known about phylogeny of the trichostome/vertebrate symbiotic systems, evolutionary correlations between trichostome extrinsic traits, and character-dependent diversification of trichostomes. These issues were investigated here, using the relaxed molecular clock technique along with stochastic mapping of character evolution, and binary-state speciation and extinction models. Clock analyses revealed that trichostomes colonized the vertebrate gastrointestinal tract ∼135 Ma, that is, near the paleontological minimum for the split of therian mammals into marsupials and placentals. According to stochastic mapping, the last common ancestor of trichostomes most likely invaded the hindgut of a mammal. Although multiple shifts to fish/amphibian or avian hosts and to the foregut compartments took place during the trichostome phylogeny, only transition to the foregut was recognized as a key innovation responsible for the explosive radiation of ophryoscolecid trichostomes after the Cretaceous/Tertiary boundary, when ungulates began their diversification. Since crown radiations of main trichostome lineages follow those of their mammalian hosts and are in agreement with their historic dispersal routes, the present time-calibrated phylogeny might help to elucidate controversies in the geological and molecular timing of the split between marsupials and placental mammals.}, } @article {pmid29610517, year = {2018}, author = {Leth, ML and Ejby, M and Workman, C and Ewald, DA and Pedersen, SS and Sternberg, C and Bahl, MI and Licht, TR and Aachmann, FL and Westereng, B and Abou Hachem, M}, title = {Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut.}, journal = {Nature microbiology}, volume = {3}, number = {5}, pages = {570-580}, doi = {10.1038/s41564-018-0132-8}, pmid = {29610517}, issn = {2058-5276}, mesh = {ATP-Binding Cassette Transporters/metabolism ; Bacterial Proteins/*metabolism ; Bacteroides/*growth & development/metabolism ; Clostridiales/*growth & development/metabolism ; Coculture Techniques ; Dietary Fiber/*metabolism ; Endo-1,4-beta Xylanases/metabolism ; Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Humans ; Substrate Specificity ; Symbiosis ; Xylans/*metabolism ; }, abstract = {Metabolism of dietary glycans is pivotal in shaping the human gut microbiota. However, the mechanisms that promote competition for glycans among gut commensals remain unclear. Roseburia intestinalis, an abundant butyrate-producing Firmicute, is a key degrader of the major dietary fibre xylan. Despite the association of this taxon to a healthy microbiota, insight is lacking into its glycan utilization machinery. Here, we investigate the apparatus that confers R. intestinalis growth on different xylans. R. intestinalis displays a large cell-attached modular xylanase that promotes multivalent and dynamic association to xylan via four xylan-binding modules. This xylanase operates in concert with an ATP-binding cassette transporter to mediate breakdown and selective internalization of xylan fragments. The transport protein of R. intestinalis prefers oligomers of 4-5 xylosyl units, whereas the counterpart from a model xylan-degrading Bacteroides commensal targets larger ligands. Although R. intestinalis and the Bacteroides competitor co-grew in a mixed culture on xylan, R. intestinalis dominated on the preferred transport substrate xylotetraose. These findings highlight the differentiation of capture and transport preferences as a possible strategy to facilitate co-growth on abundant dietary fibres and may offer a unique route to manipulate the microbiota based on glycan transport preferences in therapeutic interventions to boost distinct taxa.}, } @article {pmid29140081, year = {2018}, author = {Craft, KM and Townsend, SD}, title = {The Human Milk Glycome as a Defense Against Infectious Diseases: Rationale, Challenges, and Opportunities.}, journal = {ACS infectious diseases}, volume = {4}, number = {2}, pages = {77-83}, pmid = {29140081}, issn = {2373-8227}, support = {T32 GM065086/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/metabolism ; Bacterial Infections/immunology/metabolism/microbiology ; Communicable Diseases/etiology/*metabolism/microbiology ; *Disease Resistance/immunology ; Host-Pathogen Interactions ; Humans ; *Milk, Human/chemistry ; Oligosaccharides/chemistry/*metabolism ; Symbiosis ; }, abstract = {Each year over 3 million people die from infectious diseases with most of these deaths being poor and young children who live in low- and middle-income countries. Infectious diseases emerge for a multitude of reasons. On the social front, reasons include a breakdown of public health standards, international travel, and immigration (for financial, civil, and social reasons). At the molecular level, the modern rise of infectious diseases is tied to the juxtaposition of drug-resistant pathogens and a lack of new antimicrobials. The consequence is the possibility that humankind will return to the preantibiotic era wherein millions of people will perish from what should be trivial illnesses. Given the stakes, it is imperative that the chemistry community take leadership in delivering new antibiotic leads for clinical development. We believe this can happen through innovation in two areas. First is the development of novel chemical scaffolds to treat infections caused by multidrug-resistant pathogens. The second area, which is not exclusive to the first, is the generation of antibiotics that do not cause collateral damage to the host or the host's microbiome. Both can be enabled through advances in chemical synthesis. It is with this general philosophy in mind that we hypothesized human milk oligosaccharides (HMOs) could serve as novel chemical scaffolds for antibacterial development. We provide herein a personal account of our laboratory's progress toward the goal of using HMOs as a defense against infectious diseases.}, } @article {pmid28860659, year = {2017}, author = {Chen, R and Wang, Z and Chen, J and Jiang, LY and Qiao, GX}, title = {Insect-bacteria parallel evolution in multiple-co-obligate-aphid association: a case in Lachninae (Hemiptera: Aphididae).}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10204}, pmid = {28860659}, issn = {2045-2322}, mesh = {Animals ; Aphids/*classification/genetics/*microbiology ; Bacterial Proteins/genetics ; Buchnera/*classification/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Genome Size ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Symbiosis ; }, abstract = {Parallel phylogenies between aphid and its obligate symbiont Buchnera are hot topics which always focused on aphid lower taxonomic levels. Symbionts in the subfamily Lachninae are special. Buchnera in many lachnine species has undergone functional and genome size reduction that was replaced by other co-obligate symbionts. In this study, we constructed the phylogenetic relationships of Lachninae with a combined dataset of five genes sequenced from Buchnera to estimate the effects of a dual symbiotic system in the aphid-Buchnera cospeciation association. The phylogeny of Buchnera in Lachninae was well-resolved in the combined dataset. Each of the genera formed strongly supported monophyletic groups, with the exception of the genus Cinara. The phylogeny based on sequences from Buchnera was divided into five tribes according to the clades of the Lachninae hosts tree, with the phylogenies of Buchnera and Lachninae being generally congruent. These results first provided evidence of parallel evolution at the aphid subfamily level comprehensively and supported the view that topological congruence between the phylogenies of Buchnera and Lachninae would not be interfered with the other co-obligate symbionts, such as Sarretia, in aphid-entosymbiont association. These results also provided new insight in understanding host-plant coevolution in lachnine lineages.}, } @article {pmid31189014, year = {2019}, author = {Guo, X and Zhao, Z and Mar, SS and Zhang, D and Saunders, RMK}, title = {A symbiotic balancing act: arbuscular mycorrhizal specificity and specialist fungus gnat pollination in the mycoheterotrophic genus Thismia (Thismiaceae).}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcz087}, pmid = {31189014}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Mycorrhizal associations in mycoheterotrophic plants are generally more specialized than in autotrophs. Mycoheterotrophs typically bear small, inconspicuous flowers that often self-pollinate to maximize seed set, although some have structurally complex flowers indicative of xenogamy. A trade-off has previously been proposed between specialization in these above- and below-ground symbioses, although empirical data are lacking.

METHODS: We used next-generation DNA sequencing to compare the mycorrhizal communities from the roots of a mycoheterotrophic species, Thismia tentaculata (Thismiaceae), and its neighbouring autotrophs. We furthermore conducted detailed assessments of floral phenology and pollination ecology, and performed artificial pollination experiments to determine the breeding system.

KEY RESULTS: Thismia tentaculata maintains a symbiotic association with a single arbuscular mycorrhizal Rhizophagus species. The flowers are pollinated by a single species of fungus gnats (Corynoptera, Sciaridae), which are attracted by the yellow pigments and are temporarily restrained within the perianth chamber before departing via apertures between the anthers. The plants are self-compatible but predominantly xenogamous.

CONCLUSIONS: Our findings demonstrate that T. tentaculata maintains highly specialized associations with pollinators and mycorrhizal fungi, both of which are widely distributed. We suggest that specialization in multiple symbiotic interactions is possible in mycoheterotrophs if redundant selective pressures are not exerted to further restrict an already constrained suite of life-history traits.}, } @article {pmid31186513, year = {2019}, author = {Gabay, Y and Parkinson, JE and Wilkinson, SP and Weis, VM and Davy, SK}, title = {Inter-partner specificity limits the acquisition of thermotolerant symbionts in a model cnidarian-dinoflagellate symbiosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0429-5}, pmid = {31186513}, issn = {1751-7370}, abstract = {The ability of corals and other cnidarians to survive climate change depends partly on the composition of their endosymbiont communities. The dinoflagellate family Symbiodiniaceae is genetically and physiologically diverse, and one proposed mechanism for cnidarians to acclimate to rising temperatures is to acquire more thermally tolerant symbionts. However, cnidarian-dinoflagellate associations vary in their degree of specificity, which may limit their capacity to alter symbiont communities. Here, we inoculated symbiont-free polyps of the sea anemone Exaiptasia pallida (commonly referred to as 'Aiptasia'), a model system for the cnidarian-dinoflagellate symbiosis, with simultaneous or sequential mixtures of thermally tolerant and thermally sensitive species of Symbiodiniaceae. We then monitored symbiont success (relative proportional abundance) at normal and elevated temperatures across two to four weeks. All anemones showed signs of bleaching at high temperature. During simultaneous inoculations, the native, thermally sensitive Breviolum minutum colonized polyps most successfully regardless of temperature when paired against the non-native but more thermally tolerant Symbiodinium microadriaticum or Durusdinium trenchii. Furthermore, anemones initially colonized with B. minutum and subsequently exposed to S. microadriaticum failed to acquire the new symbiont. These results highlight how partner specificity may place strong limitations on the ability of certain cnidarians to acquire more thermally tolerant symbionts, and hence their adaptive potential under climate change.}, } @article {pmid31186318, year = {2019}, author = {Chrostek, E and Gerth, M}, title = {Is Anopheles gambiae a Natural Host of Wolbachia?.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00784-19}, pmid = {31186318}, issn = {2150-7511}, abstract = {Wolbachia (Alphaproteobacteria, Rickettsiales) is an intraovarially transmitted symbiont of insects able to exert striking phenotypes, including reproductive manipulations and pathogen blocking. These phenotypes make Wolbachia a promising tool to combat mosquito-borne diseases. Although Wolbachia is present in the majority of terrestrial arthropods, including many disease vectors, it was considered absent from Anopheles gambiae mosquitos, the main vectors of malaria in sub-Saharan Africa. In 2014, Wolbachia sequences were detected in A. gambiae samples collected in Burkina Faso. Subsequently, similar evidence came from collections all over Africa, revealing a high Wolbachia 16S rRNA sequence diversity, low abundance, and a lack of congruence between host and symbiont phylogenies. Here, we reanalyze and discuss recent evidence on the presence of Wolbachia sequences in A. gambiae. We find that although detected at increasing frequencies, the unusual properties of these Wolbachia sequences render them insufficient to diagnose natural infections in A. gambiae Future studies should focus on uncovering the origin of Wolbachia sequence variants in Anopheles and seeking sequence-independent evidence for this new symbiosis. Understanding the ecology of Anopheles mosquitos and their interactions with Wolbachia will be key in designing successful, integrative approaches to limit malaria spread. Although the prospect of using Wolbachia to fight malaria is intriguing, the newly discovered strains do not bring it closer to realization.IMPORTANCEAnopheles gambiae mosquitos are the main vectors of malaria, threatening around half of the world's population. The bacterial symbiont Wolbachia can interfere with disease transmission by other important insect vectors, but until recently, it was thought to be absent from natural A. gambiae populations. Here, we critically analyze the genomic, metagenomic, PCR, imaging, and phenotypic data presented in support of the presence of natural Wolbachia infections in A. gambiae We find that they are insufficient to diagnose Wolbachia infections and argue for the need of obtaining robust data confirming basic Wolbachia characteristics in this system. Determining the Wolbachia infection status of Anopheles is critical due to its potential to influence Anopheles population structure and Plasmodium transmission.}, } @article {pmid31186308, year = {2019}, author = {Septer, AN}, title = {The Vibrio-Squid Symbiosis as a Model for Studying Interbacterial Competition.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00108-19}, pmid = {31186308}, issn = {2379-5077}, abstract = {The symbiosis between Euprymna scolopes squid and its bioluminescent bacterial symbiont, Vibrio fischeri, is a valuable model system to study a natural, coevolved host-microbe association. Over the past 30 years, researchers have developed and optimized many experimental methods to study both partners in isolation and during symbiosis. These powerful tools, along with a strong foundational knowledge about the system, position the Vibrio-squid symbiosis at the forefront of host-microbe interactions because this system is uniquely suited to investigation of symbiosis from both host and bacterial perspectives. Moreover, the ability to isolate and characterize different strains of V. fischeri has revealed exciting new insights about how different genotypes evolve to compete for a host niche, including deploying interbacterial weapons early during host colonization. This Perspective explores how interbacterial warfare influences the diversity and spatial structure of the symbiotic population, as well as the possible effects that intraspecific competition might have on the host.}, } @article {pmid31184576, year = {2019}, author = {Gomes, DF and Tullio, LD and Del Cerro, P and Nakatani, AS and Rolla-Santos, AAP and Gil-Serrano, A and Megías, M and Ollero, FJ and Hungria, M}, title = {Regulation of hsnT, nodF and nodE genes in Rhizobium tropici CIAT 899 and their roles in the synthesis of Nod factors and in the symbiosis.}, journal = {Microbiology (Reading, England)}, volume = {}, number = {}, pages = {}, doi = {10.1099/mic.0.000824}, pmid = {31184576}, issn = {1465-2080}, abstract = {Rhizobium tropici strain CIAT 899 possesses outstanding agronomic properties as it displays tolerance to environmental stresses, a broad host range and high effectiveness in fixing nitrogen with the common bean (Phaseolus vulgaris L.); in addition, it carries intriguing features such as five copies of the regulatory nodD gene, and the capacity to synthesize a variety of nodulation factors (NFs), even in a flavonoid-independent manner, when submitted to abiotic stresses. However, the roles of several nod genes of the repertoire of CIAT 899 remain to be determined. In this study, we obtained mutants for the hsnT, nodF and nodE genes of CIAT 899 and investigated their expression, NF structures and symbiotic properties. Either in the presence of the flavonoid apigenin, or of salt the expression of hsnT, nodF and nodE in wild-type CIAT 899 was highly up-regulated in comparison to the mutants of all five copies of nodD, indicating the roles that regulatory nodD genes play in the activation of hsnT, nodF and nodE; however, NodD1 was recognized as the main inducer. In total, 29 different NF structures were synthesized by wild-type CIAT 899 induced by apigenin, and 36 when induced by salt, being drastically reduced by mutations in hsnT, nodF and nodE, especially under osmotic stress, with specific changes related to each gene, indicating that the three genes participate in the synthesis of NFs. Mutations in hsnT, nodF and nodE affected differently symbiotic performance (nodule number and shoot dry weight), according to the host plant. Our results indicate that the expression of hsnT, nodF and nodE genes of CIAT 899 is mediated by nodD genes, and although these three genes do not belong to the main set of genes controlling nodulation, they contribute to the synthesis of NFs that will impact symbiotic performance and host specificity.}, } @article {pmid31182796, year = {2019}, author = {Gruber-Vodicka, HR and Leisch, N and Kleiner, M and Hinzke, T and Liebeke, M and McFall-Ngai, M and Hadfield, MG and Dubilier, N}, title = {Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0475-9}, pmid = {31182796}, issn = {2058-5276}, abstract = {Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans1,2. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host3-6. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)7,8 and has a genomic repertoire similar to that of rickettsial parasites9,10, but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host's internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations11-13. This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan's nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter.}, } @article {pmid31182497, year = {2019}, author = {Lamouche, F and Chaumeret, A and Guefrachi, I and Barrière, Q and Pierre, O and Guérard, F and Gilard, F and Giraud, E and Dessaux, Y and Gakière, B and Timchenko, T and Kereszt, A and Mergaert, P and Alunni, B}, title = {From intracellular bacteria to differentiated bacteroids: transcriptome and metabolome analysis in Aeschynomene nodules using the Bradyrhizobium sp. ORS285 bclA mutant.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00191-19}, pmid = {31182497}, issn = {1098-5530}, abstract = {Soil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells where they differentiate into nitrogen-fixing bacteroids. Several legume lineages enforce their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. ORS285, a symbiont of Aeschynomene spp.. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells but they cannot differentiate into enlarged polyploid and functional bacteroids. The bclA nodule bacteria constitute thus an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied with a first transcriptome switch involving several hundreds of upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving less genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a non-symbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.ImportanceThe legume-rhizobium symbiosis is a major ecological process fueling the biogeochemical nitrogen cycle with reduced nitrogen. It represents also a promising strategy to cut down the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.}, } @article {pmid31182189, year = {2019}, author = {Strohm, E and Herzner, G and Ruther, J and Kaltenpoth, M and Engl, T}, title = {Nitric oxide radicals are emitted by wasp eggs to kill mold fungi.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.43718}, pmid = {31182189}, issn = {2050-084X}, abstract = {Detrimental microbes caused the evolution of a great diversity of antimicrobial defenses in plants and animals. Insects developing underground seem particularly threatened. Here we show that the eggs of a solitary digger wasp, the European beewolf Philanthus triangulum, emit large amounts of gaseous nitric oxide (NO⋅) to protect themselves and their provisions, paralyzed honeybees, against mold fungi. We provide evidence that a NO-synthase (NOS) is involved in the generation of the extraordinary concentrations of nitrogen radicals in brood cells (~1500 ppm NO⋅ and its oxidation product NO2⋅). Sequencing of the beewolf NOS gene revealed no conspicuous differences to related species. However, due to alternative splicing, the NOS-mRNA in beewolf eggs lacks an exon near the regulatory domain. This preventive external application of high doses of NO⋅ by wasp eggs represents an evolutionary key innovation that adds a remarkable novel facet to the array of functions of the important biological effector NO⋅.}, } @article {pmid31181739, year = {2019}, author = {Hao, Z and Xie, W and Chen, B}, title = {Arbuscular Mycorrhizal Symbiosis Affects Plant Immunity to Viral Infection and Accumulation.}, journal = {Viruses}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/v11060534}, pmid = {31181739}, issn = {1999-4915}, support = {41571250//National Natural Science Foundation of China/ ; 2016YFC0500702//National Key Research and Development Program of China/ ; }, abstract = {Arbuscular mycorrhizal (AM) fungi, as root symbionts of most terrestrial plants, improve plant growth and fitness. In addition to the improved plant nutritional status, the physiological changes that trigger metabolic changes in the root via AM fungi can also increase the host ability to overcome biotic and abiotic stresses. Plant viruses are one of the important limiting factors for the commercial cultivation of various crops. The effect of AM fungi on viral infection is variable, and considerable attention is focused on shoot virus infection. This review provides an overview of the potential of AM fungi as bioprotection agents against viral diseases and emphasizes the complex nature of plant-fungus-virus interactions. Several mechanisms, including modulated plant tolerance, manipulation of induced systemic resistance (ISR), and altered vector pressure are involved in such interactions. We propose that using "omics" tools will provide detailed insights into the complex mechanisms underlying mycorrhizal-mediated plant immunity.}, } @article {pmid31181676, year = {2019}, author = {Ho, YS}, title = {Comment to: Qi, Yi, et al. "Bibliometric Analysis of Algal-Bacterial Symbiosis in Wastewater Treatment", Int. J. Environ. Res. Public Health 2019, 16, 1077.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ijerph16112034}, pmid = {31181676}, issn = {1660-4601}, abstract = {Qi et al. recently published an article in the journal, entitled "Bibliometric Analysis of Algal-Bacterial Symbiosis in Wastewater Treatment" [...].}, } @article {pmid31179246, year = {2019}, author = {Thapa, V and Roossinck, MJ}, title = {Determinants of Coinfection in the Mycoviruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {169}, doi = {10.3389/fcimb.2019.00169}, pmid = {31179246}, issn = {2235-2988}, } @article {pmid31178314, year = {2019}, author = {Whiteside, MD and Werner, GDA and Caldas, VEA and Van't Padje, A and Dupin, SE and Elbers, B and Bakker, M and Wyatt, GAK and Klein, M and Hink, MA and Postma, M and Vaitla, B and Noë, R and Shimizu, TS and West, SA and Kiers, ET}, title = {Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2019.04.061}, pmid = {31178314}, issn = {1879-0445}, abstract = {The world's ecosystems are characterized by an unequal distribution of resources [1]. Trade partnerships between organisms of different species-mutualisms-can help individuals cope with such resource inequality [2-4]. Trade allows individuals to exchange commodities they can provide at low cost for resources that are otherwise impossible or more difficult to access [5, 6]. However, as resources become increasingly patchy in time or space, it is unknown how organisms alter their trading strategies [7, 8]. Here, we show how a symbiotic fungus mediates trade with a host root in response to different levels of resource inequality across its network. We developed a quantum-dot-tracking technique to quantify phosphorus-trading strategies of arbuscular mycorrhizal fungi simultaneously exposed to rich and poor resource patches. By following fluorescent nanoparticles of different colors across fungal networks, we determined where phosphorus was hoarded, relocated, and transferred to plant hosts. We found that increasing exposure to inequality stimulated trade. Fungi responded to high resource variation by (1) increasing the total amount of phosphorus distributed to host roots, (2) decreasing allocation to storage, and (3) differentially moving resources within the network from rich to poor patches. Using single-particle tracking and high-resolution video, we show how dynamic resource movement may help the fungus capitalize on value differences across the trade network, physically moving resources to areas of high demand to gain better returns. Such translocation strategies can help symbiotic organisms cope with exposure to resource inequality.}, } @article {pmid31178238, year = {2019}, author = {Spagnoletti, FN and Chiocchio, VM}, title = {Tolerance of dark septate endophytic fungi (DSE) to agrochemicals in vitro.}, journal = {Revista Argentina de microbiologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ram.2019.02.003}, pmid = {31178238}, issn = {0325-7541}, abstract = {Dark septate endophytes (DSE) are a heterogeneous group of fungi, mostly belonging to the Phylum Ascomycota, that are involved in a mutualistic symbiosis with plant roots. The aim of this study is to evaluate the behavior of two strains of DSE isolated from wheat roots of two cropping areas in the province of Buenos Aires, Argentina, against some agrochemicals. Of all the isolates obtained, two strains were identified as Alternaria alternata and Cochliobolus sp. These DSE were found to be tolerant to glyphosate, carbendazim and cypermethrin when evaluated at the recommended agronomic dose (AD), 2 AD and, in some cases, 10 AD. This work contributes to the study of the biology of this group of fungi and their tolerance in the presence of xenobiotics widely used in agriculture.}, } @article {pmid31177643, year = {2019}, author = {Wang, S and Lu, T and Xue, Q and Xu, K and Cheng, G}, title = {Antioxidation and symbiotic nitrogen fixation function of prxA gene in Mesorhizobium huakuii.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e889}, doi = {10.1002/mbo3.889}, pmid = {31177643}, issn = {2045-8827}, support = {31772399//National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities/ ; CZY18022//South-Central University for Nationalities/ ; }, abstract = {Peroxiredoxins (Prxs) play an essential role in the antioxidant activity and symbiotic capacity of Mesorhizobium huakuii. A mutation in the M. huakuii prxA gene (encoding a Prx5-like peroxiredoxin) was generated by homologous recombination. The mutation of prxA did not affect M. huakuii growth, but the strain displayed decreased antioxidative capacity under organic cumene hydroperoxide (CUOOH) conditions. The higher resistance of the prxA mutant strain compared with the wild-type strain to more than 1 mmol/L H2 O2 was associated with a significantly higher level of glutathione reductase activity and a significantly lower level of intracellular hydrogen peroxide content. Real-time quantitative PCR showed that under 1 mmol/L H2 O2 conditions, expression of the stress-responsive genes katG and katE was significantly upregulated in the prxA mutant. Although the prxA mutant can form nodules, the symbiotic ability was severely impaired, which led to an abnormal nodulation phenotype coupled to a 53.25% reduction in nitrogen fixation capacity. This phenotype was linked to an absence of bacteroid differentiation and deregulation of the transcription of the symbiotic genes nifH, nifD, and fdxN. Expression of the prxA gene was induced during symbiosis. Thus, the PrxA protein is essential for antioxidant capacity and symbiotic nitrogen fixation, playing independent roles in bacterial differentiation and cellular antioxidative systems.}, } @article {pmid31176943, year = {2019}, author = {Rempel, A and de Souza Sossella, F and Margarites, AC and Astolfi, AL and Steinmetz, RLR and Kunz, A and Treichel, H and Colla, LM}, title = {Bioethanol from Spirulina platensis biomass and the use of residuals to produce biomethane: An energy efficient approach.}, journal = {Bioresource technology}, volume = {288}, number = {}, pages = {121588}, doi = {10.1016/j.biortech.2019.121588}, pmid = {31176943}, issn = {1873-2976}, abstract = {This study aimed to produce bioethanol using Spirulina platensis biomass and the use of saccharification and fermentation wastes of bioethanol production to produce biomethane. The potential for energy generation in each technological route was quantified. Both, the enzymatic hydrolysis of the microalgae polysaccharides and the fermentation process, presented efficiencies above 80%. The fermentation of the hydrolyzate into ethanol was possible without the addition of synthetic nutrients to the must. The direct conversion of Spirulina biomass to biomethane had an energy potential of 16,770 kJ.kg-1, while bioethanol production from the hydrolysed biomass presented 4,664 kJ.kg-1. However, the sum of the energy potential obtained by producing bioethanol followed by the production of biomethane with the saccharification and fermentation residues was 13,945 kJ.kg-1. Despite this, the same raw material was able to produce both biofuels, demonstrating that Spirulina microalgae is a promising alternative to contribute in the field of renewable energies.}, } @article {pmid31176662, year = {2019}, author = {Olivieri, E and Epis, S and Castelli, M and Varotto Boccazzi, I and Romeo, C and Desirò, A and Bazzocchi, C and Bandi, C and Sassera, D}, title = {Tissue tropism and metabolic pathways of Midichloria mitochondrii suggest tissue-specific functions in the symbiosis with Ixodes ricinus.}, journal = {Ticks and tick-borne diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ttbdis.2019.05.019}, pmid = {31176662}, issn = {1877-9603}, abstract = {A wide range of arthropod species harbour bacterial endosymbionts in various tissues, many of them playing important roles in the fitness and biology of their hosts. In several cases, many different symbionts have been reported to coexist simultaneously within the same host and synergistic or antagonistic interactions can occur between them. While the associations with endosymbiotic bacteria have been widely studied in many insect species, in ticks such interactions are less investigated. The females and immatures of Ixodes ricinus (Ixodidae), the most common hard tick in Europe, harbour the intracellular endosymbiont "Candidatus Midichloria mitochondrii" with a prevalence up to 100%, suggesting a mutualistic relationship. Considering that the tissue distribution of a symbiont might be indicative of its functional role in the physiology of the host, we investigated M. mitochondrii specific localization pattern and the corresponding abundance in selected organs of I. ricinus females. We paired these experiments with in silico analysis of the metabolic pathways of M. mitochondrii, inferred from the available genome sequence, and additionally compared the presence of these pathways in seven other symbionts commonly harboured by ticks to try to obtain a comparative understanding of their biological effects on the tick hosts. M. mitochondrii was found to be abundant in ovaries and tracheae of unfed I. ricinus, and in ovaries, Malpighian tubules and salivary glands of semi-engorged females. These results, together with the in silico metabolic reconstruction allow to hypothesize that the bacterium could play multiple tissue-specific roles in the host, both enhancing the host fitness (supplying essential nutrients, enhancing the reproductive fitness, helping in the anti-oxidative defence, in the energy production and in the maintenance of homeostasis and water balance) and/or for ensuring its presence in the host population (nutrients acquisition, vertical and horizontal transmission). The ability of M. mitochondrii to colonize different tissues allows to speculate that distinctive sub-populations may display different specializations in accordance with tissue tropism. Our hypotheses should be corroborated with future nutritional and physiological experiments for a better understanding of the mechanisms underlying this symbiotic interaction.}, } @article {pmid31174466, year = {2019}, author = {Baião, GC and Schneider, DI and Miller, WJ and Klasson, L}, title = {The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {465}, doi = {10.1186/s12864-019-5816-9}, pmid = {31174466}, issn = {1471-2164}, support = {2014-4353//Vetenskapsrådet/ ; P28255-B22//Austrian Science Fund/ ; }, abstract = {BACKGROUND: The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer. Here we use RNA-seq to study the impact of Wolbachia on D. paulistorum and investigate the hypothesis that the symbiont may play a role in host speciation. For that goal, we analyze samples of heads and abdomens of both sexes of the Amazonian, Centro American and Orinocan semispecies of D. paulistorum.

RESULTS: We identify between 175 and 1192 differentially expressed genes associated with a variety of biological processes that respond either globally or according to tissue, sex or condition in the three semispecies. Some of the functions associated with differentially expressed genes are known to be affected by Wolbachia in other species, such as metabolism and immunity, whereas others represent putative novel phenotypes involving muscular functions, pheromone signaling, and visual perception.

CONCLUSIONS: Our results show that Wolbachia affect a large number of biological functions in D. paulistorum, particularly when present in high titer. We suggest that the significant metabolic impact of the infection on the host may cause several of the other putative and observed phenotypes. We also speculate that the observed differential expression of genes associated with chemical communication and reproduction may be associated with the emergence of pre- and postmating barriers between semispecies, which supports a role for Wolbachia in the speciation of D. paulistorum.}, } @article {pmid31172251, year = {2019}, author = {Taboada, H and Dunn, MF and Meneses, N and Vargas-Lagunas, C and Buchs, N and Andrade-Domínguez, A and Encarnación, S}, title = {Qualitative changes in proteins contained in outer membrane vesicles produced by Rhizobium etli grown in the presence of the nod gene inducer naringenin.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-019-01682-4}, pmid = {31172251}, issn = {1432-072X}, support = {220790//CONACYT/ ; IN213216//DGAPA-PAPIIT-UNAM/ ; IN207519//DGAPA-PAPIIT-UNAM/ ; }, abstract = {In this work, we compared the proteomic profiles of outer membrane vesicles (OMVs) isolated from Rhizobium etli CE3 grown in minimal medium (MM) with and without exogenous naringenin. One-hundred and seven proteins were present only in OMVs from naringenin-containing cultures (N-OMVs), 57 proteins were unique to OMVs from control cultures lacking naringenin (C-OMVs) and 303 proteins were present in OMVs from both culture conditions (S-OMVs). Although we found no absolute predominance of specific types of proteins in the N-, C- or S-OMV classes, there were categories of proteins that were significantly less or more common in the different OMV categories. Proteins for energy production, translation and membrane and cell wall biogenesis were overrepresented in C-OMVs relative to N-OMVs. Proteins for carbohydrate metabolism and transport and those classified as either general function prediction only, function unknown, or without functional prediction were more common in N-OMVs than C-OMVs. This indicates that naringenin increased the proportion of these proteins in the OMVs, although NodD binding sites were only slightly more common in the promoters of genes for proteins found in the N-OMVs. In addition, OMVs from naringenin-containing cultures contained nodulation factor.}, } @article {pmid31170026, year = {2019}, author = {Belin, BJ and Tookmanian, ET and de Anda, J and Wong, GCL and Newman, D}, title = {Extended hopanoid loss reduces bacterial motility and surface attachment, and leads to heterogeneity in root nodule growth kinetics in a Bradyrhizobium-Aeschynomene symbiosis.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-04-19-0111-R}, pmid = {31170026}, issn = {0894-0282}, abstract = {Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Roughly 10% of bacteria contain genes involved in hopanoid biosynthesis, and these genes are particularly conserved in plant-associated organisms. We previously found that the extended class of hopanoids (C35) in the nitrogen-fixing soil bacterium Bradyrhizobium diazoefficiens promotes its root nodule symbiosis with the tropical legume Aeschynomene afraspera. By quantitatively modeling root nodule development, we identify independent consequences of extended hopanoid loss in the initiation of root nodule formation and in the rate of root nodule maturation. In vitro studies demonstrate that extended hopanoids support B. diazoefficiens motility and surface attachment, which may correlate with stable root colonization in planta. Confocal microscopy of maturing root nodules reveals that root nodules infected with extended hopanoid-deficient B. diazoefficiens contain unusually low densities of bacterial symbionts, indicating that extended hopanoids are necessary for persistent, high levels of host infection.}, } @article {pmid31167992, year = {2019}, author = {Ohbayashi, T and Itoh, H and Lachat, J and Kikuchi, Y and Mergaert, P}, title = {Burkholderia Gut Symbionts Associated with European and Japanese Populations of the Dock Bug Coreus marginatus (Coreoidea: Coreidae).}, journal = {Microbes and environments}, volume = {}, number = {}, pages = {}, doi = {10.1264/jsme2.ME19011}, pmid = {31167992}, issn = {1347-4405}, abstract = {Insects of the heteropteran superfamilies Coreoidea and Lygaeoidea are consistently associated with symbionts of a specific group of the genus Burkholderia, called the "stinkbug-associated beneficial and environmental (SBE)" group. The symbiosis is maintained by the environmental transmission of symbionts. We investigated European and Japanese populations of the dock bug Coreus marginatus (Coreoidea: Coreidae). High nymphal mortality in reared aposymbiotic insects suggested an obligate host-symbiont association in this species. Molecular phylogenetic analyses based on 16S rRNA gene sequences revealed that all 173 individuals investigated were colonized by Burkholderia, which were further assigned to different subgroups of the SBE in a region-dependent pattern.}, } @article {pmid30624120, year = {2018}, author = {Shipway, JR and Altamia, MA and Haga, T and Velásquez, M and Albano, J and Dechavez, R and Concepcion, GP and Haygood, MG and Distel, DL}, title = {Observations on the Life History and Geographic Range of the Giant Chemosymbiotic Shipworm Kuphus polythalamius (Bivalvia: Teredinidae).}, journal = {The Biological bulletin}, volume = {235}, number = {3}, pages = {167-177}, doi = {10.1086/700278}, pmid = {30624120}, issn = {1939-8697}, support = {U19 TW008163/TW/FIC NIH HHS/United States ; }, mesh = {*Animal Distribution ; Animals ; Bivalvia/*physiology ; Chemoautotrophic Growth ; Pacific Ocean ; Symbiosis ; }, abstract = {Kuphus polythalamius (Teredinidae) is one of the world's largest, most rarely observed, and least understood bivalves. Kuphus polythalamius is also among the few shallow-water marine species and the only teredinid species determined to harbor sulfur-oxidizing chemoautotrophic (thioautotrophic) symbionts. Until the recent discovery of living specimens in the Philippines, this species was known only from calcareous hard parts, fossils, and the preserved soft tissues of a single large specimen. As a result, the anatomy, biology, life history, and geographic range of K. polythalamius remain obscure. Here we report the collection and description of the smallest living specimens of K. polythalamius yet discovered and confirm the species identity of these individuals by using sequences of three genetic markers. Unlike previously collected specimens, all of which have been reported to occur in marine sediments, these specimens were observed burrowing in wood, the same substrate utilized by all other members of the family. These observations suggest that K. polythalamius initially settles on wood and subsequently transitions into sediment, where this species may grow to enormous sizes. This discovery led us to search for and find previously unidentified and misidentified wood-boring specimens of this species within museum collections, and it allowed us to show that the recent geographic range (since 1933) of this species extends across a 3000-mile span from the Philippines to Papua New Guinea and the Solomon Islands.}, } @article {pmid30624116, year = {2018}, author = {Dossi, FCA and da Silva, EP and Cônsoli, FL}, title = {Shifting the Balance: Heat Stress Challenges the Symbiotic Interactions of the Asian Citrus Psyllid, Diaphorina citri (Hemiptera, Liviidae).}, journal = {The Biological bulletin}, volume = {235}, number = {3}, pages = {195-203}, doi = {10.1086/699755}, pmid = {30624116}, issn = {1939-8697}, mesh = {Animals ; Hemiptera/*physiology ; *Hot Temperature ; Symbiosis/*physiology ; }, abstract = {Global warming may impact biodiversity by disrupting biological interactions, including long-term insect-microbe mutualistic associations. Symbiont-mediated insect tolerance to high temperatures is an ecologically important trait that significantly influences an insect's life history. Disruption of microbial symbionts that are required by insects would substantially impact their pest status. Diaphorina citri, a worldwide citrus pest, is associated with the mutualistic symbionts Candidatus Carsonella ruddii and Candidatus Profftella armatura. Wolbachia is also associated with D. citri, but its contribution to the host is unknown. Symbiont density is dependent on a range of factors, including the thermosensitivity of the host and/or symbiont to heat stress. Here, we predicted that short-term heat stress of D. citri would disrupt the host-symbiont phenological synchrony and differentially affect the growth and density of symbionts. We investigated the effects of exposing D. citri eggs to different temperatures for different periods of time on the growth dynamics of symbionts during the nymphal development of D. citri (first instar to fifth instar) by real-time polymerase chain reaction. Symbiont densities were assessed as the number of gene copies, using specific molecular markers: 16S rRNA for Carsonella and Profftella and ftsZ for Wolbachia. Statistical modeling of the copy numbers of symbionts revealed differences in their growth patterns, particularly in the early instars of heat-shocked insects. Wolbachia was the only symbiont to benefit from heat-shock treatment. Although the symbionts responded differently to heat stress, the lack of differences in symbiont densities between treated and control late nymphs suggests the existence of an adaptive genetic process to restore phenological synchrony during the development of immatures in preparation for adult life. Our findings contribute to the understanding of the potential deleterious effects of high temperatures on host-symbiont interactions. Our data also suggest that the effects of host exposure to high temperatures in symbiont growth are highly variable and dependent on the interactions among members of the community of symbionts harbored by a host. Such dependence points to unpredictable consequences for agroecosystems worldwide due to climate change-related effects on the ecological traits of symbiont-dependent insect pests.}, } @article {pmid30542952, year = {2019}, author = {Dhaneesha, M and Hasin, O and Sivakumar, KC and Ravinesh, R and Naman, CB and Carmeli, S and Sajeevan, TP}, title = {DNA Binding and Molecular Dynamic Studies of Polycyclic Tetramate Macrolactams (PTM) with Potential Anticancer Activity Isolated from a Sponge-Associated Streptomyces zhaozhouensis subsp. mycale subsp. nov.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {21}, number = {1}, pages = {124-137}, doi = {10.1007/s10126-018-9866-9}, pmid = {30542952}, issn = {1436-2236}, support = {292/2016/KSCSTE dated 07.07.2016//Kerala State Council for Science, Technology and Environment/ ; }, mesh = {Animals ; Antineoplastic Agents/*chemistry/isolation & purification/pharmacology ; Apoptosis/*drug effects/genetics ; Binding Sites ; Cell Line, Tumor ; Cell Survival/drug effects ; DNA/*chemistry ; Epithelial Cells/drug effects/metabolism/pathology ; G1 Phase Cell Cycle Checkpoints/drug effects/genetics ; Humans ; Inhibitory Concentration 50 ; Lactams/*chemistry/isolation & purification/pharmacology ; Lactams, Macrocyclic/*chemistry/isolation & purification/pharmacology ; Molecular Docking Simulation ; Nucleic Acid Conformation ; Phylogeny ; Porifera/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; S Phase Cell Cycle Checkpoints/drug effects/genetics ; Streptomyces/*chemistry/classification/metabolism ; Symbiosis/physiology ; }, abstract = {A sponge-associated actinomycete (strain MCCB267) was isolated from a marine sponge Mycale sp. collected in the Indian Ocean off the Southeast coast of India. Phylogenetic studies of this strain using 16S rRNA gene sequencing showed high sequence similarity to Streptomyces zhaozhouensis. However, strain MCCB267 showed distinct physiological and biochemical characteristic features and was thus designated as S. zhaozhouensis subsp. mycale. subsp. nov. A cytotoxicity-guided fractionation of the crude ethyl acetate extract of strain MCCB267 culture medium yielded four pure compounds belonging to the polycyclic tetramate macrolactam (PTM) family of natural products: ikarugamycin (IK) (1), clifednamide A (CF) (2), 30-oxo-28-N-methylikarugamycin (OI) (3), and 28-N-methylikarugamycin (MI) (4). The four compounds exhibited promising cytotoxic activity against NCI-H460 lung carcinoma cells in vitro, by inducing cell death via apoptosis. Flow cytometric analysis revealed that 1, 3, and 4 induced cell cycle arrest during G1 phase in the NCI-H460 cell line, whereas 2 induced cell arrest in the S phase. A concentration-dependent accumulation of cells in the sub-G1 phase was also detected upon treatment of the cancer cell line with compounds 1-4. The in vitro cytotoxicity studies were supported by molecular docking and molecular dynamic simulation analyses. An in silico study revealed that the PTMs can bind to the minor groove of DNA and subsequently induce the apoptotic stimuli leading to cell death. The characterization of the isolated actinomycete, the study of the mode of action of the four PTMs, 1-4, and the molecular docking and molecular dynamic simulations analyses are herein described.}, } @article {pmid30540788, year = {2018}, author = {Pietri, JE and Tiffany, C and Liang, D}, title = {Disruption of the microbiota affects physiological and evolutionary aspects of insecticide resistance in the German cockroach, an important urban pest.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207985}, doi = {10.1371/journal.pone.0207985}, pmid = {30540788}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Blattellidae/drug effects/*microbiology/physiology ; Feces/microbiology ; Female ; Insecticide Resistance/drug effects ; Insecticides/*metabolism/pharmacology ; Male ; Microbiota/drug effects/*physiology ; Oxazines/*metabolism/pharmacology ; Symbiosis ; }, abstract = {The German cockroach, Blatella germanica, is a common pest in urban environments and is among the most resilient insects in the world. The remarkable ability of the German cockroach to develop resistance when exposed to toxic insecticides is a prime example of adaptive evolution and makes control of this insect an ongoing struggle. Like many other organisms, the German cockroach is host to a diverse community of symbiotic microbes that play important roles in its physiology. In some insect species, there is a strong correlation between the commensal microbial community and insecticide resistance. In particular, several bacteria have been implicated in the detoxification of xenobiotics, including synthetic insecticides. While multiple mechanisms that mediate insecticide resistance in cockroaches have been discovered, significant knowledge gaps still exist in this area of research. Here, we examine the effects of altering the microbiota on resistance to a common insecticide using antibiotic treatments. We describe an indoxacarb-resistant laboratory strain in which treatment with antibiotic increases susceptibility to orally administered insecticide. We further reveal that this strains harbors a gut microbial community that differs significantly from that of susceptible cockroaches in which insecticide resistance is unaffected by antibiotic. More importantly, we demonstrate that transfer of gut microbes from the resistant to the susceptible strain via fecal transplant increases its resistance. Lastly, our data show that antibiotic treatment adversely affects several reproductive life-history traits that may contribute to the dynamics of resistance at the population level. Together these results suggest that the microbiota contributes to both physiological and evolutionary aspects of insecticide resistance and that targeting this community may be an effective strategy to control the German cockroach.}, } @article {pmid30297831, year = {2018}, author = {Lin, JS and Li, X and Luo, Z and Mysore, KS and Wen, J and Xie, F}, title = {NIN interacts with NLPs to mediate nitrate inhibition of nodulation in Medicago truncatula.}, journal = {Nature plants}, volume = {4}, number = {11}, pages = {942-952}, doi = {10.1038/s41477-018-0261-3}, pmid = {30297831}, issn = {2055-0278}, mesh = {Gene Expression Regulation, Plant ; Medicago truncatula/*metabolism ; Nitrates/*metabolism/physiology ; Plant Proteins/metabolism/*physiology ; Plant Root Nodulation/*physiology ; Rhizobium ; Symbiosis ; }, abstract = {Legume plants can assimilate inorganic nitrogen and have access to fixed nitrogen through symbiotic interaction with diazotrophic bacteria called rhizobia. Symbiotic nitrogen fixation is an energy-consuming process and is strongly inhibited when sufficient levels of fixed nitrogen are available, but the molecular mechanisms governing this regulation are largely unknown. The transcription factor nodule inception (NIN) is strictly required for nodulation and belongs to a family of NIN-like proteins (NLPs), which have been implicated in the regulation of nitrogen homeostasis in Arabidopsis. Here, we show that mutation or downregulation of NLP genes prevents nitrate inhibition of infection, nodule formation and nitrogen fixation. We find that NIN and NLPs physically interact through their carboxy-terminal PB1 domains. Furthermore, we find that NLP1 is required for the expression of nitrate-responsive genes and that nitrate triggers NLP1 re-localization from the cytosol to the nucleus. Finally, we show that NLP1 can suppress NIN activation of CRE1 expression in Nicotiana benthamiana and Medicago truncatula. Our findings highlight a central role for NLPs in the suppression of nodulation by nitrate.}, } @article {pmid30194504, year = {2019}, author = {Miura, N and Motone, K and Takagi, T and Aburaya, S and Watanabe, S and Aoki, W and Ueda, M}, title = {Ruegeria sp. Strains Isolated from the Reef-Building Coral Galaxea fascicularis Inhibit Growth of the Temperature-Dependent Pathogen Vibrio coralliilyticus.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {21}, number = {1}, pages = {1-8}, doi = {10.1007/s10126-018-9853-1}, pmid = {30194504}, issn = {1436-2236}, support = {17J07458//Japan Society for the Promotion of Science/ ; 16J08791//Japan Society for the Promotion of Science/ ; 17J05024//Japan Society for the Promotion of Science/ ; 18K14479//Japan Society for the Promotion of Science/ ; JPMJCR16G2//Core Research for Evolutional Science and Technology/ ; JPMJCR16G2//Core Research for Evolutional Science and Technology/ ; JPMJCR16G2//Core Research for Evolutional Science and Technology/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; *Antibiosis ; Coral Reefs ; High-Throughput Nucleotide Sequencing ; Japan ; Microbiota/genetics ; Pacific Ocean ; RNA, Ribosomal, 16S/*genetics ; Rhodobacteraceae/classification/*genetics/isolation & purification ; Symbiosis/physiology ; Vibrio/*growth & development/pathogenicity ; }, abstract = {The coral microbiome has attracted increased attention because of its potential roles in host protection against deadly diseases. However, little is known about the role of coral-associated bacteria against the temperature-dependent opportunistic pathogen Vibrio coralliilyticus. In this study, we tested whether bacteria associated with the reef-building coral Galaxea fascicularis could inhibit the growth of V. coralliilyticus. Twenty-nine cultivable bacteria were successfully isolated from a healthy colony of G. fascicularis kept in an aquarium. Among the bacterial isolates, three Ruegeria sp. strains inhibited the growth of V. coralliilyticus P1 as a reference strain and Vibrio sp. isolated in this study. Ruegeria sp. strains were also detected from other G. fascicularis colonies in the aquarium and in previous field studies by 16S rRNA amplicon sequencing, suggesting that Ruegeria sp. strains are common among G. fascicularis colonies. These results illuminate the potential role of Ruegeria sp. in protecting corals against pathogenic Vibrio species.}, } @article {pmid31166165, year = {2019}, author = {Jani, K and Feng, GD and Zhu, HH and Prakash, O and Bandal, J and Rale, V and Shouche, Y and Sharma, A}, title = {Chakrabartia godavariana gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Godavari River, India.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003512}, pmid = {31166165}, issn = {1466-5034}, abstract = {A Gram-stain-negative, aerobic, yellow-pigmented, oxidase-positive and rod-shaped bacterium, designated PRB40T, was isolated from the Godavari River in India during the course of 'Kumbh Mela', the world's largest mass gathering event. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRB40T formed a lineage within the family Sphingomonadaceae and was distinct from the most closely related genera Sphingorhabdus, Novosphingobiumand Sphingomonas with sequence similarity values ≤95.2 %. Growth of strain PRB40T occurred at 10-40 °C (optimum 30 °C), at pH 6.0-9.0 (pH 7.0) and with 0-0.5 % (w/v) NaCl concentration (0 %). The major respiratory quinone was ubiquinone-10 (Q-10). It contained C17 : 1ω6c, C14 : 0 2-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major cellular fatty acids. The predominant polar lipids were phospholipid, phosphatidylethanolamine and sphingoglycolipid. It took sym-homospermidine as the major polyamine. The DNA G+C content based on its draft genome sequence was 63.7 mol%. The polyphasic taxonomic analyses indicated that strain PRB40T represents a novel species of a novel genus within the family Sphingomonadaceae, for which the name Chakrabartia godavariana gen. nov., sp. nov. is proposed. The type strain of Chakrabartia godavariana is PRB40T (=MCC 3406T=GDMCC 1.1197T=KCTC 52678T=LMG 29985T).}, } @article {pmid31166074, year = {2019}, author = {Guerrieri, A and Dong, L and Bouwmeester, HJ}, title = {Role and exploitation of underground chemical signaling in plants.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.5507}, pmid = {31166074}, issn = {1526-4998}, abstract = {The soil ecosystem is composed of a mixture of living organisms and non-living matter as well as the complex interactions between them. In the past 100 years or so, agricultural soil ecosystems were strongly affected by agricultural practices, such as tillage and the use of pesticides and fertilizers, which strongly affected soil nutrient composition, pH and biodiversity. In modern pest management, however, the focus is gradually shifting from crop production through agricultural practices to soil ecosystem protection. In this review we discuss how the underground chemical signals secreted by plant roots play a role in keeping the soil ecosystem in balance and how they affect plant fitness, by shaping the root biome, increasing nutrient availability, promoting symbiosis, attracting beneficial organisms and repelling harmful ones, including other plants. We review a number of fascinating cases like signaling molecules with dual, positive and negative, functions and bacterial quorum sensing mimicking molecules. Finally, examples of how these compounds can be exploited in modern pest management are reviewed, and the prospects for future developments discussed. This article is protected by copyright. All rights reserved.}, } @article {pmid31165947, year = {2019}, author = {Sakamoto, K and Ogiwara, N and Kaji, T and Sugimoto, Y and Ueno, M and Sonoda, M and Matsui, A and Ishida, J and Tanaka, M and Totoki, Y and Shinozaki, K and Seki, M}, title = {Transcriptome analysis of soybean (Glycine max) root genes differentially expressed in rhizobial, arbuscular mycorrhizal, and dual symbiosis.}, journal = {Journal of plant research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10265-019-01117-7}, pmid = {31165947}, issn = {1618-0860}, support = {23380042//Japan Society for the Promotion of Science/ ; }, abstract = {Soybean (Glycine max) roots establish associations with nodule-inducing rhizobia and arbuscular mycorrhizal (AM) fungi. Both rhizobia and AM fungi have been shown to affect the activity of and colonization by the other, and their interactions can be detected within host plants. Here, we report the transcription profiles of genes differentially expressed in soybean roots in the presence of rhizobial, AM, or rhizobial-AM dual symbiosis, compared with those in control (uninoculated) roots. Following inoculation, soybean plants were grown in a glasshouse for 6 weeks; thereafter their root transcriptomes were analyzed using an oligo DNA microarray. Among the four treatments, the root nodule number and host plant growth were highest in plants with dual symbiosis. We observed that the expression of 187, 441, and 548 host genes was up-regulated and 119, 1,439, and 1,298 host genes were down-regulated during rhizobial, AM, and dual symbiosis, respectively. The expression of 34 host genes was up-regulated in each of the three symbioses. These 34 genes encoded several membrane transporters, type 1 metallothionein, and transcription factors in the MYB and bHLH families. We identified 56 host genes that were specifically up-regulated during dual symbiosis. These genes encoded several nodulin proteins, phenylpropanoid metabolism-related proteins, and carbonic anhydrase. The nodulin genes up-regulated by the AM fungal colonization probably led to the observed increases in root nodule number and host plant growth. Some other nodulin genes were down-regulated specifically during AM symbiosis. Based on the results above, we suggest that the contribution of AM fungal colonization is crucial to biological N2-fixation and host growth in soybean with rhizobial-AM dual symbiosis.}, } @article {pmid31164991, year = {2019}, author = {Oishi, S and Moriyama, M and Koga, R and Fukatsu, T}, title = {Morphogenesis and development of midgut symbiotic organ of the stinkbug Plautia stali (Hemiptera: Pentatomidae).}, journal = {Zoological letters}, volume = {5}, number = {}, pages = {16}, doi = {10.1186/s40851-019-0134-2}, pmid = {31164991}, issn = {2056-306X}, abstract = {Diverse insects are intimately associated with microbial symbionts, which play a variety of biological roles in their adaptation to and survival in the natural environment. Such insects often possess specialized organs for hosting the microbial symbionts. What developmental processes and mechanisms underlie the formation of the host organs for microbial symbiosis is of fundamental biological interest but poorly understood. Here we investigate the morphogenesis of the midgut symbiotic organ and the process of symbiont colonization therein during the developmental course of the stinkbug Plautia stali. Upon hatching, the midgut is a simple and smooth tube. Subsequently, symbiont colonization to the posterior midgut occurs, and thickening and folding of the midgut epithelium proceed during the first instar period. By the second instar, rudimentary crypts have formed, and their inner cavities are colonized by the symbiotic bacteria. From the second instar to the fourth instar, while the alimentary tract grows and the posterior midgut is established as the symbiotic organ with numerous crypts, the anterior midgut and the posterior midgut are structurally and functionally isolated by a strong constriction in the middle. By the early fifth instar, the midgut symbiotic organ attains the maximal length, but toward the mid fifth instar, the basal region of each crypt starts to constrict and narrow, which deforms the midgut symbiotic organ as a whole into a shorter, thicker and twisted shape. By the late fifth instar to adulthood, the crypts are constricted off, by which the symbiotic bacteria are confined in the crypt cavities and isolated from the midgut main tract, and concurrently, the strong midgut constriction in the middle becomes loose and open, by which the food flow from the anterior midgut to the posterior midgut recovers. This study provides the most detailed and comprehensive descriptions ever reported on the morphogenesis of the symbiotic organ and the process of symbiont colonization in an obligatory insect-bacterium gut symbiotic system. Considering that P. stali is recently emerging as a useful model system for experimentally studying the intimate insect-microbe gut symbiosis, the knowledge obtained in this study establishes the foundation for the further development of this research field.}, } @article {pmid31030835, year = {2019}, author = {Bosák, J and Hrala, M and Pirková, V and Micenková, L and Čížek, A and Smola, J and Kučerová, D and Vacková, Z and Budinská, E and Koláčková, I and Šmajs, D}, title = {Porcine pathogenic Escherichia coli strains differ from human fecal strains in occurrence of bacteriocin types.}, journal = {Veterinary microbiology}, volume = {232}, number = {}, pages = {121-127}, doi = {10.1016/j.vetmic.2019.04.003}, pmid = {31030835}, issn = {1873-2542}, mesh = {Animals ; Bacterial Adhesion ; Bacteriocins/*genetics ; Carrier Proteins/genetics ; Colicins/*genetics ; Diarrhea/microbiology ; Enterotoxigenic Escherichia coli/genetics/*pathogenicity ; Escherichia coli Proteins/genetics ; Feces/microbiology ; Fimbriae Proteins/genetics ; Gastrointestinal Tract/microbiology ; Humans ; Iron/metabolism ; Phylogeny ; Plasmids ; Polymerase Chain Reaction ; Shiga-Toxigenic Escherichia coli/genetics/*pathogenicity ; Swine ; Symbiosis ; Virulence Factors/genetics ; }, abstract = {Enterotoxigenic and Shiga-toxigenic Escherichia coli (i.e., ETEC and STEC) are important causative agents of human and animal diseases. In humans, infections range from mild diarrhea to severe life-threating conditions, while infections of piglets result in lower weight gain and higher pig mortality with the accompanying significant economic losses. In this study, frequencies of four phylogenetic groups, fourteen virulence- and thirty bacteriocin determinants were analyzed in a set of 443 fecal E. coli isolates from diseased pigs and compared to a previously characterized set of 1283 human fecal E. coli isolates collected in the same geographical region. In addition, these characteristics were compared among ETEC, STEC, and non-toxigenic porcine E. coli isolates. Phylogenetic group A was prevalent among porcine pathogenic E. coli isolates, whereas the frequency of phylogroup B2, adhesion/invasion (fimA, pap, sfa, afaI, ial, ipaH, and pCVD432) and iron acquisition (aer and iucC) determinants were less frequent compared to human fecal isolates. Additionally, porcine isolates differed from human isolates relative to the spectrum of produced bacteriocins. While human fecal isolates encoded colicins and microcins with a similar prevalence, porcine pathogenic E. coli isolates produced predominantly colicins (94% of isolates); especially colicins B (42.6%), M (40.1%), and Ib (34.0%), which are encoded on large conjugative plasmids. The observed high prevalence of these colicin determinants suggests the importance of large colicinogenic plasmids and/or the importance of colicin production in intestinal inflammatory conditions.}, } @article {pmid31011888, year = {2019}, author = {Bengyella, L and Iftikhar, S and Nawaz, K and Fonmboh, DJ and Yekwa, EL and Jones, RC and Njanu, YMT and Roy, P}, title = {Biotechnological application of endophytic filamentous bipolaris and curvularia: a review on bioeconomy impact.}, journal = {World journal of microbiology & biotechnology}, volume = {35}, number = {5}, pages = {69}, doi = {10.1007/s11274-019-2644-7}, pmid = {31011888}, issn = {1573-0972}, support = {3240223450//The World Academy of Sciences (TWAS)/ ; }, mesh = {*Ascomycota/classification/enzymology/metabolism ; Biodegradation, Environmental ; *Bioengineering ; Biofuels ; Biological Control Agents ; *Biotechnology ; Biotransformation ; *Endophytes/classification/enzymology/metabolism ; Fertilizers ; Flocculation ; Fungal Viruses ; Herbicides ; Metallurgy ; Nanoparticles ; Soil/chemistry ; Symbiosis ; Thermotolerance ; Uranium ; }, abstract = {The filamentous Bipolaris and Curvularia genera consist of species known to cause severe diseases in plants and animals amounting to an estimated annual loss of USD $10 billion worldwide. Despite the harmful effect of Bipolaris and Curvularia species, scarce attention is paid on beneficial areas where the fungi are used in industrial processes to generate biotechnological products. Catalytic potential of Bipolaris and Curvularia species in the production of biodiesel, bioflucculant, biosorbent, and mycoherbicide are promising for the bioeconomy. It is herein demonstrated that knowledge-based application of some endophytic Bipolaris and Curvularia species are indispensable vectors of sustainable economic development. In the twenty-first century, India, China, and the USA have taken progress in the biotechnological application of these fungi to generate wealth. As such, some Bipolaris and Curvularia species significantly impact on global crop improvement, act as catalyst in batch-reactors for biosynthesis of industrial enzymes and medicines, bioengineer of green-nanoparticle, agent of biofertilizer, bioremediation and bio-hydrometallurgy. For the first time, this study discusses the current advances in biotechnological application of Bipolaris and Curvularia species and provide new insights into the prospects of optimizing their bioengineering potential for developing bioeconomy.}, } @article {pmid29643214, year = {2018}, author = {Norin, T and Mills, SC and Crespel, A and Cortese, D and Killen, SS and Beldade, R}, title = {Anemone bleaching increases the metabolic demands of symbiont anemonefish.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1876}, pages = {}, pmid = {29643214}, issn = {1471-2954}, mesh = {Animals ; Climate Change ; Locomotion/physiology ; Oxygen Consumption/physiology ; Perciformes/*metabolism/physiology ; Sea Anemones/*physiology ; Symbiosis/*physiology ; }, abstract = {Increased ocean temperatures are causing mass bleaching of anemones and corals in the tropics worldwide. While such heat-induced loss of algal symbionts (zooxanthellae) directly affects anemones and corals physiologically, this damage may also cascade on to other animal symbionts. Metabolic rate is an integrative physiological trait shown to relate to various aspects of organismal performance, behaviour and locomotor capacity, and also shows plasticity during exposure to acute and chronic stressors. As climate warming is expected to affect the physiology, behaviour and life history of animals, including ectotherms such as fish, we measured if residing in bleached versus unbleached sea anemones (Heteractis magnifica) affected the standard (i.e. baseline) metabolic rate and behaviour (activity) of juvenile orange-fin anemonefish (Amphiprion chrysopterus). Metabolic rate was estimated from rates of oxygen uptake [Formula: see text], and the standard metabolic rate [Formula: see text] of anemonefish from bleached anemones was significantly higher by 8.2% compared with that of fish residing in unbleached anemones, possibly due to increased stress levels. Activity levels did not differ between fish from bleached and unbleached anemones. As [Formula: see text] reflects the minimum cost of living, the increased metabolic demands may contribute to the negative impacts of bleaching on important anemonefish life history and fitness traits observed previously (e.g. reduced spawning frequency and lower fecundity).}, } @article {pmid29618548, year = {2018}, author = {Jacobsen, RM and Sverdrup-Thygeson, A and Kauserud, H and Birkemoe, T}, title = {Revealing hidden insect-fungus interactions; moderately specialized, modular and anti-nested detritivore networks.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1876}, pages = {}, pmid = {29618548}, issn = {1471-2954}, mesh = {Animals ; *Biota ; Coleoptera/*microbiology ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/*analysis ; Ecosystem ; Fungi/*classification ; Norway ; Plant Diseases/microbiology ; Symbiosis ; Wood ; }, abstract = {Ecological networks are composed of interacting communities that influence ecosystem structure and function. Fungi are the driving force for ecosystem processes such as decomposition and carbon sequestration in terrestrial habitats, and are strongly influenced by interactions with invertebrates. Yet, interactions in detritivore communities have rarely been considered from a network perspective. In the present study, we analyse the interaction networks between three functional guilds of fungi and insects sampled from dead wood. Using DNA metabarcoding to identify fungi, we reveal a diversity of interactions differing in specificity in the detritivore networks, involving three guilds of fungi. Plant pathogenic fungi were relatively unspecialized in their interactions with insects inhabiting dead wood, while interactions between the insects and wood-decay fungi exhibited the highest degree of specialization, which was similar to estimates for animal-mediated seed dispersal networks in previous studies. The low degree of specialization for insect symbiont fungi was unexpected. In general, the pooled insect-fungus networks were significantly more specialized, more modular and less nested than randomized networks. Thus, the detritivore networks had an unusual anti-nested structure. Future studies might corroborate whether this is a common aspect of networks based on interactions with fungi, possibly owing to their often intense competition for substrate.}, } @article {pmid29393559, year = {2018}, author = {Michalik, A and Schulz, F and Michalik, K and Wascher, F and Horn, M and Szklarzewicz, T}, title = {Coexistence of novel gammaproteobacterial and Arsenophonus symbionts in the scale insect Greenisca brachypodii (Hemiptera, Coccomorpha: Eriococcidae).}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {1148-1157}, doi = {10.1111/1462-2920.14057}, pmid = {29393559}, issn = {1462-2920}, mesh = {Animals ; Enterobacteriaceae/*classification/*genetics/growth & development ; Hemiptera/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Symbiosis/genetics/*physiology ; }, abstract = {Scale insects are commonly associated with obligate, intracellular microorganisms which play important roles in complementing their hosts with essential nutrients. Here we characterized the symbiotic system of Greenisca brachypodii, a member of the family Eriococcidae. Histological and ultrastructural analyses have indicated that G. brachypodii is stably associated with coccoid and rod-shaped bacteria. Phylogenetic analyses have revealed that the coccoid bacteria represent a sister group to the secondary symbiont of the mealybug Melanococcus albizziae, whereas the rod-shaped symbionts are close relatives of Arsenophonus symbionts in insects - to our knowledge, this is the first report of the presence of Arsenophonus bacterium in scale insects. As a comparison of 16S and 23S rRNA genes sequences of the G. brachypodii coccoid symbiont with other gammaprotebacterial sequences showed only low similarity (∼90%), we propose the name 'Candidatus Kotejella greeniscae' for its tentative classification. Both symbionts are transovarially transmitted from one generation to the next. The infection takes place in the neck region of the ovariole. The bacteria migrate between follicular cells, as well as through the cytoplasm of those cells to the perivitelline space, where they form a characteristic 'symbiont ball'. Our findings provide evidence for a polyphyletic origin of symbionts of Eriococcidae.}, } @article {pmid29345102, year = {2018}, author = {Martin, E and Varotto Boccazzi, I and De Marco, L and Bongiorno, G and Montagna, M and Sacchi, L and Mensah, P and Ricci, I and Gradoni, L and Bandi, C and Epis, S}, title = {The mycobiota of the sand fly Phlebotomus perniciosus: Involvement of yeast symbionts in uric acid metabolism.}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {1064-1077}, doi = {10.1111/1462-2920.14044}, pmid = {29345102}, issn = {1462-2920}, mesh = {Animals ; Female ; Genome, Fungal/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; In Situ Hybridization, Fluorescence ; Insect Vectors ; Larva/microbiology ; Male ; Malpighian Tubules/microbiology ; Microbiota/genetics ; Phlebotomus/*microbiology ; RNA, Ribosomal/genetics ; Saccharomycetales/*genetics/isolation & purification/*metabolism ; Symbiosis/*physiology ; Uric Acid/*metabolism ; }, abstract = {The knowledge of the fungal mycobiota of arthropods, including the vectors of human and animal diseases, is still limited. Here, the mycobiota associated with the sand fly Phlebotomus perniciosus, the main vector of leishmaniasis in the western Mediterranean area, by a culture-dependent approach (microbiological analyses and sequencing of the 26S rRNA gene), internal transcribed spacer (ITS) rRNA amplicon-based next-generation sequencing, fluorescence in situ hybridisation (FISH), and genome sequencing of the dominant yeast species was investigated. The dominant species was Meyerozyma guilliermondii, known for its biotechnological applications. The focus was on this yeast and its prevalence in adults, pupae and larvae of reared sand flies (overall prevalence: 57.5%) and of field-collected individuals (overall prevalence: 9%) was investigated. Using whole-mount FISH and microscopic examination, it was further showed that M. guilliermondii colonizes the midgut of females, males and larvae and the distal part of Malpighian tubules of female sand flies, suggesting a possible role in urate degradation. Finally, the sequencing and analysis of the genome of M. guilliermondii allowed predicting the complete uric acid degradation pathway, suggesting that the yeast could contribute to the removal of the excess of nitrogenous wastes after the blood meal of the insect host.}, } @article {pmid29144582, year = {2017}, author = {Wood, CW and Stinchcombe, JR}, title = {A window into the transcriptomic basis of genotype-by-genotype interactions in the legume-rhizobia mutualism.}, journal = {Molecular ecology}, volume = {26}, number = {21}, pages = {5869-5871}, doi = {10.1111/mec.14370}, pmid = {29144582}, issn = {1365-294X}, mesh = {Biological Evolution ; *Fabaceae ; Genotype ; *Rhizobium ; Symbiosis ; }, abstract = {The maintenance of genetic variation in the benefits provided by mutualists is an evolutionary puzzle (Heath & Stinchcombe,). Over time, natural selection should favour the benefit strategy that confers the highest fitness, eroding genetic variation in partner quality. Yet abundant genetic variation in partner quality exists in many systems (Heath & Stinchcombe,). One possible resolution to this puzzle is that the genetic identity of both a host and its partner affects the benefits each mutualist provides to the other, a pattern known as a genotype-by-genotype interaction (Figure). Mounting evidence suggests that genotype-by-genotype interactions between partners are pervasive at the phenotypic level (Barrett, Zee, Bever, Miller, & Thrall, ; Heath, ; Hoeksema & Thompson,). Ultimately, however, to link these phenotypic patterns to the maintenance of genetic variation in mutualisms we need to answer two questions: How much variation in mutualism phenotypes is attributable to genotype-by-genotype interactions, and what mutualistic functions are influenced by each partner and by the interaction between their genomes? In this issue of Molecular Ecology, Burghardt et al. (2017) use transcriptomics to address both questions in the legume-rhizobia mutualism.}, } @article {pmid28607345, year = {2017}, author = {Chen, HK and Wang, LH and Chen, WU and Mayfield, AB and Levy, O and Lin, CS and Chen, CS}, title = {Coral lipid bodies as the relay center interconnecting diel-dependent lipidomic changes in different cellular compartments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3244}, pmid = {28607345}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/cytology/*microbiology/*physiology ; Circadian Rhythm ; Dinoflagellida/physiology ; Lipid Droplets ; Lipid Metabolism/*physiology ; Symbiosis/physiology ; }, abstract = {Lipid bodies (LBs) in the coral gastrodermal tissues are key organelles in the regulation of endosymbiosis and exhibit a diel rhythmicity. Using the scleractinian Euphyllia glabrescens collected across the diel cycle, we observed temporally dynamic lipid profiles in three cellular compartments: host coral gastrodermal cells, LBs, and in hospite Symbiodinium. Particularly, the lipidome varied over time, demonstrating the temporally variable nature of the coral-Symbiodinium endosymbiosis. The lipidome-scale data highlight the dynamic, light-driven metabolism of such associations and reveal that LBs are not only lipid storage organelles but also act as a relay center in metabolic trafficking. Furthermore, lipogenesis in LBs is significantly regulated by coral hosts and the lipid metabolites within holobionts featured predominantly triacylglycerols, sterol esters, and free fatty acids. Given these findings through a time-varied lipidome status, the present study provided valuable insights likely to be crucial to understand the cellular biology of the coral-Symbiodinium endosymbiosis.}, } @article {pmid28091933, year = {2017}, author = {Givaudan, A and Lanois, A}, title = {Flagellar Regulation and Virulence in the Entomopathogenic Bacteria-Xenorhabdus nematophila and Photorhabdus luminescens.}, journal = {Current topics in microbiology and immunology}, volume = {402}, number = {}, pages = {39-51}, doi = {10.1007/82_2016_53}, pmid = {28091933}, issn = {0070-217X}, mesh = {*Flagella/physiology ; *Photorhabdus ; Symbiosis ; Virulence ; *Xenorhabdus ; }, abstract = {There is a complex interplay between the regulation of flagellar motility and the expression of virulence factors in many bacterial pathogens. Here, we review the literature on the direct and indirect roles of flagellar motility in mediating the tripartite interaction between entomopathogenic bacteria (Photorhabdus and Xenorhabdus), their nematode hosts, and their insect targets. First, we describe the swimming and swarming motility of insect pathogenic bacteria and its impact on insect colonization. Then, we describe the coupling between the expression of flagellar and virulence genes and the dynamic of expression of the flagellar regulon during invertebrate infection. We show that the flagellar type 3 secretion system (T3SS) is also an export apparatus for virulence proteins in X. nematophila. Finally, we demonstrate that phenotypic variation, a common property of the bacterial symbionts of nematodes, also alters flagellar motility in Photorhabdus and Xenorhabdus. Finally, the so-called phenotypic heterogeneity phenomenon in the flagellar gene expression network will be also discussed. As the main molecular studies were performed in X. nematophila, future perspectives for the study of the interplay between flagellum and invertebrate interactions in Photorhabdus will be discussed.}, } @article {pmid27995342, year = {2017}, author = {Eleftherianos, I and Shokal, U and Yadav, S and Kenney, E and Maldonado, T}, title = {Insect Immunity to Entomopathogenic Nematodes and Their Mutualistic Bacteria.}, journal = {Current topics in microbiology and immunology}, volume = {402}, number = {}, pages = {123-156}, doi = {10.1007/82_2016_52}, pmid = {27995342}, issn = {0070-217X}, support = {R01 AI110675/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Bacteria ; Biological Control Agents ; Humans ; *Insecta/immunology ; *Nematoda/parasitology ; Symbiosis ; }, abstract = {Entomopathogenic nematodes are important organisms for the biological control of insect pests and excellent models for dissecting the molecular basis of the insect immune response against both the nematode parasites and their mutualistic bacteria. Previous research involving the use of various insects has found distinct differences in the number and nature of immune mechanisms that are activated in response to entomopathogenic nematode parasites containing or lacking their associated bacteria. Recent studies using model insects have started to reveal the identity of certain molecules with potential anti-nematode or antibacterial activity as well as the molecular components that nematodes and their bacteria employ to evade or defeat the insect immune system. Identification and characterization of the genes that regulate the insect immune response to nematode-bacteria complexes will contribute significantly to the development of improved practices to control insects of agricultural and medical importance, and potentially nematode parasites that infect mammals, perhaps even humans.}, } @article {pmid31163164, year = {2019}, author = {Havird, JC and Forsythe, ES and Williams, AM and Werren, JH and Dowling, DK and Sloan, DB}, title = {Selfish Mitonuclear Conflict.}, journal = {Current biology : CB}, volume = {29}, number = {11}, pages = {R496-R511}, doi = {10.1016/j.cub.2019.03.020}, pmid = {31163164}, issn = {1879-0445}, abstract = {Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.}, } @article {pmid31162896, year = {2019}, author = {Polienko, AK}, title = {[Peculiarities morphology and structure of the uroliths].}, journal = {Urologiia (Moscow, Russia : 1999)}, volume = {}, number = {2}, pages = {21-25}, pmid = {31162896}, issn = {1728-2985}, abstract = {THE AIM: According to statistical data of a number of the countries, have an urolithic disease from 5% to 15% of the population today. A recurrence arises at 50-85% of patients. The purpose of this work was complex studying of morphology, structure, mineral structure of urolit, identification of regularities of their formation, establishment of interrelation between mineral and organic matter in structure of urolit.

MATERIALS: the urinary stones from the urology departments of hospitals and clinics of the Tomsk region (Russia).

METHOD: s: crystallomorphological (the study of the surface morphology of uroliths binocular and trinocular microscopes); polarizing optical (study of the mineral composition of uroliths on a polarizing microscope); x-ray crystallography (the study of spectral composition on the apparatus DRON-3); electron microscopic (study of the peculiarities of morphology of crystals in an electron microscope).

RESULTS: On features of morphology of a surface four types of urolit are allocated: druzovidny, sferolitovy, combined, korallovidny. Structural kinds of urolit: crystal and granular, dendritovidny, combined, rhythmic - zone. In structure of urolit the following types of rhythms are established: zone, granular, combined. In the urolitakh with rhythmic - the zone structure allocated elements of their building: kernel, layer, zone, rhythm. A mineral part of uric stones is presented by the crystals belonging to the classes: oxalates, phosphates, urat .

SUMMARY: The peculiarities of the morphology of the selected four types of uroliths: druzoid, with, combined, coral. Structural variations uroliths: crystal-grained Shelly, dendritic, combined, rhythmically zoned. In the structure of uroliths, the following types of rhythms: zoned, granular, combined. In urolith with rhythmically zoned structure selected elements of their structure: core, layer, area, rhythm.

DISCUSSION: Morphological and structural features of the structure of urolites, especially the presence of rhythmic zoning, due to the alternation of layers of mineral and organic matter, indicate a close relationship between the living organism and the organo-mineral aggregate in the human urinary system. With a high degree of confidence we can talk about the symbiosis of living and mineral matter in the human body; as a result of this symbiosis, organic-mineral formations are formed, which are often the further cause of some diseases (for example, urolithiasis and cholelithiasis).

CONCLUSION: The complex research of uric stones allows to obtain important information on their structure, structure and features of morphology. Morphological and structural features of the structure of urolit, in particular existence of the rhythmic zonality caused by alternation of layers of mineral and organic matter demonstrate close interrelation between a live organism and the organo-mineral unit in an urinary system of the person.}, } @article {pmid31162893, year = {2019}, author = {Shchuplova, EA and Kuzmin, MD}, title = {[The additional criterion for the diagnosis of purulent-destructive forms of acute pyelonephritis].}, journal = {Urologiia (Moscow, Russia : 1999)}, volume = {}, number = {2}, pages = {5-8}, pmid = {31162893}, issn = {1728-2985}, abstract = {AIM: to develop an additional criterion for objective diagnosis of purulent-destructive forms of acute pyelonephritis.

MATERIALS AND METHODS: A total of 35 blood samples from patients with acute pyelonephritis aged from 19 to 85 years (mean age was 52 years) were studied. For the analysis, a classical bacteriological method of isolating blood culture and a modern molecular genetic method of fluorescent in situ hybridization (FISH) using DNA probes complementary to species-specific regions of the 16S rRNA gene of microorganisms were used. The obtained results were processed using the Statistica 6.0 program.

RESULTS: The bacteriological study showed that only in one patient (2.9%) a blood culture was positive, whereas with FISH, polymicrobial infection consisting of two associates was observed in five patients (14.3%), and 207 specific luminescence from different DNA probes were detected in blood samples. The associations of members of the Enterobacteriaceae with S. aureus were 2.4 times more frequent than associations of the Enterobacteriaceae with S. epidermidis, indicating a development of the polymicrobial infection and, accordingly, the development of purulent stage of acute pyelonephritis.

CONCLUSION: For the diagnosis of acute pyelonephritis, we suggest to use an additional criterion, which consists in applying of FISH method for the detection and simultaneous identification of bacteria that were adhered on the surface of erythrocytes and located intracellularly. This method may allow for the differential diagnosis of serous and purulent stages of acute pyelonephritis.}, } @article {pmid31161314, year = {2019}, author = {Prasad, S and Pandey, U and Saini, J and Ingalhalikar, M and Pal, PK}, title = {Atrophy of cerebellar peduncles in essential tremor: a machine learning-based volumetric analysis.}, journal = {European radiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00330-019-06269-7}, pmid = {31161314}, issn = {1432-1084}, support = {ECR/2016/000808//Science and Engineering Research Board/ ; }, abstract = {BACKGROUND: Subtle cerebellar signs are frequently observed in essential tremor (ET) and may be associated with cerebellar dysfunction. This study aims to evaluate the macrostructural integrity of the superior, middle, and inferior cerebellar peduncles (SCP, MCP, ICP) and cerebellar gray and white matter (GM, WM) volumes in patients with ET, and compare these volumes between patients with and without cerebellar signs (ETc and ETnc).

METHODS: Forty patients with ET and 37 age- and gender-matched healthy controls were recruited. Atlas-based region-of-interest analysis of the SCP, MCP, and ICP and automated analysis of cerebellar GM and WM volumes were performed. Peduncular volumes were employed in a multi-variate classification framework to attempt discrimination of ET from controls.

RESULTS: Significant atrophy of bilateral MCP and ICP and bilateral cerebellar GM was observed in ET. Cerebellar signs were present in 20% of subjects with ET. Comparison of peduncular and cerebellar volumes between ETnc and ETc revealed atrophy of right SCP, bilateral MCP and ICP, and left cerebellar WM in ETc. The multi-variate classifier could discriminate between ET and controls with a test accuracy of 86.66%.

CONCLUSIONS: Patients with ET have significant atrophy of cerebellar peduncles, particularly the MCP and ICP. Additional atrophy of the SCP is observed in the ETc group. These abnormalities may contribute to the pathogenesis of cerebellar signs in ET.

KEY POINTS: • Patients with ET have significant atrophy of bilateral middle and inferior cerebellar peduncles and cerebellar gray matter in comparison with healthy controls. • Patients of ET with cerebellar signs have significant atrophy of right superior cerebellar peduncle, bilateral middle and inferior cerebellar peduncle, and left cerebellar white matter in comparison with ET without cerebellar signs. • A multi-variate classifier employing peduncular volumes could discriminate between ET and controls with a test accuracy of 86.66%.}, } @article {pmid31161283, year = {2019}, author = {Mu, X and Luo, J}, title = {Evolutionary analyses of NIN-like proteins in plants and their roles in nitrate signaling.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00018-019-03164-8}, pmid = {31161283}, issn = {1420-9071}, support = {2662017QD001//Fundamental Research Funds for the Central Universities/ ; 2017CFB338//Hubei Province Natural Science Foundation of China/ ; 30500487//Research Start-up Fund for Henan Agricultural Universities/ ; }, abstract = {Nitrogen (N) is one of the most important essential macro-elements for plant growth and development, and nitrate represents the most abundant inorganic form of N in soils. The nitrate uptake and assimilation processes are finely tuned according to the available nitrate in the surroundings as well as by the internal finely coordinated signaling pathways. The NIN-like proteins (NLPs) harbor both RWP-RK, and Phox and Bem1 (PB1) domains, and they belong to the well-characterized plant-specific RWP-RK transcription factor gene family. NLPs are known to be involved in the nitrate signaling pathway by activating downstream target genes, and thus they are implicated in the primary nitrate response in the nucleus via their RWP-RK domains. The PB1 domain is a ubiquitous protein-protein interaction domain and it comprises another regulatory layer for NLPs via the protein interactions within NLPs or with other essential components. Recently, Ca2+-Ca2+ sensor protein kinase-NLP signaling cascades have been identified and they allow NLPs to have central roles in mediating the nitrate signaling pathway. NLPs play essential roles in many aspects of plant growth and development via the finely tuned nitrate signaling pathway. Furthermore, recent studies have highlighted the emerging roles played by NLPs in the N starvation response, nodule formation in legumes, N and P interactions, and root cap release in higher plants. In this review, we consider recent advances in the identification, evolution, molecular characteristics, and functions of the NLP gene family in plant growth and development.}, } @article {pmid31160787, year = {2019}, author = {Klimovich, A and Wittlieb, J and Bosch, TCG}, title = {Transgenesis in Hydra to characterize gene function and visualize cell behavior.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41596-019-0173-3}, pmid = {31160787}, issn = {1750-2799}, abstract = {The freshwater polyp Hydra is a cnidarian used as a model organism in a number of fields, including the study of the origin and evolution of developmental mechanisms, aging, symbiosis and host-microbe interactions. Here, we describe a procedure for the establishment of stable transgenic Hydra lines by embryo microinjection. The three-stage protocol comprises (i) the design and preparation of a transgenic construct, (ii) the microinjection of the vector into early embryos of Hydra vulgaris, and (iii) the selection and enrichment of mosaic animals in order to develop uniformly transgenic clonal lines. The preparation of a transgenic construct requires ~2 weeks, and transgenic lines can be obtained within 3 months. The method allows constitutive or inducible gain- and loss-of-function approaches, as well as in vivo tracing of individual cells. Hydra polyps carrying transgenic cells reveal functional properties of the ancestral circuitry controlling animal development.}, } @article {pmid31159921, year = {2019}, author = {Hambleton, EA and Jones, VAS and Maegele, I and Kvaskoff, D and Sachsenheimer, T and Guse, A}, title = {Sterol transfer by atypical cholesterol-binding NPC2 proteins in coral-algal symbiosis.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.43923}, pmid = {31159921}, issn = {2050-084X}, support = {GU 1128/3-1//Deutsche Forschungsgemeinschaft/ ; FP7-PEOPLE-2013-CIG//European Commission/ ; 724715//Horizon 2020 Framework Programme/ ; Exploration Grant//Boehringer Ingelheim Stiftung/ ; LTF//European Molecular Biology Organization/ ; Excellence Initiative//Universität Heidelberg/ ; TRR83//Deutsche Forschungsgemeinschaft/ ; SFB1324//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Reef-building corals depend on intracellular dinoflagellate symbionts that provide nutrients. Besides sugars, the transfer of sterols is essential for corals and other sterol-auxotrophic cnidarians. Sterols are important cell components, and variants of the conserved Niemann-Pick Type C2 (NPC2) sterol transporter are vastly up-regulated in symbiotic cnidarians. Types and proportions of transferred sterols and the mechanism of their transfer, however, remain unknown. Using different pairings of symbiont strains with lines of Aiptasia anemones or Acropora corals, we observe both symbiont- and host-driven patterns of sterol transfer, revealing plasticity of sterol use and functional substitution. We propose that sterol transfer is mediated by the symbiosis-specific, non-canonical NPC2 proteins, which gradually accumulate in the symbiosome. Our data suggest that non-canonical NPCs are adapted to the symbiosome environment, including low pH, and play an important role in allowing corals to dominate nutrient-poor shallow tropical seas worldwide.}, } @article {pmid31159445, year = {2019}, author = {Shen, G and Ju, W and Liu, Y and Guo, X and Zhao, W and Fang, L}, title = {Impact of Urea Addition and Rhizobium Inoculation on Plant Resistance in Metal Contaminated Soil.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ijerph16111955}, pmid = {31159445}, issn = {1660-4601}, abstract = {Legume-rhizobium symbiosis has been heavily investigated for their potential to enhance plant metal resistance in contaminated soil. However, the extent to which plant resistance is associated with the nitrogen (N) supply in symbiont is still uncertain. This study investigates the effect of urea or/and rhizobium (Sinorhizobium meliloti) application on the growth of Medicago sativa and resistance in metals contaminated soil (mainly with Cu). The results show that Cu uptake in plant shoots increased by 41.7%, 69%, and 89.3% with urea treatment, rhizobium inoculation, and their combined treatment, respectively, compared to the control group level. In plant roots, the corresponding values were 1.9-, 1.7-, and 1.5-fold higher than the control group values, respectively. Statistical analysis identified that N content was the dominant variable contributing to Cu uptake in plants. Additionally, a negative correlation was observed between plant oxidative stress and N content, indicating that N plays a key role in plant resistance. Oxidative damage decreased after rhizobium inoculation as the activities of antioxidant enzymes (catalase and superoxide dismutase in roots and peroxidase in plant shoots) were stimulated, enhancing plant resistance and promoting plant growth. Our results suggest that individual rhizobium inoculation, without urea treatment, is the most recommended approach for effective phytoremediation of contaminated land.}, } @article {pmid30832430, year = {2019}, author = {Alaswad, AA and Oehrle, NW and Krishnan, HB}, title = {Classical Soybean (Glycine max (L.) Merr) Symbionts, Sinorhizobium fredii USDA191 and Bradyrhizobium diazoefficiens USDA110, Reveal Contrasting Symbiotic Phenotype on Pigeon Pea (Cajanus cajan (L.) Millsp).}, journal = {International journal of molecular sciences}, volume = {20}, number = {5}, pages = {}, doi = {10.3390/ijms20051091}, pmid = {30832430}, issn = {1422-0067}, mesh = {Bradyrhizobium/genetics/metabolism/*pathogenicity ; Cajanus/metabolism/*microbiology ; Host Specificity ; Nitrogen Fixation ; *Phenotype ; Root Nodules, Plant/metabolism/microbiology/ultrastructure ; Sinorhizobium fredii/genetics/metabolism/*pathogenicity ; Soybeans/microbiology ; *Symbiosis ; Type III Secretion Systems/genetics ; }, abstract = {Pigeon pea (Cajanus cajan (L.) Millspaugh) is cultivated widely in semiarid agricultural regions in over 90 countries around the world. This important legume can enter into symbiotic associations with a wide range of rhizobia including Bradyrhizobium and fast-growing rhizobia. In comparison with other major legumes such as soybean and common bean, only limited information is available on the symbiotic interaction of pigeon pea with rhizobia. In this study, we investigated the ability of two classical soybean symbionts-S. fredii USDA191 and B. diazoefficiens USDA110-and their type 3 secretion system (T3SS) mutants, to nodulate pigeon pea. Both S. fredii USDA191 and a T3SS mutant S. fredii RCB26 formed nitrogen-fixing nodules on pigeon pea. Inoculation of pigeon pea roots with B. diazoefficiens USDA110 and B. diazoefficiens Δ136 (a T3SS mutant) resulted in the formation of Fix- and Fix+ nodules, respectively. Light and transmission electron microscopy of Fix- nodules initiated by B. diazoefficiens USDA110 revealed the complete absence of rhizobia within these nodules. In contrast, Fix+ nodules formed by B. diazoefficiens Δ136 revealed a central region that was completely filled with rhizobia. Ultrastructural investigation revealed the presence of numerous bacteroids surrounded by peribacteroid membranes in the infected cells. Analysis of nodule proteins by one- and two-dimensional gel electrophoresis revealed that leghemoglobin was absent in B. diazoefficiens USDA110 nodules, while it was abundantly present in B. diazoefficiens Δ136 nodules. Results of competitive nodulation assays indicated that B. diazoefficiens Δ136 had greater competitiveness for nodulation on pigeon pea than did the wild type strain. Our results suggest that this T3SS mutant of B. diazoefficiens, due to its greater competitiveness and ability to form Fix+ nodules, could be exploited as a potential inoculant to boost pigeon pea productivity.}, } @article {pmid30773714, year = {2019}, author = {Estellé, J}, title = {Benefits from the joint analysis of host genomes and metagenomes: Select the holobiont.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {136}, number = {2}, pages = {75-76}, doi = {10.1111/jbg.12383}, pmid = {30773714}, issn = {1439-0388}, mesh = {Animals ; Genetic Variation ; *Genome ; Genotyping Techniques ; *Metagenome ; Symbiosis/*genetics ; }, } @article {pmid30241612, year = {2018}, author = {Cadwell, K}, title = {Sugar Turns Bacteria Sweet: A Peace Offering in the Gut.}, journal = {Cell}, volume = {175}, number = {1}, pages = {36-37}, doi = {10.1016/j.cell.2018.08.053}, pmid = {30241612}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Asymptomatic Infections ; Bacteria ; Humans ; *Sugars ; Symbiosis ; Virulence ; }, abstract = {Following an infection, a subset of individuals can remain disease free despite harboring a pathogen for a prolonged period. In this issue of Cell, Sanchez et al. demonstrate that a metabolically favorable host response can drive an otherwise lethal bacterial pathogen to abandon virulence and become a commensal microorganism.}, } @article {pmid30127409, year = {2018}, author = {Taylor, BN and Menge, DNL}, title = {Light regulates tropical symbiotic nitrogen fixation more strongly than soil nitrogen.}, journal = {Nature plants}, volume = {4}, number = {9}, pages = {655-661}, doi = {10.1038/s41477-018-0231-9}, pmid = {30127409}, issn = {2055-0278}, mesh = {Fabaceae/growth & development/metabolism/physiology ; Light ; Nitrogen/*metabolism ; Nitrogen Fixation/*radiation effects ; Rhizobiaceae/metabolism ; Seedlings/growth & development ; Soil ; Symbiosis/*radiation effects ; Trees/growth & development/metabolism/physiology ; Tropical Climate ; }, abstract = {Nitrogen limits primary production in almost every biome on Earth1,2. Symbiotic nitrogen fixation, conducted by certain angiosperms and their endosymbiotic bacteria, is the largest potential natural source of new nitrogen into the biosphere3, influencing global primary production, carbon sequestration and element cycling. Because symbiotic nitrogen fixation represents an alternative to soil nitrogen uptake, much of the work on symbiotic nitrogen fixation regulation has focused on soil nitrogen availability4-8. However, because symbiotic nitrogen fixation is an energetically expensive process9, light availability to the plant may also regulate symbiotic nitrogen fixation rates10,11. Despite the importance of symbiotic nitrogen fixation to biosphere functioning, the environmental factors that most strongly regulate this process remain unresolved. Here we show that light regulates symbiotic nitrogen fixation more strongly than does soil nitrogen and that light mediates the response of symbiotic nitrogen fixation to soil nitrogen availability. In a shadehouse experiment, low light levels (comparable with forest understories) completely shut down symbiotic nitrogen fixation, whereas soil nitrogen levels that far exceeded plant demand did not fully downregulate symbiotic nitrogen fixation at high light. For in situ forest seedlings, light was a notable predictor of symbiotic nitrogen fixation activity, but soil-extractable nitrogen was not. Light as a primary regulator of symbiotic nitrogen fixation is a departure from decades of focus on soil nitrogen availability. This shift in our understanding of symbiotic nitrogen fixation regulation can resolve a long-standing biogeochemical paradox12, and it will improve our ability to predict how symbiotic nitrogen fixation will fuel the global forest carbon sink and respond to human alteration of the global nitrogen cycle.}, } @article {pmid29245006, year = {2017}, author = {Douglas, AE}, title = {Big Role for a Tiny Genome.}, journal = {Cell}, volume = {171}, number = {7}, pages = {1472-1473}, doi = {10.1016/j.cell.2017.11.038}, pmid = {29245006}, issn = {1097-4172}, mesh = {Animals ; Bacteria ; *Coleoptera ; *Herbivory ; Insecta ; Symbiosis ; }, abstract = {In this issue of Cell, Salem et al. demonstrate a remarkable instance of herbivory dependent on a co-evolved mutualism with specialized bacteria. Despite having a tiny genome and limited metabolic repertoire, the bacteria in Cassida beetles produce pectinases predicted to mediate degradation of plant cell walls in the insect diet.}, } @article {pmid28855622, year = {2017}, author = {Fan, W and Guo, W and Van Etten, JL and Mower, JP}, title = {Multiple origins of endosymbionts in Chlorellaceae with no reductive effects on the plastid or mitochondrial genomes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10101}, pmid = {28855622}, issn = {2045-2322}, support = {P30 GM103509/GM/NIGMS NIH HHS/United States ; }, mesh = {Chlorella/genetics ; Chlorophyta/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; Introns ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {Ancient endosymbiotic relationships have led to extreme genomic reduction in many bacterial and eukaryotic algal endosymbionts. Endosymbionts in more recent and/or facultative relationships can also experience genomic reduction to a lesser extent, but little is known about the effects of the endosymbiotic transition on the organellar genomes of eukaryotes. To understand how the endosymbiotic lifestyle has affected the organellar genomes of photosynthetic green algae, we generated the complete plastid genome (plastome) and mitochondrial genome (mitogenome) sequences from three green algal endosymbionts (Chlorella heliozoae, Chlorella variabilis and Micractinium conductrix). The mitogenomes and plastomes of the three newly sequenced endosymbionts have a standard set of genes compared with free-living trebouxiophytes, providing no evidence for functional genomic reduction. Instead, their organellar genomes are generally larger and more intron rich. Intron content is highly variable among the members of Chlorella, suggesting very high rates of gain and/or loss of introns during evolution. Phylogenetic analysis of plastid and mitochondrial genes demonstrated that the three endosymbionts do not form a monophyletic group, indicating that the endosymbiotic lifestyle has evolved multiple times in Chlorellaceae. In addition, M. conductrix is deeply nested within the Chlorella clade, suggesting that taxonomic revision is needed for one or both genera.}, } @article {pmid31158486, year = {2019}, author = {Titus, BM and Benedict, C and Laroche, R and Gusmão, LC and Van Deusen, V and Chiodo, T and Meyer, CP and Berumen, ML and Bartholomew, A and Yanagi, K and Reimer, JD and Fujii, T and Daly, M and Rodríguez, E}, title = {Phylogenetic relationships among the clownfish-hosting sea anemones.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {106526}, doi = {10.1016/j.ympev.2019.106526}, pmid = {31158486}, issn = {1095-9513}, abstract = {The clownfish-sea anemone symbiosis has been a model system for understanding fundamental evolutionary and ecological processes. However, our evolutionary understanding of this symbiosis comes entirely from studies of clownfishes. A holistic understanding of a model mutualism requires systematic, biogeographic, and phylogenetic insight into both partners. Here, we conduct the largest phylogenetic analysis of sea anemones (Order Actiniaria) to date, with a focus on expanding the biogeographic and taxonomic sampling of the 10 nominal clownfish-hosting species. Using a combination of mtDNA and nuDNA loci we test 1) the monophyly of each clownfish-hosting family and genus, 2) the current anemone taxonomy that suggests symbioses with clownfishes evolved multiple times within Actiniaria, and 3) whether, like the clownfishes, there is evidence that host anemones have a Coral Triangle biogeographic origin. Our phylogenetic reconstruction demonstrates widespread poly- and para-phyly at the family and genus level, particularly within the family Stichodactylidae and genus Stichodactyla, and suggests that symbioses with clownfishes evolved minimally three times within sea anemones. We further recover evidence for a Tethyan biogeographic origin for some clades. Our data provide the first evidence that clownfish and some sea anemone hosts have different biogeographic origins, and that there may be cryptic species of host anemones. Finally, our findings reflect the need for a major taxonomic revision of the clownfish-hosting sea anemones.}, } @article {pmid31156674, year = {2019}, author = {Gómez-Gallego, T and Benabdellah, K and Merlos, MA and Jiménez-Jiménez, AM and Alcon, C and Berthomieu, P and Ferrol, N}, title = {The Rhizophagus irregularis Genome Encodes Two CTR Copper Transporters That Mediate Cu Import Into the Cytosol and a CTR-Like Protein Likely Involved in Copper Tolerance.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {604}, doi = {10.3389/fpls.2019.00604}, pmid = {31156674}, issn = {1664-462X}, abstract = {Arbuscular mycorrhizal fungi increase fitness of their host plants under Cu deficient and toxic conditions. In this study, we have characterized two Cu transporters of the CTR family (RiCTR1 and RiCTR2) and a CTR-like protein (RiCTR3A) of Rhizophagus irregularis. Functional analyses in yeast revealed that RiCTR1 encodes a plasma membrane Cu transporter, RiCTR2 a vacuolar Cu transporter and RiCTR3A a plasma membrane protein involved in Cu tolerance. RiCTR1 was more highly expressed in the extraradical mycelia (ERM) and RiCTR2 in the intraradical mycelia (IRM). In the ERM, RiCTR1 expression was up-regulated by Cu deficiency and down-regulated by Cu toxicity. RiCTR2 expression increased only in the ERM grown under severe Cu-deficient conditions. These data suggest that RiCTR1 is involved in Cu uptake by the ERM and RiCTR2 in mobilization of vacuolar Cu stores. Cu deficiency decreased mycorrhizal colonization and arbuscule frequency, but increased RiCTR1 and RiCTR2 expression in the IRM, which suggest that the IRM has a high Cu demand. The two alternatively spliced products of RiCTR3, RiCTR3A and RiCTR3B, were more highly expressed in the ERM. Up-regulation of RiCTR3A by Cu toxicity and the yeast complementation assays suggest that RiCTR3A might function as a Cu receptor involved in Cu tolerance.}, } @article {pmid31156662, year = {2019}, author = {Pucciariello, C and Boscari, A and Tagliani, A and Brouquisse, R and Perata, P}, title = {Exploring Legume-Rhizobia Symbiotic Models for Waterlogging Tolerance.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {578}, doi = {10.3389/fpls.2019.00578}, pmid = {31156662}, issn = {1664-462X}, abstract = {Unexpected and increasingly frequent extreme precipitation events result in soil flooding or waterlogging. Legumes have the capacity to establish a symbiotic relationship with endosymbiotic atmospheric dinitrogen-fixing rhizobia, thus contributing to natural nitrogen soil enrichment and reducing the need for chemical fertilization. The impact of waterlogging on nitrogen fixation and legume productivity needs to be considered for crop improvement. This review focuses on the legumes-rhizobia symbiotic models. We aim to summarize the mechanisms underlying symbiosis establishment, nodule development and functioning under waterlogging. The mechanisms of oxygen sensing of the host plant and symbiotic partner are considered in view of recent scientific advances.}, } @article {pmid31156660, year = {2019}, author = {von Sivers, L and Jaspar, H and Johst, B and Roese, M and Bitterlich, M and Franken, P and Kühn, C}, title = {Brassinosteroids Affect the Symbiosis Between the AM Fungus Rhizoglomus irregularis and Solanaceous Host Plants.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {571}, doi = {10.3389/fpls.2019.00571}, pmid = {31156660}, issn = {1664-462X}, abstract = {Together with several proteins involved in brassinosteroid (BR) signaling and synthesis, the membrane steroid binding protein 1 (MSBP1) was identified within the interactome of the sucrose transporter of tomato (SlSUT2). We asked whether MSBP1 is also involved in BR signaling as assumed for the AtMSBP1 protein from Arabidopsis and whether it impacts root colonization with arbuscular mycorrhizal (AM) fungi in a similar way as shown previously for SlSUT2. In addition, we asked whether brassinosteroids per se affect efficiency of root colonization by AM fungi. We carried out a set of experiments with transgenic tobacco plants with increased and decreased MSBP1 expression levels. We investigated the plant and the mycorrhizal phenotype of these transgenic plants and tested the involvement of MSBP1 in BR metabolism by application of epi-brassinolide and brassinazole, an inhibitor of BR biosynthesis. We show that the phenotype of the transgenic tobacco plants with increased or reduced MSBP1 expression is consistent with an inhibitory role of MSBP1 in BR signaling. MSBP1 overexpression could be mimicked by brassinazole treatment. Interestingly, manipulation of MSBP1 expression in transgenic tobacco plants not only affected plant growth and development, but also the host plant responses toward colonization with AM fungi, as well as arbuscular architecture. Moreover, we observed that brassinosteroids indeed have a direct impact on the nutrient exchange in AM symbiosis and on the biomass production of colonized host plants. Furthermore, arbuscular morphology is affected by changes in MSBP1 expression and brassinolide or brassinazole treatments. We conclude that host plant growth responses and nutrient exchange within the symbiosis with AM fungi is controlled by brassinosteroids and might be impeded by the MSBP1 protein.}, } @article {pmid31156595, year = {2019}, author = {Bertolazi, AA and de Souza, SB and Ruas, KF and Campostrini, E and de Rezende, CE and Cruz, C and Melo, J and Colodete, CM and Varma, A and Ramos, AC}, title = {Inoculation With Piriformospora indica Is More Efficient in Wild-Type Rice Than in Transgenic Rice Over-Expressing the Vacuolar H+-PPase.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1087}, doi = {10.3389/fmicb.2019.01087}, pmid = {31156595}, issn = {1664-302X}, abstract = {Achieving food security in a context of environmental sustainability is one of the main challenges of the XXI century. Two competing strategies to achieve this goal are the use of genetically modified plants and the use of plant growth promoting microorganisms (PGPMs). However, few studies assess the response of genetically modified plants to PGPMs. The aim of this study was to compare the response of over-expressing the vacuolar H+-PPase (AVP) and wild-type rice types to the endophytic fungus; Piriformospora indica. Oryza sativa plants (WT and AVP) were inoculated with P. indica and 30 days later, morphological, ecophysiological and bioenergetic parameters, and nutrient content were assessed. AVP and WT plant heights were strongly influenced by inoculation with P. indica, which also promoted increases in fresh and dry matter of shoot in both genotypes. This may be related with the stimulatory effect of P. indica on ecophysiological parameters, especially photosynthetic rate, stomatal conductance, intrinsic water use efficiency and carboxylation efficiency. However, there were differences between the genotypes concerning the physiological mechanisms leading to biomass increment. In WT plants, inoculation with P. indica stimulated all H+ pumps. However, in inoculated AVP plants, H+-PPase was stimulated, but P- and V-ATPases were inhibited. Fungal inoculation enhanced nutrient uptake in both shoots and roots of WT and AVP plants, compared to uninoculated plants; but among inoculated genotypes, the nutrient uptake was lower in AVP than in WT plants. These results clearly demonstrate that the symbiosis between P. indica and AVP plants did not benefit those plants, which may be related to the inefficient colonization of this fungus on the transgenic plants, demonstrating an incompatibility of this symbiosis, which needs to be further studied.}, } @article {pmid31153721, year = {2019}, author = {Sobotková, K and Parker, W and Levá, J and Růžková, J and Lukeš, J and Jirků Pomajbíková, K}, title = {Helminth Therapy - From the Parasite Perspective.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2019.04.009}, pmid = {31153721}, issn = {1471-5007}, abstract = {Studies in animal models and humans suggest that intentional exposure to helminths or helminth-derived products may hold promise for treating chronic inflammatory-associated diseases (CIADs). Although the mechanisms underlying 'helminth therapy' are being evaluated, little attention has been paid to the actual organisms in use. Here we examine the notion that, because of the complexity of biological symbiosis, intact helminths rather than helminth-derived products are likely to prove more useful for clinical purposes. Further, weighing potential cost/benefit ratios of various helminths along with other factors, such as feasibility of production, we argue that the four helminths currently in use for CIAD treatments in humans were selected more by happenstance than by design, and that other candidates not yet tested may prove superior.}, } @article {pmid31152905, year = {2019}, author = {Rostami, M and Rostami, S}, title = {Effect of salicylic acid and mycorrhizal symbiosis on improvement of fluoranthene phytoremediation using tall fescue (Festuca arundinacea Schreb).}, journal = {Chemosphere}, volume = {232}, number = {}, pages = {70-75}, doi = {10.1016/j.chemosphere.2019.05.171}, pmid = {31152905}, issn = {1879-1298}, abstract = {Polycyclic aromatic hydrocarbons are an important group of pollutants that are widely distributed in the environment. The present study aimed to investigate the effect of salicylic acid (a phenolic phytohormone) and mycorrhizal fungi on the growth and phytoremediation ability of tall fescue in the soil contaminated by fluoranthene. The initial concentrations of fluoranthene in this study were 100, 200, and 300 mg kg-1. The experimental treatments were included: T0 uncultivated soil; T1 cultivated soil with tall fescue; T2 cultivated soil with tall fescue + salicylic acid application; T3 cultivated soil with tall fescue + application of mycorrhizal fungi; T4 cultivated soil with tall fescue + salicylic acid and mycorrhizal fungi application; and P planting tall fescue in uncontaminated soil. The removal of fluoranthene was measured after 90 days. Furthermore, at the end of the experiment, the amount of shoot and root biomass, soil bacteria, and dehydrogenase activity were measured. According to the results, in all levels of contamination, removal of fluoranthene in cultivated treatments significantly was higher than uncultivated treatments. Increasing the concentration of fluoranthene had a negative effect on the shoot and root biomass in different treatments. Salicylic acid and mycorrhizal fungi significantly increased the shoot and root biomass and also the number of soil bacteria, dehydrogenase activity, and fluoranthene removal in T2, T3, and T4 treatments compared to T1. At the highest concentration of fluoranthene, as a result of simultaneous application of salicylic acid and mycorrhizal fungi (T4), the fluoranthene removal increased by 63, 21, 13, and 16% in comparison with T0, T1, T2, and T3, respectively. Based on the results, salicylic acid and mycorrhizal fungi, either alone or in combination, have a significant effect on the improvement of phytoremediation potential in tall fescue.}, } @article {pmid31152017, year = {2019}, author = {Pesce, C and Oshone, R and Hurst, SG and Kleiner, VA and Tisa, LS}, title = {Stable transformation of the actinobacteria Frankia.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00957-19}, pmid = {31152017}, issn = {1098-5336}, abstract = {A stable and efficient plasmid transfer system was developed for the nitrogen-fixing symbiotic actinobacteria Frankia, a key first step in developing a genetic system. Four derivatives of the broad-host-range cloning vector pBBR1MCS were successfully introduced into different Frankia strains by a filter mating with Escherichia coli strain BW29427. Initially, the plasmid pHKT1 that expresses the green fluorescent protein (GFP) was introduced into Frankia casuarinae strain CcI3 at a frequency of 4.0 X 10-3 resulting in transformants that were tetracycline resistant and exhibited GFP fluorescence. The presence of the plasmid was confirmed by molecular approaches including visualization on agarose gel and PCR. Several other pBBR1MCS plasmids were also introduced into F. casuarinae strain CcI3 and other Frankia strains at frequencies ranging from 10-2 to 10-4, and the presence of the plasmids was confirmed by PCR. The plasmids were stably maintained for over 2 years and through the passage in a plant host. As a proof of concept, a salt-tolerance candidate gene from the high salt-tolerance Frankia sp. strain CcI6 was cloned into pBBR1MCS-3. The resulting construct was introduced into the salt-sensitive F. casuarinae strain CcI3. End-point RT PCR showed that the gene was expressed in F. casuarinae strain CcI3. The expression provided an increased level of salt tolerance for the transformant. These results represent stable plasmid transfer and exogenous gene expression in Frankia, overcoming a major hurdle in the field. This is a step in developing genetic tools in Frankia will open up new avenues for research for actinorhizal symbiosis.ImportanceThe absence of genetic tools for Frankia research has been a major hindrance to the associated field of actinorhizal symbiosis and the use of the nitrogen-fixing Actinobacteria. This study reports on the introduction of plasmids into Frankia and their functional expression of green fluorescent protein and a cloned gene. As the first step in developing genetic tools, this technique opens up the field to a wide array of approaches in an organism with great importance and potential in the environment.}, } @article {pmid31150238, year = {2019}, author = {Zhang, W and Mace, WJ and Matthew, C and Card, SD}, title = {The impact of endophyte infection, seed aging and imbibition on selected sugar metabolite concentrations in seed.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.9b01618}, pmid = {31150238}, issn = {1520-5118}, abstract = {This study investigated effects of seed aging and imbibition on sugar metabolite levels in Epichloë endophyte-infected and endophyte-free seed of tall fescue (Festuca arundinacea Schreb.). Gas chromatography with flame ionization detection was employed for analysis of sugar metabolites within the seed tissues, with embryo and endosperm tissues analyzed separately. Mannitol, ribitol and trehalose were more abundant in embryo than endosperm tissues and were identified at consistently higher levels within endophyte-infected compared to endophyte-free seeds. The ratio of raffinose to sucrose significantly increased with seed aging in both endophyte-free and endophyte-infected embryo tissues while significantly lower concentrations of trehalose were detected in tissues dissected from aged-seed regardless of endophyte status. This research provides fundamental insight into the metabolic details of endophyte survival in seed and provides a first evaluation of key carbohydrates present in the fungal-plant symbiosis.}, } @article {pmid31150064, year = {2019}, author = {Weis, VM}, title = {Cell biology of coral symbiosis: Foundational study can inform solutions to the coral reef crisis.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icz067}, pmid = {31150064}, issn = {1557-7023}, abstract = {Coral reefs are faced with almost complete destruction by the end of the century due to global warming unless humanity can cap global temperature rise. There is now a race to develop a diverse set of solutions to save coral reefs. In this perspective, a case is made for understanding of the cell biology of coral-dinoflagellate symbiosis to help inform development of solutions for saving reefs. Laboratory model systems for the study of coral symbiosis, including the sea anemone Exaiptasia pallida, are featured as valuable tools in the fight to save corals. The roles of host innate immunity and inter-partner nutrient dynamics in the onset, ongoing maintenance and dysregulation of symbiosis are reviewed and discussed. Key innate immune genes and pathways, such as glycan-lectin interactions, the sphingosine rheostat and the cytokine TGFβ are shown to modulate a host immune response in the symbiotic state. An upset in the homeostatic inorganic nutrient balance during heat stress and high exogenous nutrient availability is credited with driving the partnership towards dysregulation and coral bleaching. Specific examples are given where knowledge of the cell biology of symbiosis is informing the development of solutions, including studies showing clear limitations in the value of partner switching and acclimatization protocols. Finally, emphasis is placed on rapid advancement of knowledge to try to meet the urgent need for solutions. This includes real-time open communication with colleagues on successes and failures, sharing of resources and information, and working together in the spirit of a collective mission to save coral reefs.}, } @article {pmid31115477, year = {2019}, author = {Gómez-Díaz, JS and Montoya-Lerma, J and Muñoz Valencia, V}, title = {Prevalence and Diversity of Endosymbionts in Cassava Whiteflies (Hemiptera: Aleyrodidae) From Colombia.}, journal = {Journal of insect science (Online)}, volume = {19}, number = {3}, pages = {}, doi = {10.1093/jisesa/iez047}, pmid = {31115477}, issn = {1536-2442}, mesh = {Animals ; Hemiptera/genetics/*microbiology ; Manihot ; Nymph/microbiology ; Phylogeny ; Symbiosis ; }, abstract = {Whiteflies cause huge economic losses for cassava (Manihot esculenta Crantz) cultivation. Damage can be caused directly when the insects feed on the phloem and/or indirectly by the transmission of viruses. It has been found that whiteflies maintain a close relationship with some endosymbiotic bacteria and that this interaction produces different effects on host biology and can also facilitate viral transmission. This study aimed to characterize the diversity of secondary endosymbionts (SE) present in whiteflies associated with cassava. Whitefly adults and nymphs were collected from cassava crops at nine locations in Southwestern Colombia. Molecular identification of insects and endosymbionts was carried out using specific mtCOI, wsp, 23s rRNA, and 16s rRNA primers. Phylogenetic trees were constructed from these sequences, both for whitefly species and the endosymbionts found. In addition, morphological identification of whitefly species was made using last instar nymphs. Molecular and morphological evaluation revealed that the most abundant whitefly species was Trialeurodes variabilis (Quaintance) followed by Aleurotrachelus socialis Bondar and Bemisia tuberculata Bondar. One hundred percent of the individuals contained the primary endosymbiont Portiera. The SE Rickettsia, Hamiltonella, Wolbachia, and Fritschea were not detected in the samples tested. Prevalence of Cardinium and Arsenophonus were variable at each locality, Cardinium being most prevalent in A. socialis adults. This study is the first report on the presence of Cardinium and Arsenophonus in A. socialis and T. variabilis. It is also the first report of endosymbiotic diversity in whiteflies associated with cassava in Colombia.}, } @article {pmid30834947, year = {2019}, author = {Pandey, PK and Samanta, R and Yadav, RNS}, title = {Inside the plant: addressing bacterial endophytes in biotic stress alleviation.}, journal = {Archives of microbiology}, volume = {201}, number = {4}, pages = {415-429}, doi = {10.1007/s00203-019-01642-y}, pmid = {30834947}, issn = {1432-072X}, support = {Grant no. BT/04/NE/2009//Department of Biotechnology, Ministry of Science and Technology/ ; }, mesh = {*Bacterial Physiological Phenomena ; Endophytes/*physiology ; Plants/microbiology ; Stress, Physiological ; Symbiosis ; }, abstract = {Bacterial endophytes are the internal association of bacteria with the plants, cherished whole or any part of their life cycle inside the plant. They are reported to improve plant health against the biotic stresses via de novo synthesis of structural compounds and stimulation of plant immunity. They are found to be vital in development of host resistance against phytopathogens and capable in reducing and elimination of deleterious effects of plant pathogens. Fungal-, bacterial-, viral-, insect- and nematode-associated negative effect can be reduced by the bacterial endophytes. They are also reported to control plant pathogens through several defense mechanisms such as by producing antimicrobial compounds and antibiotics, de novo synthesis of structural compounds, keeping out of pathogens by niche competition and induction of plant immunity or induced systemic resistance. In this review, an effort is made to summarize the exploitation of endophytic bacteria as a biological substitute to control biotic stresses in agricultural practices.}, } @article {pmid30639767, year = {2019}, author = {Davis, WJ and Amses, KR and Benny, GL and Carter-House, D and Chang, Y and Grigoriev, I and Smith, ME and Spatafora, JW and Stajich, JE and James, TY}, title = {Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).}, journal = {Molecular phylogenetics and evolution}, volume = {133}, number = {}, pages = {152-163}, doi = {10.1016/j.ympev.2019.01.006}, pmid = {30639767}, issn = {1095-9513}, support = {S10 OD016290/OD/NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Fungal Proteins/genetics ; Fungi/*classification/*genetics ; Gene Library ; *Genome, Fungal ; Genomics ; Likelihood Functions ; *Phylogeny ; Symbiosis/genetics ; }, abstract = {Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.}, } @article {pmid30621755, year = {2018}, author = {Osmanovic, D and Kessler, DA and Rabin, Y and Soen, Y}, title = {Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {24}, doi = {10.1186/s13062-018-0224-7}, pmid = {30621755}, issn = {1745-6150}, mesh = {*Adaptation, Biological ; Bacteria/*genetics ; Bacterial Physiological Phenomena/genetics ; *Host-Pathogen Interactions ; *Microbiota ; Models, Genetic ; *Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.

RESULTS: To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent ("detox"). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host's offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria).

CONCLUSIONS: These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system.

REVIEWERS: This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman.}, } @article {pmid30329064, year = {2019}, author = {Kashkouli, M and Fathipour, Y and Mehrabadi, M}, title = {Potential Management Tactics for Pistachio Stink Bugs, Brachynema germari, Acrosternum heegeri and Acrosternum arabicum (Hemiptera: Pentatomidae): High Temperature and Chemical Surface Sterilants Leading to Symbiont Suppression.}, journal = {Journal of economic entomology}, volume = {112}, number = {1}, pages = {244-254}, doi = {10.1093/jee/toy324}, pmid = {30329064}, issn = {1938-291X}, mesh = {Animals ; Fertility ; *Hemiptera/microbiology ; Hot Temperature ; Insect Control/*methods ; Longevity ; Ovum ; Sterilization ; Symbiosis ; }, abstract = {Insect symbionts offer an opportunity to deal with the anticipated elevated demand for novel pest management strategies. One approach is the disruption of essential symbionts required by the pests. In the present study, we examined the effects of symbiont elimination strategies, high temperature and sterilization agents, on the fitness of three stink bugs, Brachynema germari Kolenati, Acrosternum heegeri Fieber, and Acrosternum arabicum Wagner by using demographic approach. In the high-temperature experiments, almost all insects exhibited severe fitness defects, including elevated nymphal mortality and reduced population growth parameters (especially intrinsic rate of increase, r), as well as significant reductions in the gut symbiont titers. In the egg surface sterilization assays, we experimentally assessed the effects of sterilization agents on the bugs and their symbionts and observed similar fitness defects to those observed under the high-temperature condition. According to the results, we concluded that the host's defective phenotypes are attributable not to the heat stress itself but to the suppression of the symbiont titer, which highlights the possibility that global warming and elevated temperature may negatively affect this mutualism. Together, the results suggest the biological importance of the bacterial symbiont for the host that might help us for better management of these important pests in the future.}, } @article {pmid30071013, year = {2018}, author = {Ma, D and Leulier, F}, title = {The importance of being persistent: The first true resident gut symbiont in Drosophila.}, journal = {PLoS biology}, volume = {16}, number = {8}, pages = {e2006945}, pmid = {30071013}, issn = {1545-7885}, mesh = {Acetobacter ; Animals ; Drosophila/*microbiology/physiology ; Drosophila melanogaster/microbiology/physiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract ; Microbiota ; Symbiosis/physiology ; }, abstract = {In the animal kingdom, nutritional mutualism is a perpetual and intimate dialogue carried out between the host and its associated gut community members. This dialogue affects many aspects of the host's development and physiology. Some constituents of the animal gut microbiota can stably reside within the host for years, and such long-term persistence might be a prerequisite for these microbes to assert their beneficial impact. How long-term persistence is established and maintained is an interesting question, and several classic model organisms associated with cultivable resident strains are used to address this question. However, in Drosophila, this model has long eluded fly geneticists. In this issue of PLOS Biology, Pais and colleagues present the most rigorous and comprehensive demonstration to date that persistence and gut residency do take place in the digestive tract of Drosophila melanogaster. This natural gut isolate of Acetobacter thailandicus stably colonizes the adult fly foregut, accelerates larval maturation, and boosts host fecundity and fertility as efficiently as the known laboratory strains. The discovery of such stable association will be a boon for the Drosophila community interested in host-microbiota interaction, as it not only provides a novel model to unravel the molecular underpinnings of persistence but also opens a new arena for using Drosophila to study the implications of gut persistence in evolution and ecology.}, } @article {pmid30037568, year = {2018}, author = {Mostowy, RJ and Holt, KE}, title = {Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating.}, journal = {Trends in microbiology}, volume = {26}, number = {12}, pages = {1008-1021}, pmid = {30037568}, issn = {1878-4380}, mesh = {Animals ; Antigens, Bacterial/chemistry/genetics/physiology ; Bacteria/*genetics/*metabolism/pathogenicity ; Bacterial Capsules/*chemistry/*genetics/immunology/*physiology ; *Biodiversity ; Cell Communication ; Ecology ; Evolution, Molecular ; Genetic Loci ; Humans ; Immunity ; Lipopolysaccharides/classification/genetics/immunology/physiology ; Phage Therapy ; Polysaccharides ; Polysaccharides, Bacterial/chemistry/genetics/immunology/physiology ; Serotyping ; Symbiosis ; Vaccines, Conjugate ; }, abstract = {Bacterial pathogens and commensals are surrounded by diverse surface polysaccharides which include capsules and lipopolysaccharides. These carbohydrates play a vital role in bacterial ecology and interactions with the environment. Here, we review recent rapid advancements in this field, which have improved our understanding of the roles, structures, and genetics of bacterial polysaccharide antigens. Genetic loci encoding the biosynthesis of these antigens may have evolved as bacterial diversity-generating machines, driven by selection from a variety of forces, including host immunity, bacteriophages, and cell-cell interactions. We argue that the high adaptive potential of polysaccharide antigens should be taken into account in the design of polysaccharide-targeting medical interventions like conjugate vaccines and phage-based therapies.}, } @article {pmid29563264, year = {2018}, author = {Madden, AA and Epps, MJ and Fukami, T and Irwin, RE and Sheppard, J and Sorger, DM and Dunn, RR}, title = {The ecology of insect-yeast relationships and its relevance to human industry.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1875}, pages = {}, pmid = {29563264}, issn = {1471-2954}, mesh = {Animals ; Ascomycota/*physiology ; Biological Evolution ; Ecosystem ; *Food Industry ; Humans ; Insecta/*microbiology ; Plant Nectar/metabolism ; Symbiosis ; }, abstract = {Many species of yeast are integral to human society. They produce many of our foods, beverages and industrial chemicals, challenge us as pathogens, and provide models for the study of our own biology. However, few species are regularly studied and much of their ecology remains unclear, hindering the development of knowledge that is needed to improve the relationships between humans and yeasts. There is increasing evidence that insects are an essential component of ascomycetous yeast ecology. We propose a 'dispersal-encounter hypothesis' whereby yeasts are dispersed by insects between ephemeral, spatially disparate sugar resources, and insects, in turn, obtain the benefits of an honest signal from yeasts for the sugar resources. We review the relationship between yeasts and insects through three main examples: social wasps, social bees and beetles, with some additional examples from fruit flies. Ultimately, we suggest that over the next decades, consideration of these ecological and evolutionary relationships between insects and yeasts will allow prediction of where new yeast diversity is most likely to be discovered, particularly yeasts with traits of interest to human industry.}, } @article {pmid31089666, year = {2018}, author = {Cazzolla Gatti, R}, title = {endogenosymbiosis: from hypothesis to empirical evidence towards a Unified Symbiogenetic Theory (UST).}, journal = {Theoretical biology forum}, volume = {111}, number = {1-2}, pages = {13-26}, doi = {10.19272/201811402002}, pmid = {31089666}, issn = {0035-6050}, mesh = {*Biological Evolution ; *Eukaryota ; Eukaryotic Cells ; Phylogeny ; Plastids ; *Symbiosis ; }, abstract = {In 1967 Lynn (Sagan) Margulis proposed that mitochondria, photosynthetic plastids and cilia were acquired prokaryotes and evolved symbiotically to form anaerobic bacteria, photosynthetic bacteria and eventually algae. Although most of this theory is well-accepted now, the hypothesis that endosymbiotic spirochaetes developed into eukaryotic flagella and cilia, and the following proposals of an endosymbiotic origin of other eukaryotic organelles such as peroxisomes, glyoxysomes, etc. have not received much acceptance, since evidence suggests they lack a genome and do not show ultrastructural similarities to bacteria or archaea. Nevertheless, the idea that over millennia mitochondria, plastids, prokaryotic and eukaryotic cells and even flagella and peroxisomes, as either primary or secondary endosymbionts, transferred some or all of their own DNA to the host cell’s nucleus through a process called «endogenosymbiosis» (i.e. a symbiotic gene transfer, such as the internalisation of the endosymbiont’s DNA with lateral transfer) has been recently suggested. This endogenosymbiosis could take place during the evolutionary transition from the symbiotic interacting community, invoked by Margulis, to a fully-integrated (either prokaryotic or eukaryotic) cell. This process could explain the missing evidence of the presence of DNA in flagella and peroxisomes whose ancestor endosymbionts, during the long endogenosymbiotic evolution, could have transferred their whole genome to the host cell that subsequently integrated it in its own genome, directly controlling its expression. Furthermore, the endogenosymbiosis hypothesis could be the explanation of the transition between an RNA to a DNA world and of some cases of true sympatric evolution of species, apparently inexplicable by the canonical speciation processes. Here, after an introduction to the theoretical basis of endogenosymbiosis and a discussion of the empirical confirming evidence, I show a graphical summary of the integration between this and the former endosymbiosis theories. The Serial Endosymbiosis Theory and the Secondary Endosymbiosis are merged with the Endogenosymbiosis Theory in a Unified Symbiogenetic Theory (UST).}, } @article {pmid31148385, year = {2019}, author = {Fernandes, S and Vinnakota, R and Kumar, J and Kale, V and Limaye, L}, title = {Improved neural differentiation of normal and abnormal iPSC lines in the presence of valproic acid.}, journal = {Journal of tissue engineering and regenerative medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/term.2904}, pmid = {31148385}, issn = {1932-7005}, abstract = {During the generation of induced pluripotent stem cell (iPSC) lines from cord blood CD34+ cells, a line having complete trisomy of chromosome 1 and deletion of q23 to qTer of chromosome 11 was accidentally developed in our lab. The abnormality was consistently detected even at higher passages. These chromosomal anomalies are known to manifest neurological developmental defects. In order to examine if such defects occur during in vitro differentiation of the cell line, we set up a protocol for neural differentiation. Valproic acid (VPA) was earlier reported by us to enhance neural differentiation of placental mesenchymal stem cells. Here we induced normal and abnormal iPSC lines to neural lineage with/without VPA. Neural differentiation was observed in all 4 sets, but for both the iPSCs lines, VPA sets performed better. The characteristics tested were morphology, neural filament length, detection of neural markers and electrophysiology. In summary, the karyotypically abnormal line exhibited efficient neural differentiation. This iPSC line may serve as a useful tool to study abnormalities associated with trisomy 1 and deletion of q23 to qTer of chromosome 11.}, } @article {pmid31148173, year = {2019}, author = {An, J and Zeng, T and Ji, C and de Graaf, S and Zheng, Z and Xiao, TT and Deng, X and Xiao, S and Bisseling, T and Limpens, E and Pan, Z}, title = {A Medicago truncatula SWEET transporter implicated in arbuscule maintenance during arbuscular mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15975}, pmid = {31148173}, issn = {1469-8137}, abstract = {•Plants form a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, which facilitates the acquisition of scarce minerals from the soil. In return, the host plants provide sugars and lipids to its fungal partner. However, the mechanism by which the AM fungi obtain sugars from the plant has remained elusive. •In this study we investigated the role of potential SWEET family sugar exporters in AM symbiosis in Medicago truncatula. •We show that M. truncatula SWEET1b transporter is strongly upregulated in arbuscule-containing cells compared to roots and localizes to the peri-arbuscular membrane, across which nutrient exchange takes place. Heterologous expression of MtSWEET1b in a yeast hexose transport mutant showed that it mainly transports glucose. Overexpression of MtSWEET1b in M. truncatula roots promoted the growth of intraradical mycelium during AM symbiosis. Surprisingly, two independent Mtsweet1b mutants, which are predicted to produce truncated protein variants impaired in glucose transport, exhibited no significant defects in AM symbiosis. However, arbuscule-specific overexpression of MtSWEET1bY57A/G58D , which are considered to act in a dominant-negative manner, resulted in enhanced collapse of arbuscules. •Taken together, our results reveal a (redundant) role for MtSWEET1b in the transport of glucose across the peri-arbuscular membrane to maintain arbuscules for a healthy mutually beneficial symbiosis. This article is protected by copyright. All rights reserved.}, } @article {pmid31141960, year = {2019}, author = {Ali, A and Imran Ghani, M and Li, Y and Ding, H and Meng, H and Cheng, Z}, title = {Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China.}, journal = {International journal of molecular sciences}, volume = {20}, number = {11}, pages = {}, doi = {10.3390/ijms20112619}, pmid = {31141960}, issn = {1422-0067}, support = {2016KTCL02-01//Shaanxi Provincial Sci-Tech Innovation Plan/ ; 31772293//National Natural Science Foundation/ ; }, abstract = {Cover crops are key determinants of the ecological stability and sustainability of continuous cropping soils. However, their agro-ecological role in differentially reshaping the microbiome structure and functioning under a degraded agroecosystem remains poorly investigated. Therefore, structural and metabolic changes in soil bacterial community composition in response to diverse plant species were assessed. Winter catch leafy vegetables crops were introduced as cover plants in a cucumber-fallow period. The results indicate that cover crop diversification promoted beneficial changes in soil chemical and biological attributes, which increased crop yields in a cucumber double-cropping system. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community composition and diversity changed through changes in the soil properties. Principal component analysis (PCA) coupled with non-metric multidimensional scaling (NMDS) analysis reveals that the cover planting shaped the soil microbiome more than the fallow planting (FC). Among different cropping systems, spinach-cucumber (SC) and non-heading Chinese cabbage-cucumber (NCCC) planting systems greatly induced higher soil nutrient function, biological activity, and bacterial diversity, thus resulting in higher cucumber yield. Quantitative analysis of linear discriminant analysis effect size (LEfSe) indicated that Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were the potentially functional and active soil microbial taxa. Rhizospheres of NCCC, leaf lettuce-cucumber (LLC), coriander-cucumber (CC), and SC planting systems created hotspots for metabolic capabilities of abundant functional genes, compared to FC. In addition, the predictive metabolic characteristics (metabolism and detoxification) associated with host-plant symbiosis could be an important ecological signal that provides direct evidence of mediation of soil structure stability. Interestingly, the plant density of non-heading Chinese cabbage and spinach species was capable of reducing the adverse effect of arsenic (As) accumulation by increasing the function of the arsenate reductase pathway. Redundancy analysis (RDA) indicated that the relative abundance of the core microbiome can be directly and indirectly influenced by certain environmental determinants. These short-term findings stress the importance of studying cover cropping systems as an efficient biological tool to protect the ecological environment. Therefore, we can speculate that leafy crop diversification is socially acceptable, economically justifiable, and ecologically adaptable to meet the urgent demand for intensive cropping systems to promote positive feedback between crop-soil sustainable intensification.}, } @article {pmid30804519, year = {2019}, author = {Delavaux, CS and Weigelt, P and Dawson, W and Duchicela, J and Essl, F and van Kleunen, M and König, C and Pergl, J and Pyšek, P and Stein, A and Winter, M and Schultz, P and Kreft, H and Bever, JD}, title = {Mycorrhizal fungi influence global plant biogeography.}, journal = {Nature ecology & evolution}, volume = {3}, number = {3}, pages = {424-429}, doi = {10.1038/s41559-019-0823-4}, pmid = {30804519}, issn = {2397-334X}, mesh = {Biodiversity ; Islands ; Mycorrhizae/*physiology ; *Plant Dispersal ; Plants/*microbiology ; *Symbiosis ; }, abstract = {Island biogeography has traditionally focused primarily on abiotic drivers of colonization, extinction and speciation. However, establishment on islands could also be limited by biotic drivers, such as the absence of symbionts. Most plants, for example, form symbioses with mycorrhizal fungi, whose limited dispersal to islands could act as a colonization filter for plants. We tested this hypothesis using global-scale analyses of ~1.4 million plant occurrences, including ~200,000 plant species across ~1,100 regions. We find evidence for a mycorrhizal filter (that is, the filtering out of mycorrhizal plants on islands), with mycorrhizal associations less common among native island plants than native mainland plants. Furthermore, the proportion of native mycorrhizal plants in island floras decreased with isolation, possibly as a consequence of a decline in symbiont establishment. We also show that mycorrhizal plants contribute disproportionately to the classic latitudinal gradient of plant species diversity, with the proportion of mycorrhizal plants being highest near the equator and decreasing towards the poles. Anthropogenic pressure and land use alter these plant biogeographical patterns. Naturalized floras show a greater proportion of mycorrhizal plant species on islands than in mainland regions, as expected from the anthropogenic co-introduction of plants with their symbionts to islands and anthropogenic disturbance of symbionts in mainland regions. We identify the mycorrhizal association as an overlooked driver of global plant biogeographical patterns with implications for contemporary island biogeography and our understanding of plant invasions.}, } @article {pmid30742105, year = {2019}, author = {Davies, NG and Flasche, S and Jit, M and Atkins, KE}, title = {Within-host dynamics shape antibiotic resistance in commensal bacteria.}, journal = {Nature ecology & evolution}, volume = {3}, number = {3}, pages = {440-449}, doi = {10.1038/s41559-018-0786-x}, pmid = {30742105}, issn = {2397-334X}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Physiological Phenomena/drug effects ; Biological Evolution ; Drug Resistance, Microbial/*physiology ; Escherichia coli/*drug effects/physiology ; Europe ; *Host-Pathogen Interactions ; *Microbial Interactions ; Streptococcus pneumoniae/*drug effects/physiology ; Symbiosis ; }, abstract = {The spread of antibiotic resistance, a major threat to human health, is poorly understood. Simple population-level models of bacterial transmission predict that above a certain rate of antibiotic consumption in a population, resistant bacteria should completely eliminate non-resistant strains, while below this threshold they should be unable to persist at all. This prediction stands at odds with empirical evidence showing that resistant and non-resistant strains coexist stably over a wide range of antibiotic consumption rates. Not knowing what drives this long-term coexistence is a barrier to developing evidence-based strategies for managing the spread of resistance. Here, we argue that competition between resistant and sensitive pathogens within individual hosts gives resistant pathogens a relative fitness benefit when they are rare, promoting coexistence between strains at the population level. To test this hypothesis, we embed mechanistically explicit within-host dynamics in a structurally neutral pathogen transmission model. Doing so allows us to reproduce patterns of resistance observed in the opportunistic pathogens Escherichia coli and Streptococcus pneumoniae across European countries and to identify factors that may shape resistance evolution in bacteria by modulating the intensity and outcomes of within-host competition.}, } @article {pmid30570692, year = {2019}, author = {Olanrewaju, OS and Ayangbenro, AS and Glick, BR and Babalola, OO}, title = {Plant health: feedback effect of root exudates-rhizobiome interactions.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {3}, pages = {1155-1166}, doi = {10.1007/s00253-018-9556-6}, pmid = {30570692}, issn = {1432-0614}, support = {UID81192//National Research Foundation/ ; }, mesh = {Bacteria/metabolism ; Fungi/metabolism ; Microbiota/*physiology ; Plant Development/*physiology ; Plant Exudates ; Plant Roots/*metabolism/*microbiology ; Plants/metabolism/*microbiology ; Quorum Sensing/physiology ; Rhizosphere ; Symbiosis/*physiology ; }, abstract = {The well-being of the microbial community that densely populates the rhizosphere is aided by a plant's root exudates. Maintaining a plant's health is a key factor in its continued existence. As minute as rhizospheric microbes are, their importance in plant growth cannot be overemphasized. They depend on plants for nutrients and other necessary requirements. The relationship between the rhizosphere-microbiome (rhizobiome) and plant hosts can be beneficial, non-effectual, or pathogenic depending on the microbes and the plant involved. This relationship, to a large extent, determines the fate of the host plant's survival. Modern molecular techniques have been used to unravel rhizobiome species' composition, but the interplay between the rhizobiome root exudates and other factors in the maintenance of a healthy plant have not as yet been thoroughly investigated. Many functional proteins are activated in plants upon contact with external factors. These proteins may elicit growth promoting or growth suppressing responses from the plants. To optimize the growth and productivity of host plants, rhizobiome microbial diversity and modulatory techniques need to be clearly understood for improved plant health.}, } @article {pmid30426159, year = {2019}, author = {Mohanty, I and Rath, A and Swain, SP and Pradhan, N and Hazra, RK}, title = {Wolbachia Population in Vectors and Non-vectors: A Sustainable Approach Towards Dengue Control.}, journal = {Current microbiology}, volume = {76}, number = {2}, pages = {133-143}, doi = {10.1007/s00284-018-1596-8}, pmid = {30426159}, issn = {1432-0991}, support = {0//Lady Tata Memorial Trust/ ; }, mesh = {Aedes/microbiology ; Animals ; Biological Control Agents ; Communicable Disease Control/*methods ; Dengue/*prevention & control/transmission ; Female ; India ; Male ; Mosquito Vectors/classification/*microbiology ; Ovary/microbiology ; Polymerase Chain Reaction ; Prevalence ; Salivary Glands/microbiology ; Symbiosis ; Wolbachia/genetics/*physiology ; }, abstract = {Wolbachia is gram negative obligate endosymbiont known for reproductive manipulation in the host. It is important to study the presence of natural Wolbachia in mosquitoes which can later help in understanding the effect of transfected strain on indigenous strain. With this view, the present study is undertaken to focus on the prevalence, diversity, infection frequencies, phylogeny and density of indigenous Wolbachia strains in wild mosquito species of Odisha. Our study confirms Wolbachia presence in Ae. albopictus, Cx. quinquefasciatus, Cx. vishnui, Cx. gelidus, Ar. subalbatus, Mn. uniformis, and Mn. indiana. Wolbachia in the above mosquitoes were separated into two supergroups (A and B). Ae. albopictus, the major vector of dengue and chikungungunya had both super-infection and mono-infection. The ovaries of Ae. albopictus were highest in density of Wolbachia as compared to midguts or salivary glands. wAlBA and wAlbB density were variable in mosquitoes of F1 generation for both the sex and at different age. We also found that Wolbachia super-infection in females tends to increase whereas wAlbA density reduced completely as compared to wAlbB in males when they grew old. Giemsa stained squashed ovaries revealed pink pleomorphic Wolbachia cells with different shapes and forms. This study is unique in its kind covering the major aspects of the endosymbiont Wolbachia and focusing on its potential as a biocontrol agent in arboviral outbreaks. Knowledge on potential of the indigenous strain and interactions between Wolbachia and viruses can be utilized further to reduce the global burden of vector borne diseases.}, } @article {pmid30013162, year = {2018}, author = {Lin, XB and Wang, T and Stothard, P and Corander, J and Wang, J and Baines, JF and Knowles, SCL and Baltrūnaitė, L and Tasseva, G and Schmaltz, R and Tollenaar, S and Cody, LA and Grenier, T and Wu, W and Ramer-Tait, AE and Walter, J}, title = {The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2770-2784}, pmid = {30013162}, issn = {1751-7370}, mesh = {Animals ; Biofilms/*growth & development ; Biological Evolution ; *Gastrointestinal Microbiome ; Genomics ; Lactobacillus/genetics/isolation & purification/*physiology ; Lactobacillus reuteri/genetics/isolation & purification/*physiology ; Mice/*microbiology ; Symbiosis/genetics ; }, abstract = {The eco-evolutionary interactions among members of the vertebrate gut microbiota that ultimately result in host-specific communities are poorly understood. Here we show that Lactobacillus reuteri coexists with species that belong to the Lactobacillus johnsonii cluster (L. johnsonii, L. gasseri, and L taiwanensis) in a taxonomically wide range of rodents, suggesting cohabitation over evolutionary times. The two dominant Lactobacillus species found in wild mice establish a commensalistic relationship in gastric biofilms when introduced together into germ-free mice in which L. reuteri facilitates colonization of L. taiwanensis. Genomic analysis revealed allopatric diversification in strains of both species that originated from geographically separated locations (Scotland and France). Allopatry of the strains resulted in reduced formation of mixed biofilms in vitro, indicating that interspecies interactions in gastric Lactobacillus-biofilms are the result of an adaptive evolutionary process that occurred in a biogeographical context. In summary, these findings suggest that members within the vertebrate gut microbiota can evolve inter-dependencies through ecological facilitation, which could represent one mechanism by which host-specific bacterial communities assemble across vertebrate species and an explanation for their spatial and biogeographic patterns.}, } @article {pmid29977009, year = {2018}, author = {Røder, HL and Herschend, J and Russel, J and Andersen, MF and Madsen, JS and Sørensen, SJ and Burmølle, M}, title = {Enhanced bacterial mutualism through an evolved biofilm phenotype.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2608-2618}, pmid = {29977009}, issn = {1751-7370}, mesh = {Biofilms/*growth & development ; Cyclic GMP/analogs & derivatives/biosynthesis ; Escherichia coli Proteins/genetics ; Paenibacillus/genetics/*physiology ; Phenotype ; Phosphorus-Oxygen Lyases/genetics ; *Symbiosis ; Xanthomonas/genetics/*physiology ; }, abstract = {Microbial communities primarily consist of multiple species that affect one another's fitness both directly and indirectly. This study showed that the cocultivation of Paenibacillus amylolyticus and Xanthomonas retroflexus exhibited facultative mutualistic interactions in a static environment, during the course of which a new adapted phenotypic variant of X. retroflexus appeared. Although the emergence of this variant was not directly linked to the presence of P. amylolyticus, its establishment in the coculture enhanced the productivity of both species due to mutations that stimulated biofilm formation. The mutations were detected in genes encoding a diguanylate cyclase predicted to synthesise cyclic-di-GMP. Examinations of the biofilm formed in cocultures of P. amylolyticus and the new variant of X. retroflexus revealed a distinct spatial organisation: P. amylolyticus only resided in biofilms in association with X. retroflexus and occupied the outer layers. The X. retroflexus variant therefore facilitated increased P. amylolyticus growth as it produced more biofilm biomass. The increase in X. retroflexus biomass was thus not at the expense of P. amylolyticus, demonstrating that interspecies interactions can shape diversification in a mutualistic coculture and reinforce these interactions, ultimately resulting in enhanced communal performance.}, } @article {pmid29358683, year = {2018}, author = {Mullineaux-Sanders, C and Suez, J and Elinav, E and Frankel, G}, title = {Sieving through gut models of colonization resistance.}, journal = {Nature microbiology}, volume = {3}, number = {2}, pages = {132-140}, doi = {10.1038/s41564-017-0095-1}, pmid = {29358683}, issn = {2058-5276}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Enterobacteriaceae/growth & development/pathogenicity ; Enterobacteriaceae Infections/drug therapy/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Germ-Free Life ; Host-Pathogen Interactions/drug effects/*physiology ; Humans ; Mice ; Models, Animal ; Symbiosis ; }, abstract = {The development of innovative high-throughput genomics and metabolomics technologies has considerably expanded our understanding of the commensal microorganisms residing within the human body, collectively termed the microbiota. In recent years, the microbiota has been reported to have important roles in multiple aspects of human health, pathology and host-pathogen interactions. One function of commensals that has attracted particular interest is their role in protection against pathogens and pathobionts, a concept known as colonization resistance. However, pathogens are also able to sense and exploit the microbiota during infection. Therefore, obtaining a holistic understanding of colonization resistance mechanisms is essential for the development of microbiome-based and microbiome-targeting therapies for humans and animals. Achieving this is dependent on utilizing physiologically relevant animal models. In this Perspective, we discuss the colonization resistance functions of the gut microbiota and sieve through the advantages and limitations of murine models commonly used to study such mechanisms within the context of enteric bacterial infection.}, } @article {pmid31141718, year = {2019}, author = {Liu, XL and Ye, S and Cheng, CY and Li, HW and Lu, B and Yang, WJ and Yang, JS}, title = {Identification and characterization of a symbiotic agglutination-related C-type lectin from the hydrothermal vent shrimp Rimicaris exoculata.}, journal = {Fish & shellfish immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fsi.2019.05.057}, pmid = {31141718}, issn = {1095-9947}, abstract = {Rimicaris exoculata (Decapoda: Bresiliidae) is one of the dominant species of hydrothermal vent communities, which inside its gill chamber harbors ectosymbioses with taxonomic invariability while compositional flexibility. Several studies have revealed that the establishment of symbiosis can be initiated and selected by innate immunity-related pattern recognition receptors (PRRs), such as C-type lectins (CTLs). In this research, a CTL was identified in R. exoculata (termed RCTL), which showed high expression at both mRNA and protein levels in the scaphognathite, an organ where the ectosymbionts are attached outside its setae. Linear correlationships were oberseved between the relative quantities of two major symbionts and the expression of RCTL based on analyzing different shrimp individuals. The recombinant protein of RCTL could recognize and agglutinate the cultivable γ-proteobacterium of Escherichia coli in a Ca2+-dependent manner, obeying a dose-dependent and time-cumulative pattern. Unlike conventional crustacean CTLs, the involvement of RCTL could not affect the bacterial growth, which is a key issue for the successful establishment of symbiosis. These results implied that RCTL might play a critical role in symbiotic recognition and attachment to R. exoculata. It also provides insights to understand how R. exoculata adapted to such a chemosynthesis-based environment.}, } @article {pmid31139503, year = {2019}, author = {Pochon, X and Wecker, P and Stat, M and Berteaux-Lecellier, V and Lecellier, G}, title = {Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6898}, doi = {10.7717/peerj.6898}, pmid = {31139503}, issn = {2167-8359}, abstract = {High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.}, } @article {pmid31139158, year = {2019}, author = {Ahmed, HI and Herrera, M and Liew, YJ and Aranda, M}, title = {Long-Term Temperature Stress in the Coral Model Aiptasia Supports the "Anna Karenina Principle" for Bacterial Microbiomes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {975}, doi = {10.3389/fmicb.2019.00975}, pmid = {31139158}, issn = {1664-302X}, abstract = {The understanding of host-microbial partnerships has become a hot topic during the last decade as it has been shown that associated microbiota play critical roles in the host physiological functions and susceptibility to diseases. Moreover, the microbiome may contribute to host resilience to environmental stressors. The sea anemone Aiptasia is a good laboratory model system to study corals and their microbial symbiosis. In this regard, studying its bacterial microbiota provides a better understanding of cnidarian metaorganisms as a whole. Here, we investigated the bacterial communities of different Aiptasia host-symbiont combinations under long-term heat stress in laboratory conditions. Following a 16S rRNA gene sequencing approach we were able to detect significant differences in the bacterial composition and structure of Aiptasia reared at different temperatures. A higher number of taxa (i.e., species richness), and consequently increased α-diversity and β-dispersion, were observed in the microbiomes of heat-stressed individuals across all host strains and experimental batches. Our findings are in line with the recently proposed Anna Karenina principle (AKP) for animal microbiomes, which states that dysbiotic or stressed organisms have a more variable and unstable microbiome than healthy ones. Microbial interactions affect the fitness and survival of their hosts, thus exploring the AKP effect on animal microbiomes is important to understand host resilience. Our data contributes to the current knowledge of the Aiptasia holobiont and to the growing field of study of host-associated microbiomes.}, } @article {pmid31138619, year = {2019}, author = {Saint-Leandre, B and Nguyen, SC and Levine, MT}, title = {Diversification and collapse of a telomere elongation mechanism.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.245001.118}, pmid = {31138619}, issn = {1549-5469}, abstract = {In most eukaryotes, telomerase counteracts chromosome erosion by adding repetitive sequence to terminal ends. Drosophila melanogaster instead relies on specialized retrotransposons that insert exclusively at telomeres. This exchange of goods between host and mobile element - wherein the mobile element provides an essential genome service and the host provides a hospitable niche for mobile element propagation - has been called a 'genomic symbiosis'. However, these telomere-specialized, jockey family retrotransposons may actually evolve to 'selfishly' over-replicate in the genomes that they ostensibly serve. Under this model, we expect rapid diversification of telomere-specialized retrotransposon lineages and possibly, the breakdown of this ostensibly symbiotic relationship. Here we report data consistent with both predictions. Searching the raw reads of the 15-million-year-old melanogaster species group, we generated de novo jockey retrotransposon consensus sequences and used phylogenetic tree-building to delineate four distinct telomere-associated lineages. Recurrent gains, losses, and replacements account for this retrotransposon lineage diversity. In D. biarmipes, telomere-specialized elements have disappeared completely. De novo assembly of long reads and cytogenetics confirmed this species-specific collapse of retrotransposon-dependent telomere elongation. Instead, telomere-restricted satellite DNA and DNA transposon fragments occupy its terminal ends. We infer that D. biarmipes relies instead on a recombination-based mechanism conserved from yeast to flies to humans. Telomeric retrotransposon diversification and disappearance suggest that persistently 'selfish' machinery shapes telomere elongation across Drosophila rather than completely domesticated, symbiotic mobile elements.}, } @article {pmid30912174, year = {2019}, author = {Bing, XL and Zhao, DS and Hong, XY}, title = {Bacterial reproductive manipulators in rice planthoppers.}, journal = {Archives of insect biochemistry and physiology}, volume = {101}, number = {2}, pages = {e21548}, doi = {10.1002/arch.21548}, pmid = {30912174}, issn = {1520-6327}, support = {31672035//National Natural Science Foundation of China/ ; 31871976//National Natural Science Foundation of China/ ; 804015//the startup grant from Nanjing Agricultural University/ ; }, mesh = {Animals ; *Bacterial Physiological Phenomena ; Female ; Hemiptera/*microbiology/physiology ; Male ; Reproduction/*physiology ; Symbiosis ; }, abstract = {Rice planthoppers (Hemiptera: Delphacidae) are notorious pests for rice (Oryza sativa) in Asia, posing a serious threat to rice production and grain security. Rice planthoppers harbor diverse bacterial symbionts, including Wolbachia, Cardinium, Spiroplasma, and Arsenophonus, which are known to manipulate reproduction in arthropod hosts. This microreview is to introduce current knowledge of bacterial reproductive manipulators in rice planthoppers, including their diversity, population dynamics, localization, transmission, and biological functions.}, } @article {pmid30762095, year = {2019}, author = {Martínez-Rodríguez, P and Rolán-Alvarez, E and Del Mar Pérez-Ruiz, M and Arroyo-Yebras, F and Carpena-Catoira, C and Carvajal-Rodríguez, A and Bella, JL}, title = {Geographic and Temporal Variation of Distinct Intracellular Endosymbiont Strains of Wolbachia sp. in the Grasshopper Chorthippus parallelus: a Frequency-Dependent Mechanism?.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1036-1047}, doi = {10.1007/s00248-019-01338-2}, pmid = {30762095}, issn = {1432-184X}, support = {CGL2016-75482-P//Ministerio de Ciencia y Tecnolog?a/ ; BFU2013-44635//Ministerio de Econom?a, Industria y Competitividad, Gobierno de Espa?a/ ; }, mesh = {Animals ; Biological Coevolution ; Computer Simulation ; Geography ; Grasshoppers/*microbiology ; Linear Models ; *Polymorphism, Genetic ; Seasons ; *Symbiosis ; Wolbachia/genetics/*physiology ; }, abstract = {Wolbachia is an intracellular endosymbiont that can produce a range of effects on host fitness, but the temporal dynamics of Wolbachia strains have rarely been experimentally evaluated. We compare interannual strain frequencies along a geographical region for understanding the forces that shape Wolbachia strain frequency in natural populations of its host, Chorthippus parallelus (Orthoptera, Acrididae). General linear models show that strain frequency changes significantly across geographical and temporal scales. Computer simulation allows to reject the compatibility of the observed patterns with either genetic drift or sampling errors. We use consecutive years to estimate total Wolbachia strain fitness. Our estimation of Wolbachia fitness is significant in most cases, within locality and between consecutive years, following a negatively frequency-dependent trend. Wolbachia spp. B and F strains show a temporal pattern of variation that is compatible with a negative frequency-dependent natural selection mechanism. Our results suggest that such a mechanism should be at least considered in future experimental and theoretical research strategies that attempt to understand Wolbachia biodiversity.}, } @article {pmid30664701, year = {2019}, author = {Lu, M and Hedin, LO}, title = {Global plant-symbiont organization and emergence of biogeochemical cycles resolved by evolution-based trait modelling.}, journal = {Nature ecology & evolution}, volume = {3}, number = {2}, pages = {239-250}, doi = {10.1038/s41559-018-0759-0}, pmid = {30664701}, issn = {2397-334X}, mesh = {*Bacterial Physiological Phenomena ; Biological Evolution ; Fungi/*physiology ; Game Theory ; Life History Traits ; Models, Biological ; Plants/*microbiology ; *Symbiosis ; }, abstract = {One of the most distinct but unresolved global patterns is the apparent variation in plant-symbiont nutrient strategies across biomes. This pattern is central to our understanding of plant-soil-nutrient feedbacks in the land biosphere, which, in turn, are essential for our ability to predict the future dynamics of the Earth system. Here, we present an evolution-based trait-modelling approach for resolving (1) the organization of plant-symbiont relationships across biomes worldwide and (2) the emergent consequences for plant community composition and land biogeochemical cycles. Using game theory, we allow plants to use different belowground strategies to acquire nutrients and compete within local plant-soil-nutrient cycles in boreal, temperate and tropical biomes. The evolutionarily stable strategies that emerge from this analysis allow us to predict the distribution of belowground symbioses worldwide, the sequence and timing of plant succession, the bistability of ecto- versus arbuscular mycorrhizae in temperate and tropical forests, and major differences in the land carbon and nutrient cycles across biomes. Our findings imply that belowground symbioses have been central to the evolutionary assembly of plant communities and plant-nutrient feedbacks at the scale of land biomes. We conclude that complex global patterns emerge from local between-organism interactions in the context of Darwinian natural selection and evolution, and that the underlying dynamics can be mechanistically probed by our low-dimensional modelling approach.}, } @article {pmid30397795, year = {2019}, author = {Palacios, OA and Lopez, BR and Bashan, Y and de-Bashan, LE}, title = {Early Changes in Nutritional Conditions Affect Formation of Synthetic Mutualism Between Chlorella sorokiniana and the Bacterium Azospirillum brasilense.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {980-992}, doi = {10.1007/s00248-018-1282-1}, pmid = {30397795}, issn = {1432-184X}, support = {251102//Consejo Nacional de Ciencia y Tecnología/ ; 284562//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Azospirillum brasilense/*physiology ; Chlorella/*physiology ; Indoleacetic Acids/metabolism ; Microalgae/physiology ; Population Growth ; Starch/metabolism ; *Symbiosis ; Tryptophan/metabolism ; }, abstract = {The effect of three different nutritional conditions during the initial 12 h of interaction between the microalgae Chlorella sorokiniana UTEX 2714 and the plant growth-promoting bacterium Azospirillum brasilense Cd on formation of synthetic mutualism was assessed by changes in population growth, production of signal molecules tryptophan and indole-3-acetic acid, starch accumulation, and patterns of cell aggregation. When the interaction was supported by a nutrient-rich medium, production of both signal molecules was detected, but not when this interaction began with nitrogen-free (N-free) or carbon-free (C-free) media. Overall, populations of bacteria and microalgae were larger when co-immobilized. However, the highest starch production was measured in C. sorokiniana immobilized alone and growing continuously in a C-free mineral medium. In this interaction, the initial nutritional condition influenced the time at which the highest accumulation of starch occurred in Chlorella, where the N-free medium induced faster starch production and the richer medium delayed its accumulation. Formation of aggregates made of microalgae and bacteria occurred in all nutritional conditions, with maximum at 83 h in mineral medium, and coincided with declining starch content. This study demonstrates that synthetic mutualism between C. sorokiniana and A. brasilense can be modulated by the initial nutritional condition, mainly by the presence or absence of nitrogen and carbon in the medium in which they are interacting.}, } @article {pmid31134003, year = {2019}, author = {Fernández, N and Cabrera, JJ and Varadarajan, AR and Lutz, S and Ledermann, R and Roschitzki, B and Eberl, L and Bedmar, EJ and Fischer, HM and Pessi, G and Ahrens, CH and Mesa, S}, title = {An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {924}, doi = {10.3389/fmicb.2019.00924}, pmid = {31134003}, issn = {1664-302X}, abstract = {The adaptation of rhizobia from the free-living state in soil to the endosymbiotic state comprises several physiological changes in order to cope with the extremely low oxygen availability (microoxia) within nodules. To uncover cellular functions required for bacterial adaptation to microoxia directly at the protein level, we applied a systems biology approach on the key rhizobial model and soybean endosymbiont Bradyrhizobium diazoefficiens USDA 110 (formerly B. japonicum USDA 110). As a first step, the complete genome of B. diazoefficiens 110spc4, the model strain used in most prior functional genomics studies, was sequenced revealing a deletion of a ~202 kb fragment harboring 223 genes and several additional differences, compared to strain USDA 110. Importantly, the deletion strain showed no significantly different phenotype during symbiosis with several host plants, reinforcing the value of previous OMICS studies. We next performed shotgun proteomics and detected 2,900 and 2,826 proteins in oxically and microoxically grown cells, respectively, largely expanding our knowledge about the inventory of rhizobial proteins expressed in microoxia. A set of 62 proteins was significantly induced under microoxic conditions, including the two nitrogenase subunits NifDK, the nitrogenase reductase NifH, and several subunits of the high-affinity terminal cbb3 oxidase (FixNOQP) required for bacterial respiration inside nodules. Integration with the previously defined microoxia-induced transcriptome uncovered a set of 639 genes or proteins uniquely expressed in microoxia. Finally, besides providing proteogenomic evidence for novelties, we also identified proteins with a regulation similar to that of FixK2: transcript levels of these protein-coding genes were significantly induced, while the corresponding protein abundance remained unchanged or was down-regulated. This suggested that, apart from fixK2, additional B. diazoefficiens genes might be under microoxia-specific post-transcriptional control. This hypothesis was indeed confirmed for several targets (HemA, HemB, and ClpA) by immunoblot analysis.}, } @article {pmid31133991, year = {2019}, author = {Macedo-Raygoza, GM and Valdez-Salas, B and Prado, FM and Prieto, KR and Yamaguchi, LF and Kato, MJ and Canto-Canché, BB and Carrillo-Beltrán, M and Di Mascio, P and White, JF and Beltrán-García, MJ}, title = {Enterobacter cloacae, an Endophyte That Establishes a Nutrient-Transfer Symbiosis With Banana Plants and Protects Against the Black Sigatoka Pathogen.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {804}, doi = {10.3389/fmicb.2019.00804}, pmid = {31133991}, issn = {1664-302X}, abstract = {Banana (Musa spp.) is an important crop worldwide, but black Sigatoka disease caused by the fungus Pseudocercospora fijiensis threatens fruit production. In this work, we examined the potential of the endophytes of banana plants Enterobacter cloacae and Klebsiella pneumoniae, as antagonists of P. fijiensis and support plant growth in nutrient limited soils by N-transfer. The two bacterial isolates were identified by MALDI-TOF mass spectrometry and corroborated by 16S rRNA sequence analysis. Both bacteria were positive for beneficial traits such as N-fixation, indole acetic acid production, phosphate solubilization, negative for 1-aminocyclopropane 1-carboxylic acid deaminase and were antagonistic to P. fijiensis. To measure the effects on plant growth, the two plant bacteria and an E. coli strain (as non-endophyte), were inoculated weekly for 60 days as active cells (AC) and heat-killed cells (HKC) into plant microcosms without nutrients and compared to a water only treatment, and a mineral nutrients solution (MMN) treatment. Bacterial treatments increased growth parameters and prevented accelerated senescence, which was observed for water and mineral nutrients solution (MMN) treatments used as controls. Plants died after the first 20 days of being irrigated with water; irrigation with MMN enabled plants to develop some new leaves, but plants lost weight (-30%) during the same period. Plants treated with bacteria showed good growth, but E. cloacae AC treated plants had significantly greater biomass than the E. cloacae HKC. After 60 days, plants inoculated with E. cloacae AC showed intracellular bacteria within root cells, suggesting that a stable symbiosis was established. To evaluate the transference of organic N from bacteria into the plants, the 3 bacteria were grown with 15NH4Cl or Na15NO3 as the nitrogen source. The 15N transferred from bacteria to plant tissues was measured by pheophytin isotopomer abundance. The relative abundance of the isotopomers m/z 872.57, 873.57, 874.57, 875.57, 876.57 unequivocally demonstrated that plants acquired 15N atoms directly from bacterial cells, using them as a source of N, to support plant growth in restricted nutrient soils. E. cloacae might be a new alternative to promote growth and health of banana crops.}, } @article {pmid31132110, year = {2019}, author = {Hammer, TJ and Sanders, JG and Fierer, N}, title = {Not all animals need a microbiome.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz117}, pmid = {31132110}, issn = {1574-6968}, abstract = {It is often taken for granted that all animals host and depend upon a microbiome, yet this has only been shown for a small proportion of species. We propose that animals span a continuum of reliance on microbial symbionts. At one end are the famously symbiont-dependent species such as aphids, humans, corals, and cows, in which microbes are abundant and important to host fitness. In the middle are species that may tolerate some microbial colonization but are only minimally or facultatively dependent. At the other end are species that lack beneficial symbionts altogether. While their existence may seem improbable, animals are capable of limiting microbial growth in and on their bodies, and a microbially independent lifestyle may be favored by selection under some circumstances. There is already evidence for several 'microbiome-free' lineages that represent distantly related branches in the animal phylogeny. We discuss why these animals have received such little attention, highlighting the potential for contaminants, transients, and parasites to masquerade as beneficial symbionts. We also suggest ways to explore microbiomes that address the limitations of DNA sequencing. By studying microbially independent animals, we will gain a more complete picture of the ecology and evolution of macrobe-microbe interactions.}, } @article {pmid31128701, year = {2019}, author = {Yin, Y and Tian, L and Li, X and Huang, M and Liu, L and Wu, P and Li, M and Jiang, H and Wu, G and Chen, Y}, title = {The role of endogenous thiamine produced via THIC in root nodule symbiosis in Lotus japonicus.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {283}, number = {}, pages = {311-320}, doi = {10.1016/j.plantsci.2019.03.011}, pmid = {31128701}, issn = {1873-2259}, abstract = {Thiamine is a pivotal primary metabolite which is indispensable to all organisms. Although its biosynthetic pathway has been well documented, the mechanism by which thiamine influences the legume-rhizobium symbiosis remains uncertain. Here, we used overexpressing transgenic plants, mutants and grafting experiments to investigate the roles played by thiamine in Lotus japonicus nodulation. ljthic mutants displayed lethal phenotypes and the defect could be overcome by supplementation of thiamine or by overexpression of LjTHIC. Reciprocal grafting between L. japonicus wild-type Gifu B-129 and ljthic showed that the photosynthetic products of the aerial part made a major contribution to overcoming the nodulation defect in ljthic. Overexpression of LjTHIC in Lotus japonicus (OE-LjTHIC) decreased shoot growth and increased the activity of the enzymes 2-oxoglutarate dehydrogenase and pyruvate dehydrogenase. OE-LjTHIC plants exhibited an increase in the number of infection threads and also developed more nodules, which were of smaller size but unchanged nitrogenase activity compared to the wildtype. Taken together, our results suggest that endogenous thiamine produced via LjTHIC acts as an essential nutrient provided by the host plant for rhizobial infection and nodule growth in the Lotus japonicus - rhizobium interaction.}, } @article {pmid31127515, year = {2019}, author = {Symeonides, D and Loizia, P and Zorpas, AA}, title = {Tire waste management system in Cyprus in the framework of circular economy strategy.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-019-05131-z}, pmid = {31127515}, issn = {1614-7499}, abstract = {Worldwide, waste raised from tires counts 1.3-1.5 billion tonnes/year and by the end of 2025, is expected to be more than 2.5 billion tonnes. On 2013, the EU countries reached 3.6 million tonnes of used tires. However, the cheapest treatment method since now is landfilling and is considered to be a major threat for the environment and the public health. In Cyprus, the total tires that were imported on 2015 was 835,142 pieces (5.8% more than the 2014), which were equal to 9638 t, while at the same time, the total waste from those tires were 6629 tonnes. Moreover, the cement industry used 6691 tonnes of tires as alternative fuel. Until now, there are three management systems in place in Cyprus, for the end-of-life tires (ELTs). The collection of ELTs on 2011 was 1817 tonnes while at the end of 2016 was 7201 tonnes. The main treatment methods in Cyprus are the use of ELTs as alternative fuel in cement industry or to produce rubber granules (609-2738 tonnes/year) to be used to construct artificial surfaces or substrate for artificial lawn grounds and limited to pyrolysis (324-837 tonnes/year). At the same time, the environmental fees for the collection of tires varies and depends on the tire category. Furthermore, the market share of ELTs is up to 1.5 million € and the total recovery index from the market is closed to 90% the last 6 years (2013-2017). This paper evaluates and assess the existing tire waste management system (TWMS) in Cyprus in order to promote strength and weakness as well as to propose a holistic management system in insular communities in order to adopt the targets set by the concept of circular economy. The SWOT analysis identified as the main weaknesses the absence from the legislation of specific target for the recovery index of tires and the absence of any centralized logistic system to control the existing management systems while the main threats includes bureaucracy and the absence of technical and economic data which will guarantee the financial viability of a centralized treatment unit.}, } @article {pmid31126059, year = {2019}, author = {Li, J and Zhao, T and M Shirolkar, M and Li, M and Wang, H and Li, H}, title = {CuO/ZnO Heterojunction Nanorod Arrays Prepared by Photochemical Method with Improved UV Detecting Performance.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, doi = {10.3390/nano9050790}, pmid = {31126059}, issn = {2079-4991}, abstract = {CuO/ZnO heterojunction nanorod arrays were synthesized using a facile photochemical deposition strategy. The morphology of CuO was related to the concentration of Cu2+ in the Cu(NO3)2 solution, UV illumination time, and the air annealing temperature. A possible reaction mechanism was proposed. In the photochemical deposition process, the OH- was generated in the vicinity of the ZnO nanorod arrays and reacted with Cu2+ and NO3- in the solution to form Cu2(NO3)(OH)3/ZnO heterojunction nanorod arrays firstly, which were converted into CuO/ZnO heterojunction nanorod arrays completely after air annealing at a low temperature. The fabricated CuO/ZnO heterojunction nanorod arrays exhibits a well-defined rectifying characteristic and an improved photo-response performance compared with pure ZnO nanorod arrays.}, } @article {pmid31125808, year = {2019}, author = {Zhang, X and Han, C and Gao, H and Cao, Y}, title = {Comparative transcriptome analysis of the garden asparagus (Asparagus officinalis L.) reveals the molecular mechanism for growth with arbuscular mycorrhizal fungi under salinity stress.}, journal = {Plant physiology and biochemistry : PPB}, volume = {141}, number = {}, pages = {20-29}, doi = {10.1016/j.plaphy.2019.05.013}, pmid = {31125808}, issn = {1873-2690}, abstract = {Soil salinity is one of the most abiotic stress factors that severely affects the growth and development of many plants, which can ultimately threaten crop yield. Arbuscular mycorrhiza fungi (AMF) has been proven to be effective in mitigating salinity stress by symbiosis in many crops. Asparagus officinalis are perennial plants grown in saline-alkaline soil, however, limited information on their molecular mechanisms has restricted efficient application of AMF to garden asparagus under salinity stress. In this study, we conducted a transcriptome analysis on the leaves of garden asparagus to identify gene expression under salinity stress. Seedlings were grown in 4 treatments, including non-inoculated AMF using distilled water (NI), inoculated AMF using distilled water (AMF), non-inoculated with salinity stress (NI + S), and inoculated with salinity stress (AMF + S). A total of 6019 novel genes were obtained based on the reference-guided assembly of the garden asparagus transcriptome. Results revealed that 455 differentially expressed genes (DEGs) were identified when comparing NI + S to AMF + S. However, among the up-regulated DEGs, 41 DEGs were down-regulated, while 242 DEGs had no differences in their expression levels when comparing NI to NI + S. These DEGs' expression patterns may be key induced by AMF under salinity stress. Additionally, the GO and KEGG enrichment analyses of 455 DEGs revealed that these genes mainly participate in the improvement of the internal environment in plant cells, nitrogen metabolic-related processes, and possible photoprotection mechanisms. These findings provide insight into enhanced salinity stress adaptation by AMF inoculation, as well as salt-tolerant candidate genes for further functional analyses.}, } @article {pmid31125438, year = {2019}, author = {Lahari, Z and Ullah, C and Kyndt, T and Gershenzon, J and Gheysen, G}, title = {Strigolactones enhance root-knot nematode (Meloidogyne graminicola) infection in rice by antagonizing the jasmonate pathway.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15953}, pmid = {31125438}, issn = {1469-8137}, abstract = {•Strigolactones (SLs) are carotenoid-derived plant hormones that also act in the rhizosphere to stimulate germination of root-parasitic plants and enhance plant symbiosis with beneficial microbes. Here, the role of SLs was investigated in the interaction of rice roots with the root-knot nematode Meloidogyne graminicola. •Genetic approaches and chemical sprays were used to manipulate SL signaling in rice prior to infection with M. graminicola. Then, nematode performance was evaluated and plant defense hormones were quantified. •Meloidogyne graminicola infection induced SL biosynthesis and signaling and suppressed jasmonic acid (JA)-based defense in rice roots suggesting a potential role of SLs during nematode infection. While the application of low dose of the SL analog GR24 increased nematode infection and decreased jasmonate accumulation, the SL biosynthesis and signaling d mutants were less susceptible to M. graminicola, and constitutively accumulated JA and JA-isoleucine compared to wild-type plants. Spraying with 0.1 μM GR24 restored nematode susceptibility in SL-biosynthesis mutants but not in the signaling mutant. Furthermore, foliar application of the SL biosynthesis inhibitor TIS108 impeded nematode infection and increased jasmonate levels in rice roots. •In conclusion, SL signaling in rice suppresses jasmonate accumulation and promotes root-knot nematode infection. This article is protected by copyright. All rights reserved.}, } @article {pmid31125425, year = {2019}, author = {Xue, L and Almario, J and Fabiańska, I and Saridis, G and Bucher, M}, title = {Dysfunction in the arbuscular mycorrhizal symbiosis has consistent but small effects on the establishment of the fungal microbiota in Lotus japonicus.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15958}, pmid = {31125425}, issn = {1469-8137}, abstract = {•Most land plants establish mutualistic interactions with arbuscular mycorrhizal (AM) fungi. Intracellular accommodation of AM fungal symbionts remodels important host traits like root morphology and nutrient acquisition. How mycorrhizal colonization impacts plant microbiota is unclear. •To understand the impact of AM symbiosis on fungal microbiota, ten Lotus japonicus mutants impaired at different stages of AM formation were grown in non-sterile natural soil and their root-associated fungal communities were studied. •Plant mutants lacking the capacity to form mature arbuscules (arb-) exhibited limited growth performance associated to altered phosphorus (P) acquisition and reduction-oxidation (redox) processes. Furthermore, arb- plants assembled moderately but consistently different root-associated fungal microbiota, characterized by the depletion of Glomeromycota and the concomitant enrichment of Ascomycota, including Dactylonectria torresensis. Single and co-inoculation experiments showed strong reduction of root colonization by D. torresensis in the presence of AM fungus Rhizophagus irregularis, particularly in arbuscule-forming plants. •Our results suggest that impairment of central symbiotic functions in AM host plants leads to specific changes in root microbiomes and in tripartite interactions between the host plant, AM and non-AM fungi. This lays the foundation for mechanistic studies on microbe-microbe and microbe-host interactions in AM symbiosis of the model L. japonicus. This article is protected by copyright. All rights reserved.}, } @article {pmid31124196, year = {2019}, author = {McIntosh, M and Serrania, J and Lacanna, E}, title = {A novel LuxR-type solo of Sinorhizobium meliloti, NurR, is regulated by the chromosome replication coordinator, DnaA, and activates quorum sensing.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.14312}, pmid = {31124196}, issn = {1365-2958}, abstract = {The genome of Sinorhizobium meliloti, a model for studying plant-bacteria symbiosis, contains eight genes coding for LuxR-like proteins. Two of these, SinR and ExpR, are essential for quorum sensing (QS). Roles and regulation surrounding the others are mostly unknown. Here, we reveal the DNA recognition sequence and regulon of the LuxR-like protein SMc00877. Unlike ExpR, which uses the long chain acyl homoserine lactones (AHLs) as inducers, SMc00877 functioned independently of AHLs and was even functional in Escherichia coli. A target of SMc00877 is SinR, the major regulator of AHL production in S. meliloti. Disruption of SMc00877 decreased AHL production. A weaker production of AHLs resulted in smaller microcolonies, starting from single cells, and delayed AHL dependent regulation. SMc00877 was expressed only in growing cells in the presence of replete nutrients. Therefore, we renamed it NurR (nutrient sensitive LuxR-like regulator). We traced this nutrient-sensitive expression to transcription control by the DNA replication initiation factor, DnaA, which is essential for growth. These results indicate that NurR has a role in modulating the threshold of QS activation according to growth. We propose growth behavior as an additional prerequisite to population density for the activation of QS in S. meliloti. This article is protected by copyright. All rights reserved.}, } @article {pmid31121904, year = {2019}, author = {Zhang, Y and Hu, L and Yu, D and Xu, K and Zhang, J and Li, X and Wang, P and Chen, G and Liu, Z and Peng, C and Li, C and Guo, T}, title = {Integrative Analysis of the Wheat PHT1 Gene Family Reveals A Novel Member Involved in Arbuscular Mycorrhizal Phosphate Transport and Immunity.}, journal = {Cells}, volume = {8}, number = {5}, pages = {}, doi = {10.3390/cells8050490}, pmid = {31121904}, issn = {2073-4409}, support = {31872129//National Natural Science Foundation of China/ ; 162300410107 and 162300410346//Natural Science Foundation of Henan Province/ ; 172102110169, 182102110067, 182102110289 and 192102110001//Foundation of Henan Science and Technology Committee/ ; 18A180009//Foundation of Henan Educational Committee/ ; 2017GGJS146//Training Program of Youth Backbone Teacher of Henan Province/ ; }, abstract = {Phosphorus (P) deficiency is one of the main growth-limiting factors for plants. However, arbuscular mycorrhizal (AM) symbiosis can significantly promote P uptake. Generally, PHT1 transporters play key roles in plants' P uptake, and thus, PHT1 genes have been investigated in some plants, but the regulation and functions of these genes in wheat (TaPHT1) during AM symbiosis have not been studied in depth. Therefore, a comprehensive analysis of TaPHT1 genes was performed, including sequence, phylogeny, cis-elements, expression, subcellular localization and functions, to elucidate their roles in AM-associated phosphate transport and immunity. In total, 35 TaPHT1s were identified in the latest high-quality bread wheat genome, 34 of which were unevenly distributed on 13 chromosomes, and divided into five groups. Sequence analysis indicated that there are 11 types of motif architectures and five types of exon-intron structures in the TaPHT1 family. Duplication mode analysis indicated that the TaPHT1 family has expanded mainly through segmental and tandem duplication events, and that all duplicated gene pairs have been under purifying selection. Transcription analysis of the 35 TaPHT1s revealed that not only known the mycorrhizal-specific genes TaPht-myc, TaPT15-4B (TaPT11) and TaPT19-4D (TaPT10), but also four novel mycorrhizal-specific/inducible genes (TaPT3-2D, TaPT11-4A, TaPT29-6A, and TaPT31-7A) are highly up-regulated in AM wheat roots. Furthermore, the mycorrhizal-specific/inducible genes are significantly induced in wheat roots at different stages of infection by colonizing fungi. Transient Agrobacterium tumefaciens-mediated transformation expression in onion epidermal cells showed that TaPT29-6A is a membrane-localized protein. In contrast to other AM-specific/inducible PHT1 genes, TaPT29-6A is apparently required for the symbiotic and direct Pi pathway. TaPT29-6A-silenced lines exhibited reduced levels of AM fungal colonization and arbuscules, but increased susceptibility to biotrophic, hemi-biotrophic and necrotrophic pathogens. In conclusion, TaPT29-6A was not only essential for the AM symbiosis, but also played vital roles in immunity.}, } @article {pmid30566883, year = {2018}, author = {Grizotte-Lake, M and Zhong, G and Duncan, K and Kirkwood, J and Iyer, N and Smolenski, I and Isoherranen, N and Vaishnava, S}, title = {Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis.}, journal = {Immunity}, volume = {49}, number = {6}, pages = {1103-1115.e6}, doi = {10.1016/j.immuni.2018.11.018}, pmid = {30566883}, issn = {1097-4180}, support = {R01 DK113265/DK/NIDDK NIH HHS/United States ; R01 GM111772/GM/NIGMS NIH HHS/United States ; }, mesh = {Alcohol Oxidoreductases/genetics/metabolism ; Animals ; Bacteria/classification/genetics ; Dysbiosis/*metabolism/microbiology ; Epithelial Cells/*metabolism/microbiology ; Host Microbial Interactions ; Interleukins/*metabolism ; Intestinal Mucosa/cytology/*metabolism/microbiology ; Lymphocytes/metabolism/microbiology ; Mice, Inbred C57BL ; Mice, Knockout ; Microbiota/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Salmonella typhimurium/genetics/physiology ; Symbiosis ; Tretinoin/*metabolism ; }, abstract = {Retinoic acid (RA), a vitamin A metabolite, regulates transcriptional programs that drive protective or pathogenic immune responses in the intestine, in a manner dependent on RA concentration. Vitamin A is obtained from diet and is metabolized by intestinal epithelial cells (IECs), which operate in intimate association with microbes and immune cells. Here we found that commensal bacteria belonging to class Clostridia modulate RA concentration in the gut by suppressing the expression of retinol dehydrogenase 7 (Rdh7) in IECs. Rdh7 expression and associated RA amounts were lower in the intestinal tissue of conventional mice, as compared to germ-free mice. Deletion of Rdh7 in IECs diminished RA signaling in immune cells, reduced the IL-22-dependent antimicrobial response, and enhanced resistance to colonization by Salmonella Typhimurium. Our findings define a regulatory circuit wherein bacterial regulation of IEC-intrinsic RA synthesis protects microbial communities in the gut from excessive immune activity, achieving a balance that prevents colonization by enteric pathogens.}, } @article {pmid30374168, year = {2018}, author = {Reese, AT and Pereira, FC and Schintlmeister, A and Berry, D and Wagner, M and Hale, LP and Wu, A and Jiang, S and Durand, HK and Zhou, X and Premont, RT and Diehl, AM and O'Connell, TM and Alberts, SC and Kartzinel, TR and Pringle, RM and Dunn, RR and Wright, JP and David, LA}, title = {Microbial nitrogen limitation in the mammalian large intestine.}, journal = {Nature microbiology}, volume = {3}, number = {12}, pages = {1441-1450}, pmid = {30374168}, issn = {2058-5276}, mesh = {Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Carbon/metabolism ; Diet ; Dietary Proteins ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/physiology ; Intestine, Large/*metabolism/*microbiology ; Mammals/*microbiology ; Mice ; Nitrogen/*metabolism ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.}, } @article {pmid30297742, year = {2018}, author = {Ahrendt, SR and Quandt, CA and Ciobanu, D and Clum, A and Salamov, A and Andreopoulos, B and Cheng, JF and Woyke, T and Pelin, A and Henrissat, B and Reynolds, NK and Benny, GL and Smith, ME and James, TY and Grigoriev, IV}, title = {Leveraging single-cell genomics to expand the fungal tree of life.}, journal = {Nature microbiology}, volume = {3}, number = {12}, pages = {1417-1428}, doi = {10.1038/s41564-018-0261-0}, pmid = {30297742}, issn = {2058-5276}, mesh = {Biodiversity ; DNA, Ribosomal/genetics ; Fungi/classification/enzymology/*genetics/*metabolism ; Genetic Variation ; *Genome, Fungal ; *Genomics ; Heterozygote ; Life Cycle Stages ; Metabolic Networks and Pathways/genetics/physiology ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 18S/genetics ; Secondary Metabolism/genetics/physiology ; Sequence Analysis, DNA ; Symbiosis/genetics/physiology ; }, abstract = {Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential.}, } @article {pmid30027485, year = {2019}, author = {Gabaldón, T and Fairhead, C}, title = {Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal.}, journal = {Current genetics}, volume = {65}, number = {1}, pages = {93-98}, doi = {10.1007/s00294-018-0867-z}, pmid = {30027485}, issn = {1432-0983}, support = {BFU2015-67107//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, mesh = {Candida glabrata/classification/*genetics/physiology ; Candidiasis/microbiology ; Genes, Mating Type, Fungal/*genetics ; Genome, Fungal/*genetics ; Genomics/*methods ; Host-Pathogen Interactions ; Humans ; Phylogeny ; Reproduction/genetics ; Symbiosis ; }, abstract = {Candida glabrata is an opportunistic yeast pathogen, whose incidence has increased over the last decades. Despite its genus name, this species is actually more closely related to the budding yeast Saccharomyces cerevisiae than to other Candida pathogens, such as Candida albicans. Hence, C. glabrata and C. albicans must have acquired the ability to infect humans independently, which is reflected in the use of different mechanism for virulence, and survival in the host. Yet, research on C. glabrata suffers from assumptions carried over from the more studied C. albicans. Regarding the adaptation of C. glabrata to the human host, the prejudice was that, just as C. albicans, C. glabrata is a natural human commensal that turns deadly when immune defenses weaken. It was also considered asexual, as no one has observed mating, diploids, or spores, despite great efforts. However, the recent analysis of whole genomes from globally distributed C. glabrata isolates have shaken these assumptions. C. glabrata seems to be only secondarily associated to humans, as indicated by a lack of co-evolution with its host, and genomic footprints of recombination shows compelling evidence that this yeast is able to have sex. Here, we discuss the implications of this and other recent findings and highlight the new questions opened by this change in paradigm.}, } @article {pmid31119081, year = {2019}, author = {Jian, L and Bai, X and Zhang, H and Song, X and Li, Z}, title = {Promotion of growth and metal accumulation of alfalfa by coinoculation with Sinorhizobium and Agrobacterium under copper and zinc stress.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6875}, doi = {10.7717/peerj.6875}, pmid = {31119081}, issn = {2167-8359}, abstract = {The Legume-Rhizobium symbiosis has been proposed as a promising technique for the phytoremediation of contaminated soils due to its beneficial activity in symbiotic nitrogen fixation. However, numerous studies have shown that excessive heavy metals reduce the efficiency of symbiotic nodulation with Rhizobium and inhibit plant growth. In this study, we aimed to evaluate the synergistic effects of IAA-producing bacteria and Rhizobium on Medicago lupulina growth under Cu and Zn stress. Pot experiments showed that 400 mg kg-1 Cu2 + and Zn2 + greatly inhibited plant growth, but dual inoculation of Medicago lupulina with Sinorhizobium meliloti CCNWSX0020 and Agrobacterium tumefaciens CCNWGS0286 significantly increased the number of nodules and plant biomass by enhancing antioxidant activities. Under double stress of 400 mg kg-1 Cu2 + and Zn2 +, the nodule number and nitrogenase activities of dual-inoculated plants were 48.5% and 154.4% higher, respectively, than those of plants inoculated with Sinorhizobium meliloti. The root and above-ground portion lengths of the dual-inoculated plants were 32.6% and 14.1% greater, respectively, than those of the control, while the root and above-ground portion dry weights were 34.3% and 32.2% greater, respectively, than those of the control. Compared with S. meliloti and A. tumefaciens single inoculation, coinoculation increased total Cu uptake by 39.1% and 47.5% and increased total Zn uptake by 35.4% and 44.2%, respectively, under double metal stress conditions. Therefore, coinoculation with Sinorhizobium meliloti and Agrobacterium tumefaciens enhances metal phytoextraction by increasing plant growth and antioxidant activities under Cu/Zn stress, which provides a new approach for bioremediation in heavy metal-contaminated soil.}, } @article {pmid31118473, year = {2019}, author = {Sproles, AE and Oakley, CA and Matthews, JL and Peng, L and Owen, JG and Grossman, AR and Weis, VM and Davy, SK}, title = {Proteomics quantifies protein expression changes in a model cnidarian colonised by a thermally tolerant but suboptimal symbiont.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0437-5}, pmid = {31118473}, issn = {1751-7370}, abstract = {The acquisition of thermally tolerant algal symbionts by corals has been proposed as a natural or assisted mechanism of increasing coral reef resilience to anthropogenic climate change, but the cell-level processes determining the performance of new symbiotic associations are poorly understood. We used liquid chromatography-mass spectrometry to investigate the effects of an experimentally induced symbiosis on the host proteome of the model sea anemone Exaiptasia pallida. Aposymbiotic specimens were colonised by either the homologous dinoflagellate symbiont (Breviolum minutum) or a thermally tolerant, ecologically invasive heterologous symbiont (Durusdinium trenchii). Anemones containing D. trenchii exhibited minimal expression of Niemann-Pick C2 proteins, which have predicted biochemical roles in sterol transport and cell recognition, and glutamine synthetases, which are thought to be involved in nitrogen assimilation and recycling between partners. D. trenchii-colonised anemones had higher expression of methionine-synthesising betaine-homocysteine S-methyltransferases and proteins with predicted oxidative stress response functions. Multiple lysosome-associated proteins were less abundant in both symbiotic treatments compared with the aposymbiotic treatment. The differentially abundant proteins are predicted to represent pathways that may be involved in nutrient transport or resource allocation between partners. These results provide targets for specific experiments to elucidate the mechanisms underpinning compensatory physiology in the coral-dinoflagellate symbiosis.}, } @article {pmid29379208, year = {2018}, author = {Probst, AJ and Ladd, B and Jarett, JK and Geller-McGrath, DE and Sieber, CMK and Emerson, JB and Anantharaman, K and Thomas, BC and Malmstrom, RR and Stieglmeier, M and Klingl, A and Woyke, T and Ryan, MC and Banfield, JF}, title = {Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {328-336}, doi = {10.1038/s41564-017-0098-y}, pmid = {29379208}, issn = {2058-5276}, mesh = {Archaea/*classification/growth & development ; Autotrophic Processes ; Bacteria/*classification/growth & development ; Carbon Cycle ; Geologic Sediments/*microbiology ; Groundwater/*microbiology ; Metagenomics ; Phylogeny ; *Symbiosis ; }, abstract = {An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus "Altiarchaeum sp." and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. "Altiarchaeum". Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.}, } @article {pmid31117021, year = {2019}, author = {Beinart, RA}, title = {The Significance of Microbial Symbionts in Ecosystem Processes.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00127-19}, pmid = {31117021}, issn = {2379-5077}, abstract = {It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained. Here, I explore the idea that, in some habitats, host-associated microbes may have an outsized role in ecosystem processes relative to functionally equivalent free-living microbes due to key aspects of the physiology, ecology, and evolution of symbiotic interactions. My research quantifying symbiont metabolism has shown that microbial symbionts have the potential to make a substantial impact on carbon and sulfur cycling. It is my perspective that direct measurement of symbiont activity and comparison to free-living counterparts will expand our understanding of the significance of microbial symbioses and, more broadly, the role of microbial processes in ecosystems.}, } @article {pmid31117019, year = {2019}, author = {Kleiner, M}, title = {Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00115-19}, pmid = {31117019}, issn = {2379-5077}, abstract = {Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the "expressed" metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.}, } @article {pmid31115264, year = {2019}, author = {Vaidya, A and Singh, S and Limaye, L and Kale, V}, title = {Chimeric feeders of mesenchymal stromal cells and stromal cells modified with constitutively active AKT expand hematopoietic stem cells.}, journal = {Regenerative medicine}, volume = {}, number = {}, pages = {}, doi = {10.2217/rme-2018-0157}, pmid = {31115264}, issn = {1746-076X}, abstract = {Aim: To examine whether AKT-modified stromal cells expand human CD34+ hematopoietic stem cells (HSCs). Methods: Coculture, in vitro functional assays, immuno-fluorescence microscopy, flow cytometry. Results: M2-10B4 stromal cells (M2) modified with AKT1 (M2-AKT) expanded primitive CD34+38- HSCs, but affected their functionality. A chimeric feeder layer comprising naive human bone marrow-derived mesenchymal stromal cells and M2-AKT not only overcame the negative effects of M2-AKT, but, unexpectedly, also gave a synergistic effect on the growth and functionality of the HSCs. Conditioned medium of bone marrow stromal cells worked as effectively, but cell-cell contact between HSCs and M2-AKT cells was necessary for the synergistic effect of M2-AKT and bone marrow-derived mesenchymal stromal cells or their CM. Conclusion: Chimeric feeders expand HSCs.}, } @article {pmid31114600, year = {2019}, author = {Liu, YS and Geng, JC and Sha, XY and Zhao, YX and Hu, TM and Yang, PZ}, title = {Effect of Rhizobium Symbiosis on Low-Temperature Tolerance and Antioxidant Response in Alfalfa (Medicago sativa L.).}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {538}, doi = {10.3389/fpls.2019.00538}, pmid = {31114600}, issn = {1664-462X}, abstract = {Low temperature-induced stress is a major environmental factor limiting the growth and development of plants. Alfalfa (Medicago sativa L.) is a legume well known for its tolerance of extreme environments. In this study, we sought to experimentally investigate the role of rhizobium symbiosis in alfalfa's performance under a low-temperature stress condition. To do this, alfalfa "Ladak+" plants carrying active nodules (AN), inactive nodules (IN), or no nodules (NN) were exposed to an imposed low temperature stress and their survivorship calculated. The antioxidant defense responses, the accumulation of osmotic regulation substances, the cell membrane damage, and the expression of low temperature stress-related genes were determined in both the roots and the shoots of alfalfa plants. We found that more plants with AN survived than those with IN or NN under the same low temperature-stress condition. Greater activity of oxidation protective enzymes was observed in the AN and IN groups, conferring higher tolerance to low temperature in these plants. In addition, rhizobia nodulation also enhanced alfalfa's ability to tolerate low temperature by altering the expression of regulatory and metabolism-associated genes, which resulted in the accumulation of soluble proteins and sugars in the nodulated plants. Taken together, the findings of this study indicate that rhizobium inoculation offers a practical way to promote the persistence and growth potential of alfalfa "Ladak+" in cold areas.}, } @article {pmid31114559, year = {2019}, author = {González, V and Santamaría, RI and Bustos, P and Pérez-Carrascal, OM and Vinuesa, P and Juárez, S and Martínez-Flores, I and Cevallos, MÁ and Brom, S and Martínez-Romero, E and Romero, D}, title = {Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {910}, doi = {10.3389/fmicb.2019.00910}, pmid = {31114559}, issn = {1664-302X}, abstract = {The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.}, } @article {pmid31113823, year = {2019}, author = {Serra, L and Macchietto, M and Macias-Muñoz, A and McGill, CJ and Rodriguez, IM and Rodriguez, B and Murad, R and Mortazavi, A}, title = {Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-chromosome.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1534/g3.119.400180}, pmid = {31113823}, issn = {2160-1836}, abstract = {Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the most complete genome of the S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36 Mb. The largest scaffold, with 20.9 Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this improved genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae's chromosome X to be primarily orthologous to C. elegans' and P. pacificus' chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between adult male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for additional comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.}, } @article {pmid31113629, year = {2019}, author = {Ballinger, MJ and Perlman, SJ}, title = {The defensive Spiroplasma.}, journal = {Current opinion in insect science}, volume = {32}, number = {}, pages = {36-41}, doi = {10.1016/j.cois.2018.10.004}, pmid = {31113629}, issn = {2214-5753}, abstract = {Defensive microbes are of great interest for their roles in arthropod health, disease transmission, and biocontrol efforts. Obligate bacterial passengers of arthropods, such as Spiroplasma, confer protection against the natural enemies of their hosts to improve their own fitness. Although known for less than a decade, Spiroplasma's defensive reach extends to diverse parasites, both microbial and multicellular. We provide an overview of known defensive phenotypes against nematodes, parasitoid wasps, and fungi, and highlight recent studies supporting the role of Spiroplasma-encoded ribosome-inactivating proteins in protection. With cellular features well-suited for life in the hemolymph, broad distribution among invertebrate hosts, and the capacity to repeatedly evolve vertical transmission, Spiroplasma may be uniquely equipped to form intimate, defensive associations to combat extracellular parasites. Along with insights into defensive mechanisms, recent significant advances have been made in male-killing - a phenotype with interesting evolutionary ties to defense. Finally, we look forward to an exciting decade using the genetic tools of Drosophila, and the rapidly-advancing tractability of Spiroplasma itself, to better understand mechanisms and evolution in defensive symbiosis.}, } @article {pmid30107045, year = {2018}, author = {Yadav, S and Eleftherianos, I}, title = {The Imaginal Disc Growth Factors 2 and 3 participate in the Drosophila response to nematode infection.}, journal = {Parasite immunology}, volume = {40}, number = {10}, pages = {e12581}, doi = {10.1111/pim.12581}, pmid = {30107045}, issn = {1365-3024}, support = {1R01AI110675-01A1//National Institute of Allergy and Infectious Diseases/ ; //Columbian College of Arts and Sciences at GWU/ ; //Department of Biological Sciences at GWU/ ; //Cosmos Club Foundation/ ; }, mesh = {Animals ; Drosophila/*immunology/*parasitology ; Drosophila Proteins/biosynthesis/genetics/*immunology/metabolism ; Glycoproteins/biosynthesis/genetics/*immunology/metabolism ; Imaginal Discs/metabolism ; Larva/immunology/parasitology ; Nematode Infections/*immunology ; Species Specificity ; Strongyloidea/*immunology/microbiology ; Symbiosis ; Xenorhabdus/growth & development ; }, abstract = {The Drosophila imaginal disc growth factors (IDGFs) induce the proliferation of imaginal disc cells and terminate cell proliferation at the end of larval development. However, the participation of Idgf-encoding genes in other physiological processes of Drosophila including the immune response to infection is not fully understood. Here, we show the contribution of Idgf2 and Idgf3 in the Drosophila response to infection with Steinernema carpocapsae nematodes carrying or lacking their mutualistic Xenorhabdus nematophila bacteria (symbiotic or axenic nematodes, respectively). We find that Idgf2 and Idgf3 are upregulated in Drosophila larvae infected with symbiotic or axenic Steinernema and inactivation of Idgf2 confers a survival advantage to Drosophila larvae against axenic nematodes. Inactivation of Idgf2 induces the Imd and Jak/Stat pathways, whereas inactivation of Idgf3 induces the Imd, Toll and Jak/Stat pathways. We also show that inactivation of the Imd pathway receptor PGRP-LE upregulates Idgf2 against Steinernema nematode infection. Finally, we demonstrate that inactivation of Idgf3 induces the recruitment of larval haemocytes in response to Steinernema. Our results indicate that Idgf2 and Idgf3 might be involved in different yet crucial immune functions in the Drosophila antinematode immune response. Similar findings will promote the development of new targets for species-specific pest control strategies.}, } @article {pmid29410379, year = {2018}, author = {Shi, B and Leung, DYM and Taylor, PA and Li, H}, title = {Methicillin-Resistant Staphylococcus aureus Colonization Is Associated with Decreased Skin Commensal Bacteria in Atopic Dermatitis.}, journal = {The Journal of investigative dermatology}, volume = {138}, number = {7}, pages = {1668-1671}, pmid = {29410379}, issn = {1523-1747}, support = {R01 GM099530/GM/NIGMS NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; UL1 RR025780/RR/NCRR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Carrier State/microbiology ; Child ; Child, Preschool ; Dermatitis, Atopic/*microbiology/pathology ; Female ; Humans ; Male ; Methicillin-Resistant Staphylococcus aureus/isolation & purification/*pathogenicity ; *Microbiota ; Middle Aged ; Skin/*microbiology/pathology ; Staphylococcal Skin Infections/*microbiology/pathology ; Symbiosis ; Young Adult ; }, } @article {pmid31109137, year = {2019}, author = {Ji, J and Zhang, C and Sun, Z and Wang, L and Duanmu, D and Fan, Q}, title = {Genome Editing in Cowpea Vigna unguiculata Using CRISPR-Cas9.}, journal = {International journal of molecular sciences}, volume = {20}, number = {10}, pages = {}, doi = {10.3390/ijms20102471}, pmid = {31109137}, issn = {1422-0067}, abstract = {Cowpea (Vigna unguiculata) is widely cultivated across the world. Due to its symbiotic nitrogen fixation capability and many agronomically important traits, such as tolerance to low rainfall and low fertilization requirements, as well as its high nutrition and health benefits, cowpea is an important legume crop, especially in many semi-arid countries. However, research in Vigna unguiculata is dramatically hampered by the lack of mutant resources and efficient tools for gene inactivation in vivo. In this study, we used clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9). We applied the CRISPR/Cas9-mediated genome editing technology to efficiently disrupt the representative symbiotic nitrogen fixation (SNF) gene in Vigna unguiculata. Our customized guide RNAs (gRNAs) targeting symbiosis receptor-like kinase (SYMRK) achieved ~67% mutagenic efficiency in hairy-root-transformed plants, and nodule formation was completely blocked in the mutants with both alleles disrupted. Various types of mutations were observed near the PAM region of the respective gRNA. These results demonstrate the applicability of the CRISPR/Cas9 system in Vigna unguiculata, and therefore should significantly stimulate functional genomics analyses of many important agronomical traits in this unique crop legume.}, } @article {pmid31109096, year = {2019}, author = {Saridis, G and Chorianopoulou, SN and Ventouris, YE and Sigalas, PP and Bouranis, DL}, title = {An Exploration of the Roles of Ferric Iron Chelation-Strategy Components in the Leaves and Roots of Maize Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {8}, number = {5}, pages = {}, doi = {10.3390/plants8050133}, pmid = {31109096}, issn = {2223-7747}, abstract = {Plants have developed sophisticated mechanisms for acquiring iron from the soil. In the graminaceous species, a chelation strategy is in charge, in order to take up ferric iron from the rhizosphere. The ferric iron chelation-strategy components may also be present in the aerial plant parts. The aim of this work was to search for possible roles of those components in maize leaves. To this end, the expression patterns of ferric iron chelation-strategy components were monitored in the leaves and roots of mycorrhizal and non-mycorrhizal sulfur-deprived maize plants, both before and after sulfate supply. The two levels of sulfur supply were chosen due to the strong impact of this nutrient on iron homeostasis, whilst mycorrhizal symbiosis was chosen as a treatment that forces the plant to optimize its photosynthetic efficiency, in order to feed the fungus. The results, in combination with the findings of our previous works, suggest a role for the aforementioned components in ferric chelation and/or unloading from the xylem vessels to the aerial plant parts. It is proposed that the gene expression of the DMA exporter ZmTOM1 can be used as an early indicator for the establishment of a mycorrhizal symbiotic relationship in maize.}, } @article {pmid28397362, year = {2017}, author = {Roy, M and Vasco-Palacios, A and Geml, J and Buyck, B and Delgat, L and Giachini, A and Grebenc, T and Harrower, E and Kuhar, F and Magnago, A and Rinaldi, AC and Schimann, H and Selosse, MA and Sulzbacher, MA and Wartchow, F and Neves, MA}, title = {The (re)discovery of ectomycorrhizal symbioses in Neotropical ecosystems sketched in Florianópolis.}, journal = {The New phytologist}, volume = {214}, number = {3}, pages = {920-923}, doi = {10.1111/nph.14531}, pmid = {28397362}, issn = {1469-8137}, mesh = {Brazil ; Congresses as Topic ; DNA Barcoding, Taxonomic ; *Ecosystem ; Mycorrhizae/*physiology ; Plant Roots/*microbiology ; *Symbiosis ; }, } @article {pmid28272801, year = {2017}, author = {Truong, C and Mujic, AB and Healy, R and Kuhar, F and Furci, G and Torres, D and Niskanen, T and Sandoval-Leiva, PA and Fernández, N and Escobar, JM and Moretto, A and Palfner, G and Pfister, D and Nouhra, E and Swenie, R and Sánchez-García, M and Matheny, PB and Smith, ME}, title = {How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity.}, journal = {The New phytologist}, volume = {214}, number = {3}, pages = {913-919}, doi = {10.1111/nph.14509}, pmid = {28272801}, issn = {1469-8137}, mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*classification ; Plants/microbiology ; South America ; Symbiosis ; }, } @article {pmid28079936, year = {2017}, author = {Wurzburger, N and Brookshire, EN and McCormack, ML and Lankau, RA}, title = {Mycorrhizal fungi as drivers and modulators of terrestrial ecosystem processes.}, journal = {The New phytologist}, volume = {213}, number = {3}, pages = {996-999}, doi = {10.1111/nph.14409}, pmid = {28079936}, issn = {1469-8137}, mesh = {Congresses as Topic ; *Ecosystem ; Mycorrhizae/*physiology ; Symbiosis ; }, } @article {pmid31106828, year = {2019}, author = {Rigo, R and Bazin, J and Crespi, M and Charon, C}, title = {Alternative Splicing in the Regulation of Plant-Microbe Interactions.}, journal = {Plant & cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcz086}, pmid = {31106828}, issn = {1471-9053}, abstract = {As sessile organisms, plants are continuously exposed to a wide range of biotic interactions. While some biotic interactions are beneficial or even essential for the plant (e.g. rhizobia, mycorrhiza), others such as pathogens are detrimental and require fast adaptation. Plants partially achieve this growth and developmental plasticity by modulating the repertoire of genes they express. In the past few years, high-throughput transcriptome sequencing have revealed that, in addition to transcriptional control of gene expression, post-transcriptional processes, notably alternative splicing (AS), emerged as a key mechanism for gene regulation during plant adaptation to the environment. AS can increase proteome diversity by generating multiple transcripts from a single gene but also can reduce gene expression by yielding isoforms degraded by mechanisms such as nonsense-mediated mRNA decay. In this review, we will summarize recent discoveries detailing the contribution of alternative splicing to the regulation of plant-microbe interactions, with an emphasis on the modulation of immunity receptor function and other components of the signaling pathways that deal with pathogen responses. We will also discuss emerging evidences that AS could contribute to dynamic reprogramming of the plant transcriptome during beneficial interactions, such as the legume-symbiotic interaction.}, } @article {pmid31106065, year = {2019}, author = {Wright, RM and Strader, ME and Genuise, HM and Matz, M}, title = {Effects of thermal stress on amount, composition, and antibacterial properties of coral mucus.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6849}, doi = {10.7717/peerj.6849}, pmid = {31106065}, issn = {2167-8359}, abstract = {The surface mucus layer of reef-building corals supports feeding, sediment clearing, and protection from pathogenic invaders. As much as half of the fixed carbon supplied by the corals' photosynthetic symbionts is incorporated into expelled mucus. It is therefore reasonable to expect that coral bleaching (disruption of the coral-algal symbiosis) would affect mucus production. Since coral mucus serves as an important nutrient source for the entire reef community, this could have substantial ecosystem-wide consequences. In this study, we examined the effects of heat stress-induced coral bleaching on the composition and antibacterial properties of coral mucus. In a controlled laboratory thermal challenge, stressed corals produced mucus with higher protein (β = 2.1, p < 0.001) and lipid content (β = 15.7, p = 0.02) and increased antibacterial activity (likelihood ratio = 100, p < 0.001) relative to clonal controls. These results are likely explained by the expelled symbionts in the mucus of bleached individuals. Our study suggests that coral bleaching could immediately impact the nutrient flux in the coral reef ecosystem via its effect on coral mucus.}, } @article {pmid31105111, year = {2019}, author = {Goto, Y}, title = {[REGULATION OF INTESTINAL EPITHELIAL α1, 2-FUCOSE].}, journal = {Arerugi = [Allergy]}, volume = {68}, number = {3}, pages = {151-154}, doi = {10.15036/arerugi.68.151}, pmid = {31105111}, issn = {0021-4884}, } @article {pmid30727958, year = {2019}, author = {Kampfraath, AA and Klasson, L and Anvar, SY and Vossen, RHAM and Roelofs, D and Kraaijeveld, K and Ellers, J}, title = {Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {106}, doi = {10.1186/s12864-019-5492-9}, pmid = {30727958}, issn = {1471-2164}, support = {865.12.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 15494//Stichting voor de Technische Wetenschappen/ ; }, mesh = {Animals ; Arthropods/*microbiology/physiology ; DNA Repair ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Parthenogenesis ; Sequence Analysis, DNA ; *Symbiosis ; Wolbachia/*genetics/physiology ; }, abstract = {BACKGROUND: Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. In addition, we also search for candidate genes related to parthenogenesis induction (PI).

RESULTS: Within wFol, we found five phage WO regions representing 25.4% of the complete genome, few pseudogenized genes, and an expansion of DNA-repair genes in comparison to other Wolbachia. These signs of genome conservation were mirrored in the wFol host, the springtail F. candida, which also had an expanded DNA-repair gene family and many horizontally transferred genes. Across all Wolbachia genomes, there was a strong correlation between gene numbers of Wolbachia strains and their hosts. In order to identify genes with a potential link to PI, we assembled the genome of an additional PI strain, wLcla. Comparisons between four PI Wolbachia, including wFol and wLcla, and fourteen non-PI Wolbachia yielded a small set of potential candidate genes for further investigation.

CONCLUSIONS: The strong similarities in genome content of wFol and its host, as well as the correlation between host and Wolbachia gene numbers suggest that there may be some form of convergent evolution between endosymbiont and host genomes. If such convergent evolution would be strong enough to overcome the evolutionary forces causing genome reduction, it would enable expanded genomes within long-term obligate endosymbionts.}, } @article {pmid30681888, year = {2019}, author = {Marczak, M and Żebracki, K and Koper, P and Turska-Szewczuk, A and Mazur, A and Wydrych, J and Wójcik, M and Skorupska, A}, title = {Mgl2 Is a Hypothetical Methyltransferase Involved in Exopolysaccharide Production, Biofilm Formation, and Motility in Rhizobium leguminosarum bv. trifolii.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI01190026R}, doi = {10.1094/MPMI-01-19-0026-R}, pmid = {30681888}, issn = {0894-0282}, abstract = {In this study, functional characterization of the mgl2 gene located near the Pss-I exopolysaccharide biosynthesis region in Rhizobium leguminosarum bv. trifolii TA1 is described. The hypothetical protein encoded by the mgl2 gene was found to be similar to methyltransferases (MTases). Protein homology and template-based modeling facilitated prediction of the Mgl2 structure, which greatly resembled class I MTases with a S-adenosyl-L-methionine-binding cleft. The Mgl2 protein was engaged in exopolysaccharide, but not lipopolysaccharide, synthesis. The mgl2 deletion mutant produced exopolysaccharide comprised of only low molecular weight fractions, while overexpression of mgl2 caused overproduction of exopolysaccharide with a normal low to high molecular weight ratio. The deletion of the mgl2 gene resulted in disturbances in biofilm formation and a slight increase in motility in minimal medium. Red clover (Trifolium pratense) inoculated with the mgl2 mutant formed effective nodules, and the appearance of the plants indicated active nitrogen fixation. The mgl2 gene was preceded by an active and strong promoter. Mgl2 was defined as an integral membrane protein and formed homodimers in vivo; however, it did not interact with Pss proteins encoded within the Pss-I region. The results are discussed in the context of the possible involvement of the newly described potential MTase in various metabolic traits, such as the exopolysaccharide synthesis and motility that are important for rhizobial saprophytic and symbiotic relationships.}, } @article {pmid30356215, year = {2018}, author = {Schretter, CE and Vielmetter, J and Bartos, I and Marka, Z and Marka, S and Argade, S and Mazmanian, SK}, title = {A gut microbial factor modulates locomotor behaviour in Drosophila.}, journal = {Nature}, volume = {563}, number = {7731}, pages = {402-406}, pmid = {30356215}, issn = {1476-4687}, support = {R01 NS085910/NS/NINDS NIH HHS/United States ; }, mesh = {Aldose-Ketose Isomerases/metabolism ; Animals ; Anti-Bacterial Agents/pharmacology ; *Carbohydrate Metabolism/drug effects ; Drosophila melanogaster/drug effects/metabolism/*microbiology/*physiology ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Germ-Free Life ; Lactobacillus brevis/*enzymology/isolation & purification/*metabolism ; Locomotion/drug effects/*physiology ; Motor Activity/drug effects/physiology ; Neural Pathways ; Neurons/drug effects/metabolism ; Octopamine/metabolism/pharmacology ; Symbiosis ; }, abstract = {While research into the biology of animal behaviour has primarily focused on the central nervous system, cues from peripheral tissues and the environment have been implicated in brain development and function1. There is emerging evidence that bidirectional communication between the gut and the brain affects behaviours including anxiety, cognition, nociception and social interaction1-9. Coordinated locomotor behaviour is critical for the survival and propagation of animals, and is regulated by internal and external sensory inputs10,11. However, little is known about how the gut microbiome influences host locomotion, or the molecular and cellular mechanisms involved. Here we report that germ-free status or antibiotic treatment results in hyperactive locomotor behaviour in the fruit fly Drosophila melanogaster. Increased walking speed and daily activity in the absence of a gut microbiome are rescued by mono-colonization with specific bacteria, including the fly commensal Lactobacillus brevis. The bacterial enzyme xylose isomerase from L. brevis recapitulates the locomotor effects of microbial colonization by modulating sugar metabolism in flies. Notably, thermogenetic activation of octopaminergic neurons or exogenous administration of octopamine, the invertebrate counterpart of noradrenaline, abrogates the effects of xylose isomerase on Drosophila locomotion. These findings reveal a previously unappreciated role for the gut microbiome in modulating locomotion, and identify octopaminergic neurons as mediators of peripheral microbial cues that regulate motor behaviour in animals.}, } @article {pmid29868500, year = {2018}, author = {Ma, ZP and Song, Y and Cai, ZH and Lin, ZJ and Lin, GH and Wang, Y and Zhou, J}, title = {Anti-quorum Sensing Activities of Selected Coral Symbiotic Bacterial Extracts From the South China Sea.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {144}, pmid = {29868500}, issn = {2235-2988}, mesh = {Acyl-Butyrolactones/isolation & purification/pharmacology ; Animals ; Anthozoa/*microbiology ; Anti-Bacterial Agents/*isolation & purification/*pharmacology ; Bacteria/genetics/*isolation & purification/*metabolism ; Bacterial Adhesion/drug effects ; Bacterial Proteins/genetics ; Biofilms/drug effects/growth & development ; China ; Chromobacterium ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Gram-Positive Bacteria/isolation & purification/metabolism ; Ligases/genetics ; Metalloendopeptidases/genetics ; Microbial Consortia ; Pseudomonas aeruginosa/drug effects/genetics ; Quorum Sensing/*drug effects/genetics ; Seawater/microbiology ; Staphylococcus hominis/genetics/isolation & purification/metabolism ; Symbiosis ; Trans-Activators/genetics ; Transcription Factors/genetics ; Virulence/genetics ; Whole Genome Sequencing ; }, abstract = {The worldwide increase in antibiotic-resistant pathogens means that identification of alternative antibacterial drug targets and the subsequent development of new treatment strategies are urgently required. One such new target is the quorum sensing (QS) system. Coral microbial consortia harbor an enormous diversity of microbes, and are thus rich sources for isolating novel bioactive and pharmacologically valuable natural products. However, to date, the versatility of their bioactive compounds has not been broadly explored. In this study, about two hundred bacterial colonies were isolated from a coral species (Pocillopora damicornis) and screened for their ability to inhibit QS using the bioreporter strain Chromobacterium violaceum ATCC 12472. Approximately 15% (30 isolates) exhibited anti-QS activity, against the indicator strain. Among them, a typical Gram-positive bacterium, D11 (Staphylococcus hominis) was identified and its anti-QS activity was investigated. Confocal microscopy observations showed that the bacterial extract inhibited the biofilm formation of clinical isolates of wild-type P. aeruginosa PAO1 in a dose-dependent pattern. Chromatographic separation led to the isolation of a potent QS inhibitor that was identified by high-performance liquid chromatography-mass spectrometry (HPLC-MS) and nuclear magnetic resonance (NMR) spectroscopy as DL-homocysteine thiolactone. Gene expression analyses using RT-PCR showed that strain D11 led to a significant down-regulation of QS regulatory genes (lasI, lasR, rhlI, and rhlR), as well as a virulence-related gene (lasB). From the chemical structure, the target compound (DL-homocysteine thiolactone) is an analog of the acyl-homoserine lactones (AHLs), and we presume that DL-homocysteine thiolactone outcompetes AHL in occupying the receptor and thereby inhibiting QS. Whole-genome sequence analysis of S. hominis D11 revealed the presence of predicted genes involved in the biosynthesis of homocysteine thiolactone. This study indicates that coral microbes are a resource bank for developing QS inhibitors and they will facilitate the discovery of new biotechnologically relevant compounds that could be used instead of traditional antibiotics.}, } @article {pmid31103464, year = {2019}, author = {Vander Linden, C and Corbet, C}, title = {Reconciling environment-mediated metabolic heterogeneity with the oncogene-driven cancer paradigm in precision oncology.}, journal = {Seminars in cell & developmental biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.semcdb.2019.05.016}, pmid = {31103464}, issn = {1096-3634}, abstract = {Precision oncology is the practice of matching one therapy to one specific patient, based on particular genetic tumor alterations, in order to achieve the best clinical response. Despite an expanding arsenal of targeted therapies, many patients still have a poor outcome because tumor cells show a remarkable capacity to develop drug resistance, thereby leading to tumor relapse. Besides genotype-driven resistance mechanisms, tumor microenvironment (TME) peculiarities strongly contribute to generate an intratumoral phenotypic heterogeneity that affects disease progression and treatment outcome. In this Review, we describe how TME-mediated metabolic heterogeneities actively participate to therapeutic failure. We report how a lactate-based metabolic symbiosis acts as a mechanism of adaptive resistance to targeted therapies and we describe the role of mitochondrial metabolism, in particular oxidative phosphorylation (OXPHOS), to support the growth and survival of therapy-resistant tumor cells in a variety of cancers. Finally, we detail potential metabolism-interfering therapeutic strategies aiming to eradicate OXPHOS-dependent relapse-sustaining malignant cells and we discuss relevant (pre)clinical models that may help integrate TME-driven metabolic heterogeneity in precision oncology.}, } @article {pmid31102241, year = {2019}, author = {Steinfeld, L and Vafaei, A and Rösner, J and Merzendorfer, H}, title = {Chitin Prevalence and Function in Bacteria, Fungi and Protists.}, journal = {Advances in experimental medicine and biology}, volume = {1142}, number = {}, pages = {19-59}, doi = {10.1007/978-981-13-7318-3_3}, pmid = {31102241}, issn = {0065-2598}, abstract = {Chitin is an important structural polysaccharide, which supports and organizes extracellular matrices in a variety of taxonomic groups including bacteria, fungi, protists, and animals. Additionally, chitin has been recognized as a molecule that is required for Rhizobia-legume symbiosis and involved in arbuscular mycorrhizal signaling in the symbiotic interaction between terrestrial plants and fungi. Moreover, it serves as a unique molecular pattern in the plant defense system against pathogenic fungi and parasites, and in the innate and adaptive immune response of mammals and humans. In this review, we will focus on the prevalence and structural function of chitin in bacteria, fungi, and protists, with a particular focus on the evolution of chitin synthases and the function of chitin oligosaccharides as a signaling molecule in symbiosis and immunity.}, } @article {pmid31101941, year = {2019}, author = {Doni, F and Mispan, MS and Suhaimi, NSM and Ishak, N and Uphoff, N}, title = {Roles of microbes in supporting sustainable rice production using the system of rice intensification.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-09879-9}, pmid = {31101941}, issn = {1432-0614}, support = {FRGS/1/2015/SG03/UM/02/3//Ministry of Higher Education Malaysia/ ; BK004-2015//Universiti Malaya/ ; RU006-2017//Universiti Malaya/ ; }, abstract = {The system of rice intensification (SRI) is an agroecological approach to rice cultivation that seeks to create optimal conditions for healthy plant growth by minimizing inter-plant competition, transplanting widely spaced young single seedlings, and optimizing favorable soil conditions with organic amendments, increased soil aeration by weeding, and controlled water management. These practices improve rice plant growth with yields up to three times more than with conventional cultivation methods, and increase crop resilience under biotic and abiotic stresses. This review discusses the roles of beneficial microbes in improving rice plant growth, yield, and resilience when SRI practices are used, and how these modifications in plant, soil, water, and nutrient management affect the populations and diversity of soil microorganisms. Mechanisms whereby symbiotic microbes support rice plants' growth and performance are also discussed.}, } @article {pmid31101921, year = {2019}, author = {Queralt, M and Walker, JKM and de Miguel, AM and Parladé, J and Anderson, IC and Hortal, S}, title = {The ability of a host plant to associate with different symbiotic partners affects ectomycorrhizal functioning.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz069}, pmid = {31101921}, issn = {1574-6941}, abstract = {Some plants that associate with ectomycorrhizal (ECM) fungi are also able to simultaneously establish symbiosis with other types of partners. The presence of alternative partners that may provide similar benefits may affect ECM functioning. Here we compared potential leucine-aminopeptidase (LA) and acid phosphatase (AP) enzyme activity (involved in N and P cycling, respectively) in ECM fungi of three hosts planted under the same conditions but differing in the type of partners: Pinus (ECM fungi only), Eucalyptus (ECM and arbuscular mycorrhizal -AM- fungi) and Acacia (ECM, AM fungi and rhizobial bacteria). We found that the ECM community on Acacia and Eucalyptus had higher potential AP activity than the Pinus community. The ECM community in Acacia also showed increased potential LA activity compared to Pinus. Morphotypes present in more than one host showed higher potential AP and LA activity when colonizing Acacia than when colonizing another host. Our results suggest that competition with AM fungi and rhizobial bacteria could promote increased ECM activity in Eucalyptus and Acacia. Alternatively, other host-related differences such as ECM community composition could also play a role. We found evidence for ECM physiological plasticity when colonizing different hosts, which might be key for adaptation to future climate scenarios.}, } @article {pmid31101610, year = {2019}, author = {Feldman, D and Amedi, N and Carmeli, S and Yarden, O and Hadar, Y}, title = {Manipulating the expression of small secreted protein 1 (Ssp1) alters patterns of development and metabolism in the white-rot fungus Pleurotus ostreatus.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00761-19}, pmid = {31101610}, issn = {1098-5336}, abstract = {The function of small secreted proteins (SSPs) in saprotrophic fungi is, for the most part, unknown. The white-rot mushroom Pleurotus ostreatus produces considerable amounts of poSSPs at the onset of secondary metabolism, during colony development and in response to chemical compounds such as 5-hydroxymethylfurfural and aryl-alcohols. Genetic manipulation of Ssp1, by knockdown (KDssp1) or overexpression (OEssp1), indicated that they are, in fact, involved in regulation of the ligninolytic system. To elucidate their potential involvement in fungal development, quantitative secretome analyses was performed during the trophophase, idiophase and at a transition point between the two growth phases. The mutations conferred a time shift in the secretion and expression patterns; OEssp1 preceded the entrance to idiophase and secondary metabolism, while KDssp1 was delayed. This was also correlated with expression patterns of selected genes. The KDssp1 colony aged at a slower pace, accompanied by a slower decline in biomass over time. In contrast, OEssp1 exhibited severe lysis and aging of the colony at the same time point. These phenomena were accompanied by variations in yellow pigment production, characteristic of entrance of the wild-type into idiophase. The pigment was produced earlier and at a higher amount in the OEssp1 and was absent from KDssp1. Furthermore, the dikaryon harboring OEssp1 exhibited a delay in initiation of fruiting body formation as well as earlier aging. It is proposed that Ssp1 might function as a part of the fungal communication network and regulating the pattern of fungal development and metabolism in P. ostreatusImportanceSmall secreted proteins (SSPs) are common in fungal saprotrophs, but their roles remain elusive. As such, they comprise part of a gene pool which may be involved in governing fungal lifestyles not limited to symbiosis and pathogenicity, in which they are commonly referred as 'effectors'. It is proposed that Ssp1 in the white-rot fungus Pleurotus ostreatus regulates the transition from primary to secondary metabolism, development, aging and fruiting body initiation. Our observations uncover a novel regulatory role of effector-like SSPs in a saprotroph, suggesting that they may act in fungal communication as well as in response to environmental cues. The presence of Ssp1 homologues in other fungal species supports a common potential role in environmental sensing and fungal development.}, } @article {pmid31099411, year = {2019}, author = {Bosch, TCG and Guillemin, K and McFall-Ngai, M}, title = {Evolutionary "Experiments" in Symbiosis: The Study of Model Animals Provides Insights into the Mechanisms Underlying the Diversity of Host-Microbe Interactions.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e1800256}, doi = {10.1002/bies.201800256}, pmid = {31099411}, issn = {1521-1878}, support = {P50GM098911 and P01GM125576.//National Institute of General Medical Sciences of the National Institutes of Health/ ; P01GM125576//National Institute of General Medical Sciences of the National Institutes of Health/ ; P50GM098911//National Institute of General Medical Sciences of the National Institutes of Health/ ; Collaborative Research Centre (CRC) 1182 "Origin//Deutsche Forschungsgemeinschaft/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; 5R37AI050661-16//National Institutes of Health/ ; }, abstract = {Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host-microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host-microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease.}, } @article {pmid31097480, year = {2019}, author = {Ishii, Y and Maruyama, S and Takahashi, H and Aihara, Y and Yamaguchi, T and Yamaguchi, K and Shigenobu, S and Kawata, M and Ueno, N and Minagawa, J}, title = {Global Shifts in Gene Expression Profiles Accompanied with Environmental Changes in Cnidarian-Dinoflagellate Endosymbiosis.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1534/g3.118.201012}, pmid = {31097480}, issn = {2160-1836}, abstract = {Stable endosymbiotic relationships between cnidarian animals and dinoflagellate algae are vital for sustaining coral reef ecosystems. Recent studies have shown that elevated seawater temperatures can cause the collapse of their endosymbiosis, known as 'bleaching', and result in mass mortality. However, the molecular interplay between temperature responses and symbiotic states still remains unclear. To identify candidate genes relevant to the symbiotic stability, we performed transcriptomic analyses under multiple conditions using the symbiotic and apo-symbiotic (symbiont free) Exaiptasia diaphana, an emerging model sea anemone. Gene expression patterns showed that large parts of differentially expressed genes in response to heat stress were specific to the symbiotic state, suggesting that the host sea anemone could react to environmental changes in a symbiotic state-dependent manner. Comparative analysis of expression profiles under multiple conditions highlighted candidate genes potentially important in the symbiotic state transition under heat-induced bleaching. Many of these genes were functionally associated with carbohydrate and protein metabolisms in lysosomes. Symbiont algal genes differentially expressed in hospite encode proteins related to heat shock response, calcium signaling, organellar protein transport, and sugar metabolism. Our data suggest that heat stress alters gene expression in both the hosts and symbionts. In particular, heat stress may affect the lysosome-mediated degradation and transportation of substrates such as carbohydrates through the symbiosome (phagosome-derived organelle harboring symbiont) membrane, which potentially might attenuate the stability of symbiosis and lead to bleaching-associated symbiotic state transition.}, } @article {pmid30592732, year = {2018}, author = {Sen, A and Duperron, S and Hourdez, S and Piquet, B and Léger, N and Gebruk, A and Le Port, AS and Svenning, MM and Andersen, AC}, title = {Cryptic frenulates are the dominant chemosymbiotrophic fauna at Arctic and high latitude Atlantic cold seeps.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209273}, doi = {10.1371/journal.pone.0209273}, pmid = {30592732}, issn = {1932-6203}, mesh = {Animals ; Arctic Regions ; *Bacteria/genetics ; Cold Temperature ; DNA, Mitochondrial ; Norway ; Oceans and Seas ; Phylogeny ; Polychaeta/anatomy & histology/*microbiology/ultrastructure ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {We provide the first detailed identification of Barents Sea cold seep frenulate hosts and their symbionts. Mitochondrial COI sequence analysis, in combination with detailed morphological investigations through both light and electron microscopy was used for identifying frenulate hosts, and comparing them to Oligobrachia haakonmosbiensis and Oligobrachia webbi, two morphologically similar species known from the Norwegian Sea. Specimens from sites previously assumed to host O. haakonmosbiensis were included in our molecular analysis, which allowed us to provide new insight on the debate regarding species identity of these Oligobrachia worms. Our results indicate that high Arctic seeps are inhabited by a species that though closely related to Oligobrachia haakonmosbiensis, is nonetheless distinct. We refer to this group as the Oligobrachia sp. CPL-clade, based on the colloquial names of the sites they are currently known to inhabit. Since members of the Oligobrachia sp. CPL-clade cannot be distinguished from O. haakonmosbiensis or O. webbi based on morphology, we suggest that a complex of cryptic Oligobrachia species inhabit seeps in the Norwegian Sea and the Arctic. The symbionts of the Oligobrachia sp. CPL-clade were also found to be closely related to O. haakonmosbiensis symbionts, but genetically distinct. Fluorescent in situ hybridization and transmission electron micrographs revealed extremely dense populations of bacteria within the trophosome of members of the Oligobrachia sp. CPL-clade, which is unusual for frenulates. Bacterial genes for sulfur oxidation were detected and small rod shaped bacteria (round in cross section), typical of siboglinid-associated sulfur-oxidizing bacteria, were seen on electron micrographs of trophosome bacteriocytes, suggesting that sulfide constitutes the main energy source. We hypothesize that specific, local geochemical conditions, in particular, high sulfide fluxes and concentrations could account for the unusually high symbiont densities in members of the Oligrobrachia sp. CPL-clade.}, } @article {pmid31095296, year = {2019}, author = {Dabo, M and Jaiswal, SK and Dakora, FD}, title = {Phylogenetic evidence of allopatric speciation of bradyrhizobia nodulating cowpea (Vigna unguiculata L. walp) in South African and Mozambican soils.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz067}, pmid = {31095296}, issn = {1574-6941}, abstract = {The legume host and soil environment play a major role to establish effective symbiosis with diverse rhizobia for growth promotion and nodule formation. Aim of this study was to access morpho-physiology, distribution and phylogenetic position of rhizobia nodulating cowpea from South Africa and Mozambique. The results showed that isolate were highly diverse in their appearance on yeast mannitol agar plates. The test isolates also showed an ability to produce IAA at concentrations ranging from 0.64 to 56.46 μg.ml-1 and to solubilise phosphorus at levels from 0 to 3.55 index. Canonical correspondence analysis (CCA) showed that soil pH and mineral nutrients could significantly influence bradyrhizobial distribution. Analysis of BOX-PCR placed the isolates in eight major clusters with 0.01 to 1.00 similarity coefficient with resulted 45 unique BOX-types. Isolates' phylogenetic analyses based on 16S rRNA, atpD, glnII, gyrB and recA gene sequences showed distinct novel evolutionary lineages within the genus Bradyrhizobium, with some of them being closely related to Bradyrhizobium kavangense, B. subterraneum and B. pachyrhizi. Furthermore, symbiotic genes' phylogenies suggested that the isolates' sym loci probably relate to isolates' geographical origin. The results indicated that geographical origin did affect the isolates' phylogenetic placement and could be the basis for allopatric speciation.}, } @article {pmid31092941, year = {2019}, author = {Steidinger, BS and Crowther, TW and Liang, J and Van Nuland, ME and Werner, GDA and Reich, PB and Nabuurs, G and de-Miguel, S and Zhou, M and Picard, N and Herault, B and Zhao, X and Zhang, C and Routh, D and Peay, KG and , }, title = {Climatic controls of decomposition drive the global biogeography of forest-tree symbioses.}, journal = {Nature}, volume = {569}, number = {7756}, pages = {404-408}, doi = {10.1038/s41586-019-1128-0}, pmid = {31092941}, issn = {1476-4687}, abstract = {The identity of the dominant root-associated microbial symbionts in a forest determines the ability of trees to access limiting nutrients from atmospheric or soil pools1,2, sequester carbon3,4 and withstand the effects of climate change5,6. Characterizing the global distribution of these symbioses and identifying the factors that control this distribution are thus integral to understanding the present and future functioning of forest ecosystems. Here we generate a spatially explicit global map of the symbiotic status of forests, using a database of over 1.1 million forest inventory plots that collectively contain over 28,000 tree species. Our analyses indicate that climate variables-in particular, climatically controlled variation in the rate of decomposition-are the primary drivers of the global distribution of major symbioses. We estimate that ectomycorrhizal trees, which represent only 2% of all plant species7, constitute approximately 60% of tree stems on Earth. Ectomycorrhizal symbiosis dominates forests in which seasonally cold and dry climates inhibit decomposition, and is the predominant form of symbiosis at high latitudes and elevation. By contrast, arbuscular mycorrhizal trees dominate in aseasonal, warm tropical forests, and occur with ectomycorrhizal trees in temperate biomes in which seasonally warm-and-wet climates enhance decomposition. Continental transitions between forests dominated by ectomycorrhizal or arbuscular mycorrhizal trees occur relatively abruptly along climate-driven decomposition gradients; these transitions are probably caused by positive feedback effects between plants and microorganisms. Symbiotic nitrogen fixers-which are insensitive to climatic controls on decomposition (compared with mycorrhizal fungi)-are most abundant in arid biomes with alkaline soils and high maximum temperatures. The climatically driven global symbiosis gradient that we document provides a spatially explicit quantitative understanding of microbial symbioses at the global scale, and demonstrates the critical role of microbial mutualisms in shaping the distribution of plant species.}, } @article {pmid30810852, year = {2019}, author = {Vissa, S and Hofstetter, RW and Bonifácio, L and Khaustov, A and Knee, W and Uhey, DA}, title = {Phoretic mite communities associated with bark beetles in the maritime and stone pine forests of Setúbal, Portugal.}, journal = {Experimental & applied acarology}, volume = {77}, number = {2}, pages = {117-131}, doi = {10.1007/s10493-019-00348-6}, pmid = {30810852}, issn = {1572-9702}, mesh = {Animals ; *Forests ; Mites/*physiology ; Pinus/growth & development ; Portugal ; *Symbiosis ; Trees/growth & development ; Weevils/*physiology ; }, abstract = {The phoretic mite communities of prominent bark beetle pests associated with pine stands of southern Portugal were sampled to determine whether they vary across bark beetle species and stand type. Bark beetles were sampled for mites from two primary (aggressive) bark beetle species (Ips sexdentatus and Orthotomicus erosus) and the most common secondary species (Hylurgus ligniperda) in maritime pine (Pinus pinaster) and stone pine (Pinus pinea) in the Setúbal province of Portugal. Twelve mite species, spanning diverse ecological roles, are found associated with these bark beetle systems. The relative abundances of the 12 species that make up the phoretic mite communities of maritime and stone pine varied significantly between host beetle species as well as between stand type, indicating that the phoretic host and dominant tree type are important drivers of mite community composition. The functional roles of these mites are outlined and their ecological significance in pine forest ecosystems is discussed.}, } @article {pmid30596699, year = {2018}, author = {Xie, L and Lehvävirta, S and Timonen, S and Kasurinen, J and Niemikapee, J and Valkonen, JPT}, title = {Species-specific synergistic effects of two plant growth-promoting microbes on green roof plant biomass and photosynthetic efficiency.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209432}, doi = {10.1371/journal.pone.0209432}, pmid = {30596699}, issn = {1932-6203}, mesh = {Biomass ; Phosphorus/metabolism ; Photosynthesis/*genetics ; Plant Development/*genetics ; Species Specificity ; Symbiosis/*genetics ; Viridiplantae/genetics/growth & development ; }, abstract = {Rhizophagus irregularis, an arbuscular mycorrhizal fungus, and Bacillus amyloliquefaciens, a bacterium, are microorganisms that promote plant growth. They associate with plant roots and facilitate nutrient absorption by their hosts, increase resistance against pathogens and pests, and regulate plant growth through phytohormones. In this study, eight local plant species in Finland (Antennaria dioica, Campanula rotundifolia, Fragaria vesca, Geranium sanguineum, Lotus corniculatus, Thymus serpyllum, Trifolium repens, and Viola tricolor) were inoculated with R. irregularis and/or B. amyloliquefaciens in autoclaved substrates to evaluate the plant growth-promoting effects of different plant/microbe combinations under controlled conditions. The eight plant species were inoculated with R. irregularis, B. amyloliquefaciens, or both microbes or were not inoculated as a control. The impact of the microbes on the plants was evaluated by measuring dry shoot weight, colonization rate by the arbuscular mycorrhizal fungus, bacterial population density, and chlorophyll fluorescence using a plant phenotyping facility. Under dual inoculation conditions, B. amyloliquefaciens acted as a "mycorrhiza helper bacterium" to facilitate arbuscular mycorrhizal fungus colonization in all tested plants. In contrast, R. irregularis did not demonstrate reciprocal facilitation of the population density of B. amyloliquefaciens. Dual inoculation with B. amyloliquefaciens and R. irregularis resulted in the greatest increase in shoot weight and photosynthetic efficiency in T. repens and F. vesca.}, } @article {pmid30596693, year = {2018}, author = {Newton, AC and Boscolo, D and Ferreira, PA and Lopes, LE and Evans, P}, title = {Impacts of deforestation on plant-pollinator networks assessed using an agent based model.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209406}, doi = {10.1371/journal.pone.0209406}, pmid = {30596693}, issn = {1932-6203}, mesh = {Animals ; Bees/physiology ; Conservation of Natural Resources ; *Ecosystem ; *Forests ; Humans ; *Plant Physiological Phenomena ; Pollination/physiology ; Symbiosis/physiology ; Systems Analysis ; }, abstract = {Plant-pollinator networks have been widely used to understand the ecology of mutualistic interactions between plants and animals. While a number of general patterns have been identified, the mechanisms underlying the structure of plant-pollinator networks are poorly understood. Here we present an agent based model (ABM) that simulates the movement of bees over heterogeneous landscapes and captures pollination events, enabling the influence of landscape pattern on pollination networks to be explored. Using the model, we conducted a series of experiments using virtual landscapes representing a gradient of forest loss and fragmentation. The ABM was able to produce expected trends in network structure, from simulations of interactions between individual plants and pollinators. For example, results indicated an increase in the index of complementary specialization (H2') and a decline in network connectance with increasing forest cover. Furthermore, network nestedness was not associated with the degree of forest cover, but was positively related to forest patch size, further supporting results obtained in the field. This illustrates the potential value of ABMs for exploring the structure and dynamics of plant-pollinator networks, and for understanding the mechanisms that underlie them. We attribute the results obtained primarily to a shift from specialist to generalist pollinators with increasing forest loss, a trend that has been observed in some field situations.}, } @article {pmid29878200, year = {2018}, author = {Lee, FJ and Miller, KI and McKinlay, JB and Newton, ILG}, title = {Differential carbohydrate utilization and organic acid production by honey bee symbionts.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {8}, pages = {}, doi = {10.1093/femsec/fiy113}, pmid = {29878200}, issn = {1574-6941}, mesh = {Acetates/metabolism ; Animals ; Bacteria/genetics/*metabolism ; Bees/*microbiology ; Carbohydrate Metabolism/*physiology ; Carbohydrates ; Fatty Acids, Volatile/biosynthesis/*metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Lactic Acid/metabolism ; Metagenome ; Symbiosis/physiology ; }, abstract = {The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain. To identify metabolic contributions of symbionts within the honey bee gut, we utilized a combination of molecular and biochemical approaches. We show significant variation in the metabolic capabilities of honey bee-associated taxa, highlighting the fact that honey bee gut microbiota members of the same clade are highly variable in their ability to use specific carbohydrates and produce organic acids. Finally, we confirm that the honey bee core microbes are active in vivo, expressing key enzymatic genes critical for utilizing plant-derived molecules and producing organic acids (i.e. acetate and lactate). These results suggest that core taxa may contribute significantly to weight gain in the honey bee, specifically through the production of organic acids.}, } @article {pmid31064586, year = {2018}, author = {Marie, A}, title = {"Self-sacrifice" as an accidental outcome of extreme within-group mutualism.}, journal = {The Behavioral and brain sciences}, volume = {41}, number = {}, pages = {e210}, doi = {10.1017/S0140525X1800167X}, pmid = {31064586}, issn = {1469-1825}, mesh = {*Biological Evolution ; Marriage ; Morals ; *Symbiosis ; Warfare ; }, abstract = {Whitehouse makes no room for evolutionary approaches to extreme behaviors based on partner choice and mutualism, which have been convincingly invoked to make sense of ordinary morality. Extended to intergroup warfare, these evolutionary mechanisms may play a pivotal role in explaining the existence of extreme - though not functionally sacrificial - behaviors, benefiting non-kin fellow fighters, together with the distinctive phenomenology those behaviors display.}, } @article {pmid29194919, year = {2018}, author = {Lavy, A and Keren, R and Yu, K and Thomas, BC and Alvarez-Cohen, L and Banfield, JF and Ilan, M}, title = {A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {800-814}, pmid = {29194919}, issn = {1462-2920}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gammaproteobacteria/classification/genetics/metabolism ; Genome, Bacterial/genetics ; Indian Ocean ; Microbiota/genetics ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Polyketide Synthases/genetics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sulfides/*metabolism ; Sulfur/*metabolism ; Symbiosis/physiology ; }, abstract = {Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.}, } @article {pmid31089128, year = {2019}, author = {Ramakrishna, C and Kujawski, M and Chu, H and Li, L and Mazmanian, SK and Cantin, EM}, title = {Bacteroides fragilis polysaccharide A induces IL-10 secreting B and T cells that prevent viral encephalitis.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2153}, doi = {10.1038/s41467-019-09884-6}, pmid = {31089128}, issn = {2041-1723}, abstract = {The gut commensal Bacteroides fragilis or its capsular polysaccharide A (PSA) can prevent various peripheral and CNS sterile inflammatory disorders. Fatal herpes simplex encephalitis (HSE) results from immune pathology caused by uncontrolled invasion of the brainstem by inflammatory monocytes and neutrophils. Here we assess the immunomodulatory potential of PSA in HSE by infecting PSA or PBS treated 129S6 mice with HSV1, followed by delayed Acyclovir (ACV) treatment as often occurs in the clinical setting. Only PSA-treated mice survived, with dramatically reduced brainstem inflammation and altered cytokine and chemokine profiles. Importantly, PSA binding by B cells is essential for induction of regulatory CD4+ and CD8+ T cells secreting IL-10 to control innate inflammatory responses, consistent with the lack of PSA mediated protection in Rag-/-, B cell- and IL-10-deficient mice. Our data reveal the translational potential of PSA as an immunomodulatory symbiosis factor to orchestrate robust protective anti-inflammatory responses during viral infections.}, } @article {pmid31088928, year = {2019}, author = {Schorn, MA and Jordan, PA and Podell, S and Blanton, JM and Agarwal, V and Biggs, JS and Allen, EE and Moore, BS}, title = {Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00821-19}, pmid = {31088928}, issn = {2150-7511}, abstract = {Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation.}, } @article {pmid31088273, year = {2019}, author = {Bell-Roberts, L and Douglas, AE and Werner, GDA}, title = {Match and mismatch between dietary switches and microbial partners in plant sap-feeding insects.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1902}, pages = {20190065}, doi = {10.1098/rspb.2019.0065}, pmid = {31088273}, issn = {1471-2954}, abstract = {Some animal groups associate with the same vertically transmitted microbial symbionts over extended periods of evolutionary time, punctuated by occasional symbiont switches to different microbial taxa. Here we test the oft-repeated suggestion that symbiont switches are linked with host diet changes, focusing on hemipteran insects of the suborder Auchenorrhyncha. These insects include the only animals that feed on plant xylem sap through the life cycle, as well as taxa that feed on phloem sap and plant parenchyma cells. Ancestral state reconstruction provides strong statistical support for a xylem feeding auchenorrhynchan ancestor bearing the dual symbiosis with the primary symbiont Sulcia (Bacteroidetes) and companion symbiont 'β-Sym' (β-proteobacteria). We identified seven dietary transitions from xylem feeding (six to phloem feeding, one to parenchyma feeding), but no reversions to xylem feeding; five evolutionary losses of Sulcia, including replacements by yeast symbionts, exclusively in phloem/parenchyma-feeding lineages; and 14-15 losses of β-Sym, including nine transitions to a different bacterial companion symbiont. Our analysis indicates that, although companion symbiont switching is not associated with shifts in host diet, Sulcia is probably required for xylem-feeding. Furthermore, the ancestral auchenorrhynchan bearing Sulcia and β-Sym probably represents the sole evolutionary origin of xylem feeding in the animal kingdom.}, } @article {pmid31087385, year = {2019}, author = {Zhou, Y and Ge, S and Jin, L and Yao, K and Wang, Y and Wu, X and Zhou, J and Xia, X and Shi, K and Foyer, CH and Jingquan, Y}, title = {A novel CO2 -responsive systemic signaling pathway controlling plant mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15917}, pmid = {31087385}, issn = {1469-8137}, abstract = {Rising atmospheric carbon dioxide concentrations (eCO2) promote symbiosis between roots and arbuscular mycorrhizal fungi (AMF), modifying plant nutrient acquisition and cycling of carbon, nitrogen and phosphate. However, the biological mechanisms by which plants transmit aerial eCO2 cues to roots, to alter the symbiotic associations remain unknown. We used a range of interdisciplinary approaches, including gene silencing, grafting, transmission electron microscopy, LC-MS/MS, biochemical methodologies and gene transcript analysis to explore the complexities of environmental signal transmission from the point of perception in the leaves at the apex to the roots. Here we show that eCO2 triggers apoplastic H2 O2 -dependent auxin production in tomato shoots followed by systemic signaling that results in strigolactone biosynthesis in the roots. This redox-auxin-strigolactone systemic signaling cascade facilitates eCO2 -induced AMF symbiosis and phosphate utilization. Our results challenge the current paradigm of eCO2 effects on AMF and provide new insights into potential targets for manipulation of AMF symbiosis for high nutrient utilization under future climate change scenarios. This article is protected by copyright. All rights reserved.}, } @article {pmid31086829, year = {2019}, author = {Burgsdorf, I and Handley, KM and Bar-Shalom, R and Erwin, PM and Steindler, L}, title = {Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00057-19}, pmid = {31086829}, issn = {2379-5077}, abstract = {"Candidatus Synechococcus feldmannii" is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont "Candidatus Synechococcus spongiarum." Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of "Ca. Synechococcus feldmannii." By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by "Ca. Synechococcus feldmannii" and free-living cyanobacteria, while they are absent in the obligate symbiont "Ca. Synechococcus spongiarum." These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on "Ca. Synechococcus feldmannii" its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths-one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.}, } @article {pmid31084944, year = {2019}, author = {González-Pech, RA and Bhattacharya, D and Ragan, MA and Chan, CX}, title = {Genome Evolution of Coral Reef Symbionts as Intracellular Residents.}, journal = {Trends in ecology & evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2019.04.010}, pmid = {31084944}, issn = {1872-8383}, abstract = {Coral reefs are sustained by symbioses between corals and symbiodiniacean dinoflagellates. These symbioses vary in the extent of their permanence in and specificity to the host. Although dinoflagellates are primarily free-living, Symbiodiniaceae diversified mainly as symbiotic lineages. Their genomes reveal conserved symbiosis-related gene functions and high sequence divergence. However, the evolutionary mechanisms that underpin the transition from the free-living lifestyle to symbiosis remain poorly understood. Here, we discuss the genome evolution of Symbiodiniaceae in diverse ecological niches across the broad spectrum of symbiotic associations, from free-living to putative obligate symbionts. We pose key questions regarding genome evolution vis-à-vis the transition of dinoflagellates from free-living to symbiotic and propose strategies for future research to better understand coral-dinoflagellate and other eukaryote-eukaryote symbioses.}, } @article {pmid31084866, year = {2019}, author = {Ortiz-Castro, R and López-Bucio, J}, title = {Review: Phytostimulation and root architectural responses to quorum-sensing signals and related molecules from rhizobacteria.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {284}, number = {}, pages = {135-142}, doi = {10.1016/j.plantsci.2019.04.010}, pmid = {31084866}, issn = {1873-2259}, abstract = {Bacteria rely on chemical communication to sense the environment and to retrieve information on their population densities. Accordingly, a vast repertoire of molecules is released, which synchronizes expression of genes, coordinates behavior through a process termed quorum-sensing (QS), and determines the relationships with eukaryotic species. Already identified QS molecules from Gram negative bacteria can be grouped into two main classes, N-acyl-L-homoserine lactones (AHLs) and cyclodipeptides (CDPs), with roles in biofilm formation, bacterial virulence or symbiotic interactions. Noteworthy, plants detect each of these molecules, change their own gene expression programs, re-configurate root architecture, and activate defense responses, improving in this manner their adaptation to natural and agricultural ecosystems. AHLs may act as alarm signals, pathogen and/or microbe-associated molecular patterns, whereas CDPs function as hormonal mimics for plants via their putative interactions with the auxin receptor Transport Inhibitor Response1 (TIR1). A major challenge is to identify the molecular pathways of QS-mediated crosstalk and the plant receptors and interacting proteins for AHLs, CDPs and related signals.}, } @article {pmid30327531, year = {2019}, author = {Bennek, E and Mandić, AD and Verdier, J and Roubrocks, S and Pabst, O and Van Best, N and Benz, I and Kufer, T and Trautwein, C and Sellge, G}, title = {Subcellular antigen localization in commensal E. coli is critical for T cell activation and induction of specific tolerance.}, journal = {Mucosal immunology}, volume = {12}, number = {1}, pages = {97-107}, doi = {10.1038/s41385-018-0061-0}, pmid = {30327531}, issn = {1935-3456}, mesh = {Administration, Oral ; Animals ; Antigens, Bacterial/genetics/immunology ; Cells, Cultured ; Escherichia coli/*physiology ; Female ; Forkhead Transcription Factors/metabolism ; Gastrointestinal Microbiome/*physiology ; Homeostasis ; Immune Tolerance ; Intracellular Space ; Lymphocyte Activation ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Microorganisms, Genetically-Modified ; Ovalbumin/genetics/immunology ; Peptides/genetics/immunology ; Symbiosis ; T-Lymphocytes, Regulatory/*immunology ; }, abstract = {Oral tolerance to soluble antigens is critically important for the maintenance of immunological homeostasis in the gut. The mechanisms of tolerance induction to antigens of the gut microbiota are still less well understood. Here, we investigate whether the subcellular localization of antigens within non-pathogenic E. coli has a role for its ability to induce antigen-specific tolerance. E. coli that express an ovalbumin (OVA) peptide in the cytoplasm, at the outer membrane or as secreted protein were generated. Intestinal colonization of mice with non-pathogenic E. coli expressing OVA at the membrane induced the expansion of antigen-specific Foxp3+ Tregs and mediated systemic immune tolerance. In contrast, cytoplasmic OVA was ignored by antigen-specific CD4+ T cells and failed to induce tolerance. In vitro experiments revealed that surface-displayed OVA of viable E. coli was about two times of magnitude more efficient to activate antigen-specific CD4+ T cells than soluble antigens, surface-displayed antigens of heat-killed E. coli or cytoplasmic antigen of viable or heat-killed E. coli. This effect was independent of the antigen uptake efficiency in dendritic cells. In summary, our results show that subcellular antigen localization in viable E. coli strongly influences antigen-specific CD4+ cell expansion and tolerance induction upon intestinal colonization.}, } @article {pmid31081746, year = {2019}, author = {Elizalde-Díaz, JP and Hernández-Lucas, I and Medina-Aparicio, L and Dávalos, A and Leija, A and Alvarado-Affantranger, X and García-García, JD and Hernández, G and Garcia-de Los Santos, A}, title = {Rhizobium tropici CIAT 899 copA gene plays a fundamental role in copper tolerance in both free life and symbiosis with Phaseolus vulgaris.}, journal = {Microbiology (Reading, England)}, volume = {}, number = {}, pages = {}, doi = {10.1099/mic.0.000803}, pmid = {31081746}, issn = {1465-2080}, abstract = {Rhizobium tropici CIAT 899 is a facultative symbiotic diazotroph able to deal with stressful concentrations of metals. Nevertheless the molecular mechanisms involved in metal tolerance have not been elucidated. Copper (Cu2+) is a metal component essential for the heme-copper respiratory oxidases and enzymes that catalyse redox reactions, however, it is highly toxic when intracellular trace concentrations are surpassed. In this study, we report that R. tropici CIAT 899 is more tolerant to Cu2+ than other Rhizobium and Sinorhizobium species. Through Tn5 random mutagenesis we identify a R. tropici mutant strain with a severe reduction in Cu2+ tolerance. The Tn5 insertion disrupted the gene RTCIAT899_CH17575, encoding a putative heavy metal efflux P1B-1-type ATPase designated as copA. Phaseolus vulgaris plants inoculated with the copA::Tn5 mutant in the presence of toxic Cu2+ concentrations showed a drastic reduction in plant and nodule dry weight, as well as nitrogenase activity. Nodules induced by the copA::Tn5 mutant present an increase in H2O2 concentration, lipoperoxidation and accumulate 40-fold more Cu2+ than nodules formed by the wild-type strain. The copA::Tn5 mutant complemented with the copA gene recovered the wild-type symbiotic phenotypes. Therefore, the copA gene is essential for R. tropici CIAT 899 to survive in copper-rich environments in both free life and symbiosis with P. vulgaris plants.}, } @article {pmid31080889, year = {2019}, author = {Parekh, VS and Jacobs, MA}, title = {Deep learning and radiomics in precision medicine.}, journal = {Expert review of precision medicine and drug development}, volume = {4}, number = {2}, pages = {59-72}, doi = {10.1080/23808993.2019.1585805}, pmid = {31080889}, issn = {2380-8993}, abstract = {Introduction: The radiological reading room is undergoing a paradigm shift to a symbiosis of computer science and radiology using artificial intelligence integrated with machine and deep learning with radiomics to better define tissue characteristics. The goal is to use integrated deep learning and radiomics with radiological parameters to produce a personalized diagnosis for a patient.

Areas covered: This review provides an overview of historical and current deep learning and radiomics methods in the context of precision medicine in radiology. A literature search for 'Deep Learning', 'Radiomics', 'Machine learning', 'Artificial Intelligence', 'Convolutional Neural Network', 'Generative Adversarial Network', 'Autoencoders', Deep Belief Networks", Reinforcement Learning", and 'Multiparametric MRI' was performed in PubMed, ArXiv, Scopus, CVPR, SPIE, IEEE Xplore, and NIPS to identify articles of interest.

Expert opinion: In conclusion, both deep learning and radiomics are two rapidly advancing technologies that will unite in the future to produce a single unified framework for clinical decision support with a potential to completely revolutionize the field of precision medicine.}, } @article {pmid31079999, year = {2019}, author = {Schlöffel, MA and Käsbauer, C and Gust, AA}, title = {Interplay of plant glycan hydrolases and LysM proteins in plant-Bacteria interactions.}, journal = {International journal of medical microbiology : IJMM}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijmm.2019.04.004}, pmid = {31079999}, issn = {1618-0607}, abstract = {Plants are always found together with bacteria and other microbes. Although plants can be attacked by phytopathogenic bacteria, they are more often engaged in neutral or mutualistic bacterial interactions. In the soil, plants associate with rhizobia or other plant growth promoting rhizosphere bacteria; above ground, bacteria colonise plants as epi- and endophytes. For mounting appropriate responses, such as permitting colonisation by beneficial symbionts while at the same time fending off pathogenic invaders, plants need to distinguish between the "good" and the "bad". Plants make use of proteins containing the lysin motif (LysM) for perception of N-acetylglucosamine containing carbohydrate structures, such as chitooligosaccharides functioning as symbiotic nodulation factors or bacterial peptidoglycan. Moreover, plant hydrolytic enzymes of the chitinase family, which are able to cleave bacterial peptidoglycan or chitooligosaccharides, are essential for cellular signalling induced by rhizobial nodulation factors during symbiosis as well as bacterial peptidoglycan during pathogenesis. Hence, LysM receptors seem to work in concert with hydrolytic enzymes that fine-tune ligand availability to either allow symbiotic interactions or trigger plant immunity.}, } @article {pmid30716462, year = {2019}, author = {Odeniran, PO and Macleod, ET and Ademola, IO and Welburn, SC}, title = {Endosymbionts interaction with trypanosomes in Palpalis group of Glossina captured in southwest Nigeria.}, journal = {Parasitology international}, volume = {70}, number = {}, pages = {64-69}, doi = {10.1016/j.parint.2019.01.011}, pmid = {30716462}, issn = {1873-0329}, mesh = {Animals ; Enterobacteriaceae/*isolation & purification/physiology ; Insect Vectors/microbiology/parasitology ; Nigeria ; Polymerase Chain Reaction ; Prevalence ; *Symbiosis ; Trypanosoma/microbiology/*physiology ; Tsetse Flies/*microbiology/*parasitology ; Wolbachia ; }, abstract = {Glossina species epidemiological studies were conducted in "fly-belt" endemic zone of southwest Nigeria. Two major study areas were identified and four Nzi traps were set in each site for tsetse collection. This study was conducted to determine the prevalence of endosymbionts (Wigglesworthia glossinidia, Sodalis glossinidius and Wolbachia) in natural field-trapped populations of G. p. palpalis and G. tachinoides and investigate the corresponding interactions with African trypanosomes. A total of 64 tsetse flies were collected, these included G. p. palpalis (n = 28) and G. tachinoides (n = 36). Trypanosome infection and endosymbionts of these flies were determined using polymerase chain reaction (PCR) amplification. The infection rates of W. glossinidia was 100.0% in both species, no flies were positive for Wolbachia. Sodalis glossinidius prevalence was similar between the two-tsetse species, with G. p. palpalis and G. tachinoides showing prevalence of 35.7% (95%CI: 20.7-54.2) and 27.8% (95%CI: 15.9-44.0) respectively. No relationship was found between the endosymbionts and trypanosomes in trapped tsetse flies. More studies are needed to enhance the potential control interventions mediated by endosymbionts to reduce parasitic infections.}, } @article {pmid30684037, year = {2019}, author = {Kumar, U and Nayak, AK and Panneerselvam, P and Kumar, A and Mohanty, S and Shahid, M and Sahoo, A and Kaviraj, M and Priya, H and Jambhulkar, NN and Dash, PK and Mohapatra, SD and Nayak, PK}, title = {Cyanobiont diversity in six Azolla spp. and relation to Azolla-nutrient profiling.}, journal = {Planta}, volume = {249}, number = {5}, pages = {1435-1447}, doi = {10.1007/s00425-019-03093-7}, pmid = {30684037}, issn = {1432-2048}, mesh = {Anabaena/metabolism ; Antioxidants/metabolism ; Aspergillus/*metabolism ; Cyanobacteria/metabolism ; RNA, Ribosomal, 16S/metabolism ; Symbiosis/physiology ; }, abstract = {MAIN CONCLUSION: Illumina-Miseq®-based cyanobiont diversity and biomass were analyzed in six Azolla spp. Results revealed that 93-98% of total operational taxonomic units (OTUs) belong to Nostacaceae followed by Cylindrospermopsis with about 1-6% OTUs. The taxonomy of Azolla-cyanobiont is a long-term debate within the scientific community. Morphological and biochemical-based reports indicated the presence of Anabaena, Nostoc and/or Trichormus azollae as abundant Azolla-cyanobionts, however, molecular data did not support the abundance of Anabaena and/or Nostoc. To understand furthermore, the cyanobiont diversity in six species of Azolla (A. microphylla, A. mexicana, A. filiculoides, A. caroliniana, A. pinnata and A. rubra) was analyzed based on 16S rRNA Illumina-MiSeq sequencing. Additionally, biomass and nutrient profiling of Azolla spp. were analyzed and correlated with cyanobiont diversity. Illumina-MiSeq data revealed that 99.6-99.9% of total operational taxonomic units (OTUs) belonged to Nostocophycideae (class), Nostocales (order) and Nostacaceae (family). At genus level, the unassigned affiliation (93.4-97.9%) under Nostacaceae family was abundant followed by Cylindrospermopsis OTUs (1.1-6.0%). Interestingly, A. pinnata harboured maximum Cylindrospermopsis OTUs and also recorded higher biomass (40.67 g m-2 day-1), whereas crude protein (25.9%) and antioxidants (76.9%) were recorded to be higher in A. microphylla. Biplot analysis revealed that A. pinnata and its cyanobiont abundance were positively correlated with neutral and acid detergent fibers. Overall, the present findings deepened the understanding about cyanobiont in Azolla and its relations with Azolla nutrient profiling.}, } @article {pmid30672456, year = {2019}, author = {Angers, A and Ouimet, P and Tsyvian-Dzyabko, A and Nock, T and Breton, S}, title = {[The underestimated coding potential of mitochondrial DNA].}, journal = {Medecine sciences : M/S}, volume = {35}, number = {1}, pages = {46-54}, doi = {10.1051/medsci/2018308}, pmid = {30672456}, issn = {1958-5381}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Bacteria/genetics ; Cyclooxygenase 1/genetics ; DNA, Mitochondrial/*genetics ; Female ; Humans ; Insulin Resistance/genetics ; Intracellular Signaling Peptides and Proteins/genetics ; Male ; Mitochondrial Proteins/*genetics ; Open Reading Frames/genetics ; Peptides/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Mitochondria are ancient organelles that emerged from the endosymbiosis of free-living proto-bacteria. They still retain a semi-autonomous genetic system with a small genome. Mitochondrial DNA (mtDNA) codes for 13 essential proteins for the production of ATP, the sequences of which are relatively conserved across Metazoans. The discovery of additional mitochondria-derived peptides (MDPs) indicates an underestimated coding potential. Humanin, an anti-apoptotic peptide, is likely independently transcribed from within the 16S rRNA gene, as are recently described SHLPs. MOTS-c, discovered in silico, has been demonstrated to be involved in metabolism and insulin sensitivity. Gau, is a positionally conserved open reading frame (ORF) sequence found in the antisense strand of the COX1 gene and its corresponding peptide is strictly colocalized with mitochondrial markers. In bivalves with doubly uniparental inheritance of mtDNA, male and female mtDNAs each carry a separate additional gene possibly involved in sex determination. Other MDPs likely exist and their investigation will shed light on the underestimated functional repertoire of mitochondria.}, } @article {pmid30315353, year = {2019}, author = {Enebe, MC and Babalola, OO}, title = {The impact of microbes in the orchestration of plants' resistance to biotic stress: a disease management approach.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {9-25}, doi = {10.1007/s00253-018-9433-3}, pmid = {30315353}, issn = {1432-0614}, support = {Grants Ref: UID81192, UID95111//National Research Foundation/ ; }, mesh = {Biological Control Agents ; Disease Resistance ; Endophytes/physiology ; Food Preservation/methods ; Fruit ; Host-Pathogen Interactions/*physiology ; Plant Immunity ; Plant Physiological Phenomena ; Plants/immunology/*microbiology ; Soil Microbiology ; Stress, Physiological/*physiology ; Symbiosis ; }, abstract = {The struggle for survival is a natural and a continuous process. Microbes are struggling to survive by depending on plants for their nutrition while plants on the other hand are resisting the attack of microbes in order to survive. This interaction is a tug of war and the knowledge of microbe-plant relationship will enable farmers/agriculturists improve crop health, yield, sustain regular food supply, and minimize the use of agrochemicals such as fungicides and pesticides in the fight against plant pathogens. Although, these chemicals are capable of inhibiting pathogens, they also constitute an environmental hazard. However, certain microbes known as plant growth-promoting microbes (PGPM) aid in the sensitization and priming of the plant immune defense arsenal for it to conquer invading pathogens. PGPM perform this function by the production of elicitors such as volatile organic compounds, antimicrobials, and/or through competition. These elicitors are capable of inducing the expression of pathogenesis-related genes in plants through induced systemic resistance or acquired systemic resistance channels. This review discusses the current findings on the influence and participation of microbes in plants' resistance to biotic stress and to suggest integrative approach as a better practice in disease management and control for the achievement of sustainable environment, agriculture, and increasing food production.}, } @article {pmid30241736, year = {2018}, author = {Ferlian, O and Biere, A and Bonfante, P and Buscot, F and Eisenhauer, N and Fernandez, I and Hause, B and Herrmann, S and Krajinski-Barth, F and Meier, IC and Pozo, MJ and Rasmann, S and Rillig, MC and Tarkka, MT and van Dam, NM and Wagg, C and Martinez-Medina, A}, title = {Growing Research Networks on Mycorrhizae for Mutual Benefits.}, journal = {Trends in plant science}, volume = {23}, number = {11}, pages = {975-984}, doi = {10.1016/j.tplants.2018.08.008}, pmid = {30241736}, issn = {1878-4372}, mesh = {Mycorrhizae/*physiology ; Plant Roots/microbiology ; Symbiosis ; }, abstract = {Research on mycorrhizal interactions has traditionally developed into separate disciplines addressing different organizational levels. This separation has led to an incomplete understanding of mycorrhizal functioning. Integration of mycorrhiza research at different scales is needed to understand the mechanisms underlying the context dependency of mycorrhizal associations, and to use mycorrhizae for solving environmental issues. Here, we provide a road map for the integration of mycorrhiza research into a unique framework that spans genes to ecosystems. Using two key topics, we identify parallels in mycorrhiza research at different organizational levels. Based on two current projects, we show how scientific integration creates synergies, and discuss future directions. Only by overcoming disciplinary boundaries, we will achieve a more comprehensive understanding of the functioning of mycorrhizal associations.}, } @article {pmid29967516, year = {2018}, author = {Banks, JA}, title = {Fern genomes finally here.}, journal = {Nature plants}, volume = {4}, number = {7}, pages = {404-405}, doi = {10.1038/s41477-018-0202-1}, pmid = {29967516}, issn = {2055-0278}, mesh = {*Cyanobacteria ; *Embryophyta ; *Ferns ; Phylogeny ; Symbiosis ; }, } @article {pmid29570981, year = {2018}, author = {Kust, A and Mareš, J and Jokela, J and Urajová, P and Hájek, J and Saurav, K and Voráčová, K and Fewer, DP and Haapaniemi, E and Permi, P and Řeháková, K and Sivonen, K and Hrouzek, P}, title = {Discovery of a Pederin Family Compound in a Nonsymbiotic Bloom-Forming Cyanobacterium.}, journal = {ACS chemical biology}, volume = {13}, number = {5}, pages = {1123-1129}, doi = {10.1021/acschembio.7b01048}, pmid = {29570981}, issn = {1554-8937}, mesh = {Cyanobacteria/genetics/*metabolism ; Genes, Bacterial ; Magnetic Resonance Spectroscopy ; Multigene Family ; Peptide Synthases/metabolism ; Polyketide Synthases/metabolism ; Polyketides/*isolation & purification/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {The pederin family includes a number of bioactive compounds isolated from symbiotic organisms of diverse evolutionary origin. Pederin is linked to beetle-induced dermatitis in humans, and pederin family members possess potent antitumor activity caused by selective inhibition of the eukaryotic ribosome. Their biosynthesis is accomplished by a polyketide/nonribosomal peptide synthetase machinery employing an unusual trans-acyltransferase mechanism. Here, we report a novel pederin type compound, cusperin, from the free-living cyanobacterium Cuspidothrix issatschenkoi (earlier Aphanizomenon). The chemical structure of cusperin is similar to that of nosperin recently isolated from the lichen cyanobiont Nostoc sharing the tehrahydropyran moiety and major part of the linear backbone. However, the cusperin molecule is extended by a glycine residue and lacks one hydroxyl substituent. Pederins were previously thought to be exclusive to symbiotic relationships. However, C. issatschenkoi is a nonsymbiotic planktonic organism and a frequent component of toxic water blooms. Cusperin is devoid of the cytotoxic activity reported for other pederin family members. Hence, our findings raise questions about the role of pederin analogues in cyanobacteria and broaden the knowledge of ecological distribution of this group of polyketides.}, } @article {pmid29524256, year = {2018}, author = {Tatu, AL and Nwabudike, LC}, title = {Reply to: Kubiak K et al. Endosymbiosis and its significance in dermatology.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {32}, number = {9}, pages = {e346-e347}, doi = {10.1111/jdv.14921}, pmid = {29524256}, issn = {1468-3083}, mesh = {*Dermatology ; Humans ; *Prostatic Neoplasms ; Symbiosis ; }, } @article {pmid31078557, year = {2019}, author = {Wiles, TJ and Guillemin, K}, title = {The Other Side of the Coin: What Beneficial Microbes Can Teach us about Pathogenic Potential.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmb.2019.05.001}, pmid = {31078557}, issn = {1089-8638}, abstract = {Koch's postulates and molecular Koch's postulates have made an indelible mark on how we study and classify microbes, particularly pathogens. However, rigid adherence to these historic postulates constrains our view of not only microbial pathogenesis, but host-microbe relationships in general. Collectively the postulates imply that a 'microbial pathogen' is a clearly identifiable organism with the exclusive capacity to elicit disease through an arsenal of pathogen-specific 'virulence factors'. This narrow definition has been repeatedly contradicted. Advances in DNA sequencing technologies and new experimental systems have revealed that the outcomes of host-microbe interactions are highly contextual and dynamic, especially those involving resident microbiota and variable aspects of host biology. Clarifying what differentiates pathogenic from non-pathogenic microbes, including their paradoxical ability to masquerade as one another, is critical to developing targeted diagnostics and treatments for infectious disease. Such endeavors will also inform the design of therapeutic strategies based on microbiome engineering by providing insights into how manipulating entire host-microbe systems may directly or indirectly alter the pathogenic potential of microbial communities. With these goals in mind, we discuss the need to develop experimental models that better capture the contexts that determine the nature of host-microbe relationships. To demonstrate the potential of one such model-the zebrafish and its resident microbiota-we describe recent work that has revealed the thin line between pathogenic and mutualistic relationships, how the intestine physically shapes bacterial populations and inflammation, and the ability of microbial transmission to override the host's innate immune system.}, } @article {pmid31078551, year = {2019}, author = {Verdonk, CJ and Sullivan, JT and Williman, KM and Nicholson, L and Bastholm, TR and Hynes, MF and Ronson, CW and Bond, CS and Ramsay, JP}, title = {Delineation of the integrase-attachment and origin-of-transfer regions of the symbiosis island ICEMlSymR7A.}, journal = {Plasmid}, volume = {}, number = {}, pages = {102416}, doi = {10.1016/j.plasmid.2019.102416}, pmid = {31078551}, issn = {1095-9890}, abstract = {Integrative and conjugative elements (ICEs) are chromosomally-integrated mobile genetic elements that excise from their host chromosome and transfer to other bacteria via conjugation. ICEMlSymR7A is the prototypical member of a large family of "symbiosis ICEs" which confer upon their hosts the ability to form a nitrogen-fixing symbiosis with a variety of legume species. Mesorhizobial symbiosis ICEs carry a common core of mobilisation genes required for integration, excision and conjugative transfer. IntS of ICEMlSymR7A enables recombination between the ICEMlSymR7A attachment site attP and the 3' end of the phe-tRNA gene. Here we identified putative IntS attP arm (P) sites within the attP region and demonstrated that the outermost P1 and P5 sites demarcated the minimal region for efficient IntS-mediated integration. We also identified the ICEMlSymR7A origin-of-transfer (oriT) site directly upstream of the relaxase-gene rlxS. The ICEMlSymR7A conjugation system mobilised a plasmid carrying the cloned oriT to Escherichia coli in an rlxS-dependent manner. Surprisingly, an in-frame, markerless deletion mutation in the ICEMlSymR7A recombination directionality factor (excisionase) gene rdfS, but not a mutation in intS, abolished mobilisation, suggesting the rdfS deletion tentatively has downstream effects on conjugation or its regulation. In summary, this work defines two critical cis-acting regions required for excision and transfer of ICEMlSymR7A and related ICEs.}, } @article {pmid31077522, year = {2019}, author = {Songwattana, P and Tittabutr, P and Wongdee, J and Teamtisong, K and Wulandari, D and Teulet, A and Fardoux, J and Boonkerd, N and Giraud, E and Teaumroong, N}, title = {Symbiotic properties of a chimeric Nod-independent photosynthetic Bradyrhizobium strain obtained by conjugative transfer of a symbiotic plasmid.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14650}, pmid = {31077522}, issn = {1462-2920}, abstract = {The lateral transfer of symbiotic genes converting a predisposed soil bacteria into a legume symbiont has occurred repeatedly and independently during the evolution of rhizobia. We experimented the transfer of a symbiotic plasmid between Bradyrhizobium strains. The originality of the DOA9 donor is that it harbors a symbiotic mega-plasmid (pDOA9) containing nod, nif and T3SS genes while the ORS278 recipient has the unique property of inducing nodules on some Aeschynomene species in the absence of Nod factors (NFs). We observed that the chimeric strain ORS278-pDOA9* lost its ability to develop a functional symbiosis with A. indica and A. evenia. The mutation of rhcN and nodB led to partial restoration of nodule efficiency, indicating that T3SS effectors and NFs block the establishment of the NF-independent symbiosis. Conversely, ORS278-pDOA9* strain acquired the ability to form nodules on Crotalaria juncea and Macroptillium artropurpureum but not on NF-dependent Aeschynomene (A. afraspera and A. americana), suggesting that the ORS278 strain also harbors incompatible factors that block the interaction with these species. These data indicate that the symbiotic properties of a chimeric rhizobia cannot be anticipated due to new combination of symbiotic and non-symbiotic determinants that may interfere during the interaction with the host plant. This article is protected by copyright. All rights reserved.}, } @article {pmid31076773, year = {2019}, author = {Shiratake, K and Notaguchi, M and Makino, H and Sawai, Y and Borghi, L}, title = {Petunia PLEIOTROPIC DRUG RESISTANCE 1 is a Strigolactone Short-distance Transporter with Long-distance Outcomes.}, journal = {Plant & cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcz081}, pmid = {31076773}, issn = {1471-9053}, abstract = {Phytohormones of the strigolactone (SL) family have been characterized as negative regulators of lateral bud outgrowth and triggers of symbioses between plants and mycorrhizal fungi. Strigolactones and their precursors are synthesized in root tips as well as along shoot and root vasculature; they either move shoot-wards and regulate plant architecture or are exuded from roots into the soil to establish mycorrhizal symbiosis. Owing to the difficulty in quantification of SL in shoot tissues because of low abundance, it is not yet clear how SL distribution in plants is regulated at short- and long-distances from SL biosynthetic and target tissues. To address this question, we grafted wildtype scions and rootstocks from different petunia mutants for SL biosynthesis/transport and investigated SL activity by quantifying lateral bud outgrowth in the main shoot. Based on these results, we show that i) the previously reported petunia SL transporter PLEIOTROPIC DRUG RESISTANCE 1 (PDR1) directly accounts for short-distance SL transport and ii) long distance transport of SLs seems to be partially and not-directly dependent on PDR1. These data suggest that the root-to-shoot transport of SLs occurs either via the vasculature bundle through transporters other than PDR1 or involves SL precursors that are not substrates of PDR1.}, } @article {pmid31076245, year = {2019}, author = {Brunk, CF and Martin, WF}, title = {Archaeal Histone Contributions to the Origin of Eukaryotes.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2019.04.002}, pmid = {31076245}, issn = {1878-4380}, abstract = {The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.}, } @article {pmid31074496, year = {2019}, author = {Chaudhary, S and Gupta, P and Srivastava, S and Adholeya, A}, title = {Understanding dynamics of Rhizophagus irregularis ontogenesis in axenically developed co-culture through basic and advanced microscopic techniques.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jobm.201900138}, pmid = {31074496}, issn = {1521-4028}, abstract = {Detailed information on structural changes that occur during ontogenesis of Rhizophagus irregularis in axenically developed co-cultures is limited. Our study aims to investigate the series of events that occur during mycorrhizal ontogenesis under axenic condition through basic and advanced microscopic techniques followed by comparison amongst these to identify the suitable technique for rapid and detailed analysis of mycorrhizal structures. Three stages were identified in mycorrhizal ontogenesis from initiation (pre-infection stage of hyphae; its branching, infection and appressoria formation; epidermal opening; hyphal entry), progression (arbuscular development; hyphal coils and vesicles) to maturity (extra-radical spores). Scanning electron microscopy was found to be an efficient tool for studying spatial three-dimensional progression. Adding to the advantages of advanced microscopy, the potential of autofluorescence to explore the stages of symbiosis non-destructively was established. We also report imaging of ultrathin sections by bright field microscopy to provide finer details at subcellular interface. Owing to the merits of non-destructive sampling, ease of sample preparation, autofluorescence (no dye required), no use of toxic chemicals, rapid analysis and in depth characterization confocal laser scanning microscopy was identified as the most preferred technique. The method thus developed can be used for detailed structural inquisition of mycorrhizal symbiosis both in in planta and in an in vitro system. This article is protected by copyright. All rights reserved.}, } @article {pmid31073281, year = {2019}, author = {Gao, M and Benge, A and Wu, TJ and Javier, R}, title = {Use of Plasmid pVMG to Make Transcriptional ß-Glucuronidase Reporter Gene Fusions in the Rhizobium Genome for Monitoring the Expression of Rhizobial Genes In Vivo.}, journal = {Biological procedures online}, volume = {21}, number = {}, pages = {8}, doi = {10.1186/s12575-019-0096-y}, pmid = {31073281}, issn = {1480-9222}, abstract = {Background: The soil bacterium Sinorhizobium meliloti and its allies are important nitrogen-fixing bacterial symbionts that cause N2-fixing nodules on the roots of legumes. Chromosomal ß-glucuronidase gene (uidA) transcriptional fusions are frequently used to monitor the expression of bacterial genes during the symbiosis. However, the construction of the fusions is laborious.

Results: The narrow-host-range, fusion selective plasmid pVMG was constructed and used as a vector for the construction of chromosomal uidA transcriptional fusions in the S. meliloti genome. Translation termination codons were added in all three reading frames upstream of the promoterless uidA in this vector to ensure transcriptional fusions. pVMG replicated to high copy number in Escherichia coli, offering advantages for the isolation of fusion-containing plasmids and the restriction analysis. Genomic locations of uidA fusions were verified in a simple PCR experiment. All these helps reduce the sample processing time and efforts. As a demonstration of its usefulness, the N-acyl homoserine lactone (AHL) signal synthase gene promoter was fused to uidA and shown to be expressed by S. meliloti in the senescence zone of the nodule on the host plant, M. truncatula. This indicates the presence of AHL signals at the late stages of symbiosis.

Conclusions: A simple, pVMG-based method for construction of chromosomal uidA transcriptional fusions has been successfully used in the model rhizobium S. meliloti. It is also applicable for other rhizobial strains.}, } @article {pmid31072343, year = {2019}, author = {Chamberlain, NB and Mehari, YT and Hayes, BJ and Roden, CM and Kidane, DT and Swehla, AJ and Lorenzana-DeWitt, MA and Farone, AL and Gunderson, JH and Berk, SG and Farone, MB}, title = {Infection and nuclear interaction in mammalian cells by 'Candidatus Berkiella cookevillensis', a novel bacterium isolated from amoebae.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {91}, doi = {10.1186/s12866-019-1457-z}, pmid = {31072343}, issn = {1471-2180}, support = {R833102//U.S. Environmental Protection Agency/ ; R827111//U.S. Environmental Protection Agency/ ; }, abstract = {BACKGROUND: 'Candidatus Berkiella cookevillensis' and 'Ca. Berkiella aquae' have previously been described as intranuclear bacteria of amoebae. Both bacteria were isolated from amoebae and were described as appearing within the nuclei of Acanthamoeba polyphaga and ultimately lysing their host cells within 4 days. Both bacteria are Gammaproteobacteria in the order Legionellales with the greatest similarity to Coxiella burnetii. Neither bacterium grows axenically in artificial culture media. In this study, we further characterized 'Ca. B. cookevillensis' by demonstrating association with nuclei of human phagocytic and nonphagocytic cell lines.

RESULTS: Transmission electron microscopy (TEM) and confocal microscopy were used to confirm nuclear co-localization of 'Ca. B. cookevillensis' in the amoeba host A. polyphaga with 100% of cells having bacteria co-localized with host nuclei by 48 h. TEM and confocal microscopy demonstrated that the bacterium was also observed to be closely associated with nuclei of human U937 and THP-1 differentiated macrophage cell lines and nonphagocytic HeLa human epithelial-like cells. Immunofluorescent staining revealed that the bacteria-containing vacuole invaginates the nuclear membranes and appears to cross from the cytoplasm into the nucleus as an intact vacuole.

CONCLUSION: Results of this study indicate that a novel coccoid bacterium isolated from amoebae can infect human cell lines by associating with the host cell nuclei, either by crossing the nuclear membranes or by deeply invaginating the nuclear membranes. When associated with the nuclei, the bacteria appear to be bound within a vacuole and replicate to high numbers by 48 h. We believe this is the first report of such a process involving bacteria and human cell lines.}, } @article {pmid30693447, year = {2019}, author = {Saadani, O and Jebara, SH and Fatnassi, IC and Chiboub, M and Mannai, K and Zarrad, I and Jebara, M}, title = {Effect of Vicia faba L. var. minor and Sulla coronaria (L.) Medik associated with plant growth-promoting bacteria on lettuce cropping system and heavy metal phytoremediation under field conditions.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {8}, pages = {8125-8135}, doi = {10.1007/s11356-019-04302-2}, pmid = {30693447}, issn = {1614-7499}, support = {MOBIDOC//PASRI, Tunisia funded by European Union/ ; }, mesh = {Agricultural Inoculants/*growth & development/metabolism ; Biodegradation, Environmental ; Crop Production/methods ; Fabaceae/growth & development/metabolism/microbiology ; Lettuce/*growth & development/metabolism ; Metals, Heavy/*analysis/metabolism ; Plant Development/drug effects ; Rhizobium/*growth & development/metabolism ; Soil/chemistry ; Soil Pollutants/*analysis/metabolism ; Symbiosis ; Vicia faba/*growth & development/metabolism/microbiology ; }, abstract = {Researches involving the use of association between legumes and PGPBs (plant growth-promoting bacteria) in heavy metal phytoremediation process were mainly performed for soils highly contaminated. However, even in agriculture soils, with moderate or low contamination levels, plants can accumulate high rates of heavy metals. So, food chain contamination by these metals presents a real threat to animal and human health. This work aimed to evaluate the use of two legumes/PGPB symbioses; Vicia faba var. minor and Sulla coronaria have been inoculated with specific heavy metal-resistant inocula in a crop rotation system with Lactuca sativa as a following crop, in order to assess their effects on soil fertility, lettuce yield, and heavy metal content. Our results showed that legume inoculation significantly enhanced their biomass production, nitrogen and phosphorus content. The use of our symbioses as green manure before lettuce cultivation, as a rotation cropping system, affected positively soil fertility. In fact, we recorded a higher organic matter content, with rapid decomposition in the soil of inoculated plots. Besides, results demonstrated a greater nitrogen and phosphorus content in this soil, especially in the plot cultivated with inoculated V. faba var. minor. The improvement of soil fertility enhanced lettuce yield and its nitrogen and phosphorus content. Moreover, inoculated legumes extracted and accumulated more heavy metals than non-inoculated legumes. Our symbioses play the role of organic trap for heavy metals, making them unavailable for following crops. These facts were supported by lettuce heavy metal content, showing a significant decrease in metal accumulation, mainly zinc and cadmium, in edible parts. Results showed the usefulness of the studied symbioses, as a main part of a rotation system with lettuce. Our symbioses can be suggested for agriculture soil phytoremediation, aiming to enhance non-legume crop yield and limit heavy metal translocation to food chain.}, } @article {pmid30520104, year = {2018}, author = {Foyer, CH and Nguyen, HT and Lam, HM}, title = {A seed change in our understanding of legume biology from genomics to the efficient cooperation between nodulation and arbuscular mycorrhizal fungi.}, journal = {Plant, cell & environment}, volume = {41}, number = {9}, pages = {1949-1954}, doi = {10.1111/pce.13419}, pmid = {30520104}, issn = {1365-3040}, support = {//Worldwide University Network (WUN)/International ; }, mesh = {Fabaceae/genetics/*physiology ; Genome, Plant ; Genomics ; Mycorrhizae/*physiology ; Nitrogen Fixation ; Plant Roots/microbiology ; Seeds/*physiology ; *Soil Microbiology ; Stress, Physiological ; Symbiosis ; }, abstract = {Grain legumes play a significant role in global food security. They have an advantage over cereals in that they can form symbiotic associations with nitrogen-fixing bacteria, making them self-sufficient in terms of nitrogen acquisition. In addition to this superior agronomic trait, grain legumes have excellent nutritional properties and are thus widely used as animal feed as well as in human nutrition. Current global trends towards increased legume consumption and availability of value-added products, as well as legume production in developing countries require the provision of improved cultivars with better productivity and adaptability. Intensive efforts are thus underway to elaborate genomic resources and gain an improved knowledge base in a number of legume crops. There is also an emerging understanding of the beneficial interactions between legume-associated organisms, particularly rhizobia and arbuscular mycorrhizal fungi, which result in improved nodulation and nutrient acquisition. The emerging focus on legume breeding for high sustainable yields as well as improved biotic and abiotic stress tolerance traits will serve to close the current gap between grain legume production and demand. With the support from policymakers, this increase in knowledge can be readily translated into increased crop production to meet the demands of an increasing global population.}, } @article {pmid31071427, year = {2019}, author = {Rahnama, M and Maclean, P and Fleetwood, DJ and Johnson, RD}, title = {The LaeA orthologue in Epichloë festucae is required for symbiotic interaction with Lolium perenne.}, journal = {Fungal genetics and biology : FG & B}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fgb.2019.05.001}, pmid = {31071427}, issn = {1096-0937}, abstract = {LaeA is a conserved global regulator of secondary metabolism and development in fungi. It is often required for successful pathogenic interactions. In this study, the laeA homologue in the fungal grass endophyte E. festucae was deleted and functionally characterised in vitro and its role in the mutualistic E. festucae interaction with Lolium perenne (perennial ryegrass) was determined. We showed that laeA in E. festucae is required for normal hyphal morphology, resistance to oxidative stress, and conidiation under nutrient-limited in vitro conditions. In planta studies revealed that laeA is expressed in a tissue-specific manner and is required to form a compatible plant interaction, with the majority of seedlings inoculated with a laeA deletion mutant either dying or being uninfected. In mature infected plants no difference was observed in the number or morphology of endophytic hyphae. However, the number of epiphyllous hyphae were greatly increased. Comparative transcriptomics analyses suggested roles for plant cell wall degradation, fungal cell wall composition, secondary metabolism and small-secreted proteins in Epichloë foliar symbiosis.}, } @article {pmid31071294, year = {2019}, author = {Brown, EM and Ke, X and Hitchcock, D and Jeanfavre, S and Avila-Pacheco, J and Nakata, T and Arthur, TD and Fornelos, N and Heim, C and Franzosa, EA and Watson, N and Huttenhower, C and Haiser, HJ and Dillow, G and Graham, DB and Finlay, BB and Kostic, AD and Porter, JA and Vlamakis, H and Clish, CB and Xavier, RJ}, title = {Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.}, journal = {Cell host & microbe}, volume = {25}, number = {5}, pages = {668-680.e7}, doi = {10.1016/j.chom.2019.04.002}, pmid = {31071294}, issn = {1934-6069}, abstract = {Sphingolipids are structural membrane components and important eukaryotic signaling molecules. Sphingolipids regulate inflammation and immunity and were recently identified as the most differentially abundant metabolite in stool from inflammatory bowel disease (IBD) patients. Commensal bacteria from the Bacteroidetes phylum also produce sphingolipids, but the impact of these metabolites on host pathways is largely uncharacterized. To determine whether bacterial sphingolipids modulate intestinal health, we colonized germ-free mice with a sphingolipid-deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides-derived sphingolipids resulted in intestinal inflammation and altered host ceramide pools in mice. Using lipidomic analysis, we described a sphingolipid biosynthesis pathway and revealed a variety of Bacteroides-derived sphingolipids including ceramide phosphoinositol and deoxy-sphingolipids. Annotating Bacteroides sphingolipids in an IBD metabolomic dataset revealed lower abundances in IBD and negative correlations with inflammation and host sphingolipid production. These data highlight the role of bacterial sphingolipids in maintaining homeostasis and symbiosis in the gut.}, } @article {pmid31070991, year = {2019}, author = {Lindsay, PL and Williams, BN and MacLean, AM and Harrison, M}, title = {A phosphate-dependent requirement for the transcription factors IPD3 and IPD3L during AM symbiosis in Medicago truncatula.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-01-19-0006-R}, pmid = {31070991}, issn = {0894-0282}, abstract = {During arbuscular mycorrhizal (AM) symbiosis, activation of a symbiosis signaling pathway induces gene expression necessary for accommodation of AM fungi. Here we focus on pathway components Medicago truncatula INTERACTING PROTEIN OF DOES NOT MAKE INFECTIONS 3 (IPD3) and IPD3 LIKE (IPD3L), which are potential orthologs of Lotus japonicus CYCLOPS, a transcriptional regulator essential for AM symbiosis. In ipd3 ipd3l, hyphal entry through the epidermis and overall colonization levels are reduced relative to wild type but fully developed arbuscules are present in the cortex. In comparison with wild type, colonization of ipd3 ipd3l is acutely sensitive to higher phosphate levels in the growth medium, with a disproportionate decrease in epidermal penetration, overall colonization, and symbiotic gene expression. When constitutively expressed in ipd3 ipd3l, an autoactive DOES NOT MAKE INFECTIONS 3 (DMI3) induces the expression of transcriptional regulators REDUCED ARBUSCULAR MYCORRHIZA 1 (RAM1) and REQUIRED for ARBUSCULE DEVELOPMENT 1 (RAD1), providing a possible avenue for arbuscule development even in the absence of IPD3 and IPD3L. An increased sensitivity of ipd3 ipd3l to GA3 suggests an involvement of DELLA. The data reveal partial redundancy in the symbiosis signaling pathway which may ensure robust signaling in low-P environments, while IPD3 and IPD3L maintain signaling in higher-P environments. The latter may buffer the pathway from short-term variation in P levels encountered by roots during growth in heterogeneous soil environments.}, } @article {pmid31067698, year = {2019}, author = {Vaz Martins, T and Livina, VN}, title = {What Drives Symbiotic Calcium Signalling in Legumes? Insights and Challenges of Imaging.}, journal = {International journal of molecular sciences}, volume = {20}, number = {9}, pages = {}, doi = {10.3390/ijms20092245}, pmid = {31067698}, issn = {1422-0067}, support = {BB/J004553/1; BB/P012574/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {We review the contribution of bioimaging in building a coherent understanding of Ca 2 + signalling during legume-bacteria symbiosis. Currently, two different calcium signals are believed to control key steps of the symbiosis: a Ca 2 + gradient at the tip of the legume root hair is involved in the development of an infection thread, while nuclear Ca 2 + oscillations, the hallmark signal of this symbiosis, control the formation of the root nodule, where bacteria fix nitrogen. Additionally, different Ca 2 + spiking signatures have been associated with specific infection stages. Bioimaging is intrinsically a cross-disciplinary area that requires integration of image recording, processing and analysis. We used experimental examples to critically evaluate previously-established conclusions and draw attention to challenges caused by the varying nature of the signal-to-noise ratio in live imaging. We hypothesise that nuclear Ca 2 + spiking is a wide-range signal involving the entire root hair and that the Ca 2 + signature may be related to cytoplasmic streaming.}, } @article {pmid30420746, year = {2018}, author = {Murat, C and Payen, T and Noel, B and Kuo, A and Morin, E and Chen, J and Kohler, A and Krizsán, K and Balestrini, R and Da Silva, C and Montanini, B and Hainaut, M and Levati, E and Barry, KW and Belfiori, B and Cichocki, N and Clum, A and Dockter, RB and Fauchery, L and Guy, J and Iotti, M and Le Tacon, F and Lindquist, EA and Lipzen, A and Malagnac, F and Mello, A and Molinier, V and Miyauchi, S and Poulain, J and Riccioni, C and Rubini, A and Sitrit, Y and Splivallo, R and Traeger, S and Wang, M and Žifčáková, L and Wipf, D and Zambonelli, A and Paolocci, F and Nowrousian, M and Ottonello, S and Baldrian, P and Spatafora, JW and Henrissat, B and Nagy, LG and Aury, JM and Wincker, P and Grigoriev, IV and Bonfante, P and Martin, FM}, title = {Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle.}, journal = {Nature ecology & evolution}, volume = {2}, number = {12}, pages = {1956-1965}, doi = {10.1038/s41559-018-0710-4}, pmid = {30420746}, issn = {2397-334X}, mesh = {Ascomycota/*genetics/physiology ; DNA, Fungal/analysis ; *Genome, Fungal ; *Life History Traits ; Mycorrhizae/*genetics/physiology ; Phylogeny ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.}, } @article {pmid29124861, year = {2018}, author = {Certner, RH and Vollmer, SV}, title = {Inhibiting bacterial quorum sensing arrests coral disease development and disease-associated microbes.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {645-657}, doi = {10.1111/1462-2920.13991}, pmid = {29124861}, issn = {1462-2920}, mesh = {4-Butyrolactone/analogs & derivatives/antagonists & inhibitors ; Animals ; Anthozoa/*microbiology ; Caribbean Region ; Coral Reefs ; Flavobacteriaceae/drug effects ; Gammaproteobacteria/growth & development ; Microbiota/*drug effects ; Quorum Sensing/*drug effects ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {Among the greatest threats to coral reefs are coral epizootics, which are increasing in frequency and severity across many reef ecosystems. In particular, white band disease (WBD) has devastated Caribbean acroporid populations since its initial outbreak in 1979. However, despite its widespread and damaging effects, the aetiology of WBD remains largely unresolved. Here, we examine the role of quorum sensing within bacterial communities associated with WBD-infected Acropora cervicornis. Microbial communities isolated from WBD-infected corals were exposed to quorum sensing inhibitor (QSI) - a N-acyl homoserine lactone autoinducer antagonist - and then dosed onto healthy test corals. WBD-associated bacteria supplemented with QSI lost the ability to establish disease, while healthy corals exposed to uninhibited WBD bacterial communities became infected within two days. Microbial 16S rRNA metagenomic sequencing analyses were then used to identify shifts in bacterial communities due to QSI exposure on WBD-associated bacterial communities. Our results demonstrated that Vibrionaceae and Flavobacteriaceae abundances were strongly inhibited by the addition of QSI to WBD-infected corals, whereas putative coral symbiont Endozoicomonas and Halomonadaceae abundances decrease dramatically in diseased corals.}, } @article {pmid29098761, year = {2018}, author = {Astudillo-García, C and Slaby, BM and Waite, DW and Bayer, K and Hentschel, U and Taylor, MW}, title = {Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {561-576}, doi = {10.1111/1462-2920.13965}, pmid = {29098761}, issn = {1462-2920}, mesh = {Animals ; Bacteria, Aerobic/*classification/genetics ; Molecular Typing ; Phylogeny ; Porifera/*microbiology ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {Many marine sponges contain dense and diverse communities of associated microorganisms. Members of the 'sponge-associated unclassified lineage' (SAUL) are frequently recorded from sponges, yet little is known about these bacteria. Here we investigated the distribution and phylogenetic status of SAUL. A meta-analysis of the available literature revealed the widespread distribution of this clade and its association with taxonomically varied sponge hosts. Phylogenetic analyses, conducted using both 16S rRNA gene-based phylogeny and concatenated marker protein sequences, revealed that SAUL is a sister clade of the candidate phylum 'Latescibacteria'. Furthermore, we conducted a comprehensive analysis of two draft genomes assembled from sponge metagenomes, revealing novel insights into the physiology of this symbiont. Metabolic reconstruction suggested that SAUL members are aerobic bacteria with facultative anaerobic metabolism, with the capacity to degrade multiple sponge- and algae-derived carbohydrates. We described for the first time in a sponge symbiont the putative genomic capacity to transport phosphate into the cell and to produce and store polyphosphate granules, presumably constituting a phosphate reservoir for the sponge host in deprivation periods. Our findings suggest that the lifestyle of SAUL is symbiotic with the host sponge, and identify symbiont factors which may facilitate the establishment and maintenance of this relationship.}, } @article {pmid31066947, year = {2019}, author = {Muletz-Wolz, CR and Fleischer, RC and Lips, KR}, title = {Fungal disease and temperature alter skin microbiome structure in an experimental salamander system.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15122}, pmid = {31066947}, issn = {1365-294X}, abstract = {Pathogens compete with host microbiomes for space and resources. Their shared environment impacts pathogen-microbiome-host interactions, which can lead to variation in disease outcome. The skin microbiome of red-backed salamanders (Plethodon cinereus) can reduce infection by the pathogen Batrachochytrium dendrobatidis (Bd) at moderate infection loads, with high species richness and high abundance of competitors as putative mechanisms. However, it is unclear if the skin microbiome can reduce epizootic Bd loads across temperatures. We conducted a laboratory experiment to quantify skin microbiome and host responses (P. cinereus: n = 87) to Bd at mimicked epizootic loads across temperatures (13, 17, 21 °C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified OTUs taxonomically similar to culturable bacteria known to kill Bd (anti-Bd OTUs). Prior to pathogen exposure, temperature changed the microbiome (OTU richness decreased by 12% and abundance of anti-Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. Post exposure, Bd changed the microbiome (OTU richness decreased by 0.1% and the abundance of anti-Bd OTUs increased by 0.2% per 1% increase in Bd load) and caused high host mortality across temperatures (35/45: 78%). Temperature indirectly impacted microbiome change and mortality through its direct effect on pathogen load. We did not find support for the microbiome impacting Bd load or host survival. Our research unravels complex host, pathogen, microbiome and environmental interactions to demonstrate that during epizootic events the microbiome will be unlikely to reduce pathogen invasion, even for putatively Bd-resistant species. This article is protected by copyright. All rights reserved.}, } @article {pmid31066909, year = {2019}, author = {Martinez-Medina, A and Pescador, L and Fernandez, I and Rodríguez-Serrano, M and García, JM and Romero-Puertas, MC and Pozo, MJ}, title = {Nitric oxide and phytoglobin PHYTOGB1 are regulatory elements in the Solanum lycopersicum-Rhizophagus irregularis mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15898}, pmid = {31066909}, issn = {1469-8137}, abstract = {The regulatory role of nitric oxide (NO) and phytoglobins in plant response to pathogenic and mutualistic microbes has been evidenced. However, little is known about their function in the arbuscular mycorrhizal (AM) symbiosis. We investigated whether NO and phytoglobin PHYTOGB1 are regulatory components in the AM symbiosis. Rhizophagus irregularis in vitro-grown cultures and tomato plants were used to monitor AM-associated NO-related root responses as compared to responses triggered by the pathogen Fusarium oxysporum. A genetic approach was conducted to understand the role of PHYTOGB1 on NO signaling during both interactions. After a common early peak on NO levels in response to both fungi, a specific NO accumulation pattern was triggered in tomato roots during the onset of the AM interaction. PHYTOGB1 was upregulated by the AM interaction. By contrast, the pathogen triggered a continuous NO accumulation and a strong downregulation of PHYTOGB1. Manipulation of PHYTOGB1 levels in overexpressing and silenced roots led to a deregulation of NO levels and altered mycorrhization and pathogen infection. We demonstrate that the onset of the AM symbiosis is associated with a specific NO-related signature in the host root. We propose that NO regulation by PHYTOGB1 is a regulatory component of the AM symbiosis. This article is protected by copyright. All rights reserved.}, } @article {pmid31065250, year = {2019}, author = {Irisarri, P and Cardozo, G and Tartaglia, C and Reyno, R and Gutiérrez, P and Lattanzi, FA and Rebuffo, M and Monza, J}, title = {Selection of Competitive and Efficient Rhizobia Strains for White Clover.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {768}, doi = {10.3389/fmicb.2019.00768}, pmid = {31065250}, issn = {1664-302X}, abstract = {The practice of inoculating forage legumes with rhizobia strains is widespread. It is assumed that the inoculated strain determines the performance of the symbiosis and nitrogen fixation rates. However, native-naturalized strains can be competitive, and actual nodule occupancy is often scarcely investigated. In consequence, failures in establishment, and low productivity attributed to poor performance of the inoculant may merely reflect the absence of the inoculated strain in the nodules. This study lays out a strategy followed for selecting a Rhizobium leguminosarum sv. trifolii strain for white clover (Trifolium repens) with competitive nodule occupancy. First, the competitiveness of native-naturalized rhizobia strains selected for their efficiency to fix N2 in clover and tagged with gusA was evaluated in controlled conditions with different soils. Second, three of these experimental strains with superior nodule occupancy plus the currently recommended commercial inoculant, an introduced strain, were tested in the field in 2 years and at two sites. Plant establishment, herbage productivity, fixation of atmospheric N2 (15N natural abundance), and nodule occupancy (ERIC-PCR genomic fingerprinting) were measured. In both years and sites, nodule occupancy of the native-naturalized experimental strains was either higher or similar to that of the commercial inoculant in both primary and secondary roots. The difference was even greater in stolon roots nodules, where nodule occupancy of the native-naturalized experimental strains was at least five times greater. The amount of N fixed per unit plant mass was consistently higher with native-naturalized experimental strains, although the proportion of N derived from atmospheric fixation was similar for all strains. Plant establishment and herbage production, as well as clover contribution in oversown native grasslands, were either similar or higher in white clover inoculated with the native-naturalized experimental strains. These results support the use of our implemented strategy for developing a competitive inoculant from native-naturalized strains.}, } @article {pmid31015472, year = {2019}, author = {Molina-Santiago, C and Pearson, JR and Navarro, Y and Berlanga-Clavero, MV and Caraballo-Rodriguez, AM and Petras, D and García-Martín, ML and Lamon, G and Haberstein, B and Cazorla, FM and de Vicente, A and Loquet, A and Dorrestein, PC and Romero, D}, title = {The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1919}, doi = {10.1038/s41467-019-09944-x}, pmid = {31015472}, issn = {2041-1723}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; S10 RR029121/RR/NCRR NIH HHS/United States ; BacBio 637971//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/International ; AGL2016-78662-R//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/International ; }, mesh = {Bacillus subtilis/*genetics/growth & development/metabolism ; Bacterial Proteins/genetics/metabolism ; Colony Count, Microbial ; Cucurbitaceae/*microbiology ; Extracellular Matrix/*metabolism ; *Gene Expression Regulation, Bacterial ; Microbial Interactions/*genetics ; Phosphotransferases/genetics/metabolism ; Plant Leaves/microbiology ; Protein Kinases/genetics/metabolism ; Pseudomonas chlororaphis/*genetics/growth & development/metabolism ; Seeds/microbiology ; Spores, Bacterial/genetics/growth & development/metabolism ; Symbiosis/physiology ; Type VI Secretion Systems/genetics/metabolism ; }, abstract = {Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds.}, } @article {pmid30953430, year = {2019}, author = {Landmann, F}, title = {The Wolbachia Endosymbionts.}, journal = {Microbiology spectrum}, volume = {7}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.BAI-0018-2019}, pmid = {30953430}, issn = {2165-0497}, mesh = {Animals ; Arthropods/microbiology ; Filarioidea/microbiology ; Host Microbial Interactions/*physiology ; Insecta/microbiology ; Symbiosis ; Wolbachia/classification/genetics/pathogenicity/*physiology ; }, abstract = {The Wolbachia endosymbionts encompass a large group of intracellular bacteria of biomedical and veterinary relevance, closely related to Anaplasma, Ehrlichia, and Rickettsia. This genus of Gram-negative members of the Alphaproteobacteria does not infect vertebrates but is instead restricted to ecdysozoan species, including terrestrial arthropods and a family of parasitic filarial nematodes, the Onchocercidae. The Wolbachia profoundly impact not only the ecology and evolution but also the reproductive biology of their hosts, through a wide range of symbiotic interactions. Because they are essential to the survival and reproduction of their filarial nematode hosts, they represent an attractive target to fight filariasis. Their abilities to spread through insect populations and to affect vector competence through pathogen protection have made Wolbachia a staple for controlling vector-borne diseases. Estimated to be present in up to 66% of insect species, the Wolbachia are probably the most abundant endosymbionts on earth. Their success resides in their unique capacity to infect and manipulate the host germ line to favor their vertical transmission through the maternal lineage. Because the Wolbachia resist genetic manipulation and growth in axenic culture, our understanding of their biology is still in its infancy. Despite these limitations, the "-omics" revolution combined with the use of well-established and emerging experimental host models is accelerating our comprehension of the host phenotypes caused by Wolbachia, and the identification of Wolbachia effectors is ongoing.}, } @article {pmid31063471, year = {2019}, author = {Joshi, RK and Mehendale, SM}, title = {Determinants of consistently high HIV prevalence in Indian Districts: A multi-level analysis.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216321}, doi = {10.1371/journal.pone.0216321}, pmid = {31063471}, issn = {1932-6203}, abstract = {INTRODUCTION: Factors associated with persistently high Human Immunodeficiency Virus (HIV) prevalence levels in several districts of India are not well understood. This study was undertaken to determine the association of socio-demographic characteristics, economic factors, awareness about HIV and Sexually Transmitted Infections (STIs), and condom use with consistently high HIV prevalence in the Indian districts and to ascertain whether these associations differed across various regions of India.

METHODS: This study was carried out including all 640 districts of India. Secondary analysis of data obtained from the Census of India-2011, HIV Sentinel Surveillance in India and District Level Household Survey-III was done. Population profile, socio-economic characteristics, levels of HIV/STI/condom awareness and condom use, were compared between the districts with and without consistently high HIV prevalence. Due to the presence of collinearity among predictor variables, we used principal component analysis and the principal component scores were included as covariates for further analysis. Considering the districts at level 1 and the regions at level 2, multi-level analysis was done by generalised linear mixed models. Variance partition coefficient and median odds ratio were also calculated.

RESULTS: Sixty-three districts with consistently high HIV prevalence were found clustered in the South and the North-east regions of India. Population size, density and urbanisation were found to be positively associated with consistently high HIV prevalence in these districts. Higher levels of literacy, better socio-economic status, higher proportion of population in reproductive age group and late marriages were positively associated with consistently high HIV prevalence in all regions of India except in the Southern region. Higher levels of knowledge about the role of condoms in HIV prevention and condom use were associated with low HIV prevalence at the district level.

CONCLUSIONS: Considerable heterogeneity among factors associated with consistently high HIV prevalence at the district level in different regions of India necessitates special region-specific strategies for HIV control. Increasing awareness about HIV alone is not sufficient for controlling the HIV epidemic and there is a need to raise knowledge levels about preventive measures against HIV and promote the use of condoms amongst population.}, } @article {pmid31062028, year = {2019}, author = {Becerra-Rivera, VA and Dunn, MF}, title = {Polyamine biosynthesis and biological roles in rhizobia.}, journal = {FEMS microbiology letters}, volume = {366}, number = {7}, pages = {}, doi = {10.1093/femsle/fnz084}, pmid = {31062028}, issn = {1574-6968}, abstract = {Polyamines are ubiquitous molecules containing two or more amino groups that fulfill varied and often essential physiological and regulatory roles in all organisms. In the symbiotic nitrogen-fixing bacteria known as rhizobia, putrescine and homospermidine are invariably produced while spermidine and norspermidine synthesis appears to be restricted to the alfalfa microsymbiont Sinorhizobium meliloti. Studies with rhizobial mutants deficient in the synthesis of one or more polyamines have shown that these compounds are important for growth, stress resistance, motility, exopolysaccharide production and biofilm formation. In this review, we describe these studies and examine how polyamines are synthesized and regulated in rhizobia.}, } @article {pmid31062009, year = {2019}, author = {Dhanjal, NI and Sharma, S and Skalny, AV and Skalnaya, MG and Ajsuvakova, OP and Tinkov, AA and Zhang, F and Guo, X and Prabhu, KS and Tejo Prakash, N}, title = {Selenium-rich maize modulates the expression of prostaglandin genes in lipopolysaccharide-stimulated RAW264.7 macrophages.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/c9fo00186g}, pmid = {31062009}, issn = {2042-650X}, abstract = {Cell signaling is necessary for the organs to co-ordinate with the whole body and it includes response to external stimuli, inflammation, hormonal secretions and other various metabolic functions. In the present study, we have focused on the inflammatory signals modulated by the reactive oxygen and nitrogen species (RONS). Under homeostatic conditions, these species turn on the COX-1-dependent arachidonic acid (AA) pathway towards the release of anti-inflammatory enzymes. However, the excess release of these ions induces negative effects in the form of inflammation by turning on the COX-2-dependent AA pathway to release pro-inflammatory enzymes. In the present study, we observed the shunting of the COX-2-dependent AA pathway towards the release of anti-inflammatory enzymes with the supplementation of organic dietary selenium in the form of seleniferous maize extracts. We observed that 500 nM selenium concentration in Se-maize extracts downregulated the COX-2 and mPGES-1 expressions by 3.8- and 3.2-fold and upregulated the GPx-1 and H-PGDS expressions by 5.0- and 5.4-fold, respectively. To facilitate more availability of Se from the dietary matrices, Se-maize extracts were incubated with rMETase. It was observed that the enzyme-treated cells increased the downregulation of COX-2 and mPGES-1 expressions by 24.8- and 21.0-fold and the upregulation of GPx-1 and H-PGDS expressions by 13.2- and 16.5-fold, respectively.}, } @article {pmid31061106, year = {2019}, author = {Pislariu, CI and Sinharoy, S and Torres-Jerez, I and Nakashima, J and Blancaflor, EB and Udvardi, MK}, title = {The nodule-specific PLAT-domain protein NPD1 is required for nitrogen-fixing symbiosis.}, journal = {Plant physiology}, volume = {}, number = {}, pages = {}, doi = {10.1104/pp.18.01613}, pmid = {31061106}, issn = {1532-2548}, abstract = {Symbiotic nitrogen fixation by rhizobia in legume root nodules is a key source of nitrogen for sustainable agriculture. Genetic approaches have revealed important roles for only a few of the thousands of plant genes expressed during nodule development and symbiotic nitrogen fixation. Previously, we isolated over one hundred nodulation and nitrogen fixation mutants from a population of Tnt1-insertion mutants of Medigaco truncatula (Pislariu et al., 2011). Using Tnt1 as a tag to identify genetic lesions in these mutants, we discovered that insertions in a nodule-specific PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain-encoding gene, MtNPD1, resulted in development of ineffective nodules. Early stages of nodule development and colonization by the nitrogen fixing bacterium Sinorhizobium meliloti appeared to be normal in the npd1 mutant. However, npd1 nodules ceased to grow after a few days, resulting in abnormally small, ineffective nodules. Rhizobia that colonized developing npd1 nodules did not differentiate completely into nitrogen-fixing bacteroids and quickly degraded. MtNPD1 expression was low in roots but increased significantly in developing nodules four days post-inoculation (DPI), and expression accompanied invading rhizobia in the nodule infection zone and into the distal nitrogen fixation zone. A functional MtNPD1:GFP fusion protein localized in the space surrounding symbiosomes in infected cells. When ectopically expressed in tobacco (Nicotiana tabacum) leaves, MtNPD1 co-localized with vacuoles and the endoplasmic reticulum. MtNPD1 belongs to a cluster of 5 nodule-specific single PLAT domain-encoding genes, with apparent non-redundant functions.}, } @article {pmid30744948, year = {2019}, author = {Binetruy, F and Bailly, X and Chevillon, C and Martin, OY and Bernasconi, MV and Duron, O}, title = {Phylogenetics of the Spiroplasma ixodetis endosymbiont reveals past transfers between ticks and other arthropods.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {3}, pages = {575-584}, doi = {10.1016/j.ttbdis.2019.02.001}, pmid = {30744948}, issn = {1877-9603}, mesh = {Animals ; Arthropods/*microbiology ; Bacterial Typing Techniques ; Disease Transmission, Infectious ; Female ; Genetic Variation ; Gram-Negative Bacterial Infections/*transmission ; Infectious Disease Transmission, Vertical ; Male ; Multilocus Sequence Typing ; *Phylogeny ; Spiroplasma/classification/*genetics ; *Symbiosis ; Ticks/*microbiology ; }, abstract = {The bacterium Spiroplasma ixodetis is a maternally inherited endosymbiont primarily described from ticks but also found widespread across other arthropods. While it has been identified as a male-killing agent in some insect species, the consequences of infection with S. ixodetis in ticks are entirely unknown, and it is unclear how this endosymbiont spreads across tick species. Here, we have investigated this aspect through the examination of the diversity and evolutionary history of S. ixodetis infections in 12 tick species and 12 other arthropod species. Using a multi-locus typing approach, we identified that ticks harbor a substantial diversity of divergent S. ixodetis strains. Phylogenetic investigations revealed that these S. ixodetis strains do not cluster within a tick-specific subclade but rather exhibit distinct evolutionary origins. In their past, these strains have undergone repeated horizontal transfers between ticks and other arthropods, including aphids and flies. This diversity pattern strongly suggests that maternal inheritance and horizontal transfers are key drivers of S. ixodetis spread, dictating global incidence of infections across tick communities. We do not, however, detect evidence of S. ixodetis-based male-killing since we observed that infections were widely present in both males and females across populations of the African blue tick Rhipicephalus decoloratus.}, } @article {pmid30269177, year = {2019}, author = {Chevrette, MG and Currie, CR}, title = {Emerging evolutionary paradigms in antibiotic discovery.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {46}, number = {3-4}, pages = {257-271}, doi = {10.1007/s10295-018-2085-6}, pmid = {30269177}, issn = {1476-5535}, support = {T32 GM008505/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; U19 A1109673//National Institutes of Health/ ; T32 GM008505//National Institute of General Medical Sciences/ ; }, mesh = {Actinobacteria/metabolism ; Anti-Bacterial Agents/*chemistry ; Bacteria/metabolism ; Biological Products/*chemistry ; Biosynthetic Pathways ; *Drug Discovery ; Drug-Related Side Effects and Adverse Reactions ; Evolution, Molecular ; Fungi/metabolism ; Symbiosis ; }, abstract = {Antibiotics revolutionized medicine and remain its cornerstone. Despite their global importance and the continuous threat of resistant pathogens, few antibiotics have been discovered in recent years. Natural products, especially the secondary metabolites of Actinobacteria, have been the traditional discovery source of antibiotics. In nature, the chemistry of antibiotic natural products is shaped by the unique evolution and ecology of their producing organisms, yet these influences remain largely unknown. Here, we highlight the ecology of antibiotics employed by microbes in defensive symbioses and review the evolutionary processes underlying the chemical diversity and activity of microbe-derived antibiotics, including the dynamics of vertical and lateral transmission of biosynthetic pathways and the evolution of efficacy, targeting specificity, and toxicity. We argue that a deeper understanding of the ecology and evolution of microbial interactions and the metabolites that mediate them will allow for an alternative, rational approach to discover new antibiotics.}, } @article {pmid30265339, year = {2018}, author = {Zhao, D and Hoffmann, AA and Zhang, Z and Niu, H and Guo, H}, title = {Interactions Between Facultative Symbionts Hamiltonella and Cardinium in Bemisia tabaci (Hemiptera: Aleyrodoidea): Cooperation or Conflict?.}, journal = {Journal of economic entomology}, volume = {111}, number = {6}, pages = {2660-2666}, doi = {10.1093/jee/toy261}, pmid = {30265339}, issn = {1938-291X}, mesh = {Animals ; Bacteroidaceae/*physiology ; Enterobacteriaceae/*physiology ; Fertility ; Hemiptera/*microbiology ; Reproductive Isolation ; Symbiosis ; }, abstract = {Maternally-inherited facultative symbionts are widespread in most insect species, and it is common that several symbionts coexist in the same host individual. Hence, the symbionts may compete or share for the limited resources and space in the host. The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodoidea), harbors a diverse array of facultative symbionts, among which Hamiltonella sp. and Cardinium sp. are abundant species. Hamiltonella alone increases host fitness, while Cardinium alone confers lower fitness. Locking those different partners together creates ideal situations for the evolution of interactions between symbionts. In this study, we compared the fitness effects of whiteflies infected with only Hamiltonella to Hamiltonella-Cardnium co-infected whiteflies and measured the density of Hamiltonella and Cardinium during host aging, aiming to explore Hamiltonella-Cardinium interactions in B. tabaci. Our results illustrated that Hamiltonella-Cardinium coinfection induced lower fecundity, egg hatchability and number of female offspring, leading to a male-biased sex ratio in offspring, while there is no evidence for reproductive incompatibility between the infections. We also found an antagonistic interaction between Hamiltonella and Cardinium given that the density of the latter increased across time and led to a decrease of Hamiltonella density, which may be the underlying causes of the fitness cost in double-infected B. tabaci. Exploring the ecological consequences of co-infections of these different symbionts helps us to understand the nature of host-symbiont interactions in this species and potential for evolutionary conflict.}, } @article {pmid31059742, year = {2019}, author = {Chaubey, MG and Patel, SNK and Rastogi, RP and Srivastava, PL and Singh, AK and Madamwar, D and Singh, NK}, title = {Therapeutic potential of cyanobacterial pigment protein phycoerythrin: in silico and in vitro study of BACE1 interaction and in vivo Aβ reduction.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijbiomac.2019.05.006}, pmid = {31059742}, issn = {1879-0003}, abstract = {Cyanobacteria are an immense source of innovative classes of pharmacologically active compounds exhibiting various biological activities ranging from antioxidants, antibiotics, anticancer, anti-inflammatory to anti-Alzheimer's disease. In the present study, we primarily targeted the inhibition of Beta-site amyloid precursor protein cleaving enzyme-1 (BACE1) by a naturally occurring cyanobacterial protein phycoerythrin (C-PE). BACE1 cleaves amyloid-β precursor protein (APP) and leads to accumulation of neurotoxic amyloid beta (Aβ) plaques in the brain, as an attribute of Alzheimer's disease (AD). Inhibition of BACE1 was measured in terms of their association and dissociation rate constants, thermodynamics of binding using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). The kinetic parameters for enzyme activity were also measured using synthetic decapeptide as a substrate. We further validated the potential of PE by in-vivo histopathological staining of Aβ aggregate mutant Caenorhabditis elegans CL4176 by Thioflavin-T. The present studies pave the way for the application of naturally occurring C-PE as a putative therapeutic drug for the AD.}, } @article {pmid31059378, year = {2019}, author = {Aasen, DM and Vergara, MN}, title = {New Drug Discovery Paradigms for Retinal Diseases: A Focus on Retinal Organoids.}, journal = {Journal of ocular pharmacology and therapeutics : the official journal of the Association for Ocular Pharmacology and Therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1089/jop.2018.0140}, pmid = {31059378}, issn = {1557-7732}, abstract = {Retinal disease represents a growing global problem, both in terms of quality of life and economic impact, yet new therapies are not being developed at a sufficient rate to meet this mounting need. In this context, retinal organoids derived from human induced pluripotent stem cells hold significant promise for improving upon the current drug development process, increasing the speed and efficiency of moving potential therapeutic agents from bench to bedside. These organoid systems display the cell-cell and cell-matrix interactions, cellular heterogeneity, and physiological responses reflective of human biology and, thus, have the ability to replicate retinal disease pathology in a way that 2-dimensional cell cultures and animal models have been heretofore unable to achieve. However, organoid technology is not yet mature enough to meet the high-throughput demands of the first stages of drug screening. Hence, the augmentation of the existing drug development pipeline with retinal organoids, rather than the replacement of existing pathway components, may provide a way to harness the benefits of this improved pathological modeling. In this study, we outline the possible benefits of such a symbiosis, discuss other potential uses, and highlight barriers that remain to be overcome.}, } @article {pmid31059123, year = {2019}, author = {Sorroche, F and Walch, M and Zou, L and Rengel, D and Maillet, F and Gibelin-Viala, C and Poinsot, V and Chervin, C and Masson-Boivin, C and Gough, C and Batut, J and Garnerone, AM}, title = {Endosymbiotic Sinorhizobium meliloti modulate Medicago root susceptibility to secondary infection via ethylene.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15883}, pmid = {31059123}, issn = {1469-8137}, abstract = {A complex network of pathways coordinates nodulation and epidermal root hair infection in the symbiotic interaction between rhizobia and legume plants. Whereas nodule formation was known to be autoregulated, it was so far unclear whether a similar control is exerted on the infection process. We assessed the capacity of Medicago plants nodulated by Sinorhizobium meliloti to modulate root susceptibility to secondary bacterial infection or to purified Nod factors in split-root and volatile assays using bacterial and plant mutant combinations. Ethylene implication in this process emerged from gas production measurements, use of a chemical inhibitor of ethylene biosynthesis and of a Medicago mutant affected in ethylene signal transduction. We identified a feedback mechanism that we named AOI (for Autoregulation Of Infection) by which endosymbiotic bacteria control secondary infection thread formation by their rhizospheric peers. AOI involves activation of a cAMP cascade in endosymbiotic bacteria, which decreases both root infectiveness and root susceptibility to bacterial Nod factors. These latter two effects are mediated by ethylene. AOI is a novel component of the complex regulatory network controlling the interaction between Sinorhizobium meliloti and its host plants that emphasizes the implication of endosymbiotic bacteria in fine-tuning the interaction. This article is protected by copyright. All rights reserved.}, } @article {pmid31059122, year = {2019}, author = {Zhang, L and Yuan, L and Staehelin, C and Li, Y and Ruan, J and Liang, Z and Xie, Z and Wang, W and Xie, J and Huang, S}, title = {The LYSIN MOTIF-CONTAINING RECEPTOR-LIKE KINASE 1 protein of banana is required for perception of pathogenic and symbiotic signals.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15888}, pmid = {31059122}, issn = {1469-8137}, abstract = {● How plants can distinguish pathogenic and symbiotic fungi remains largely unknown. Here, we characterized the role of MaLYK1, a lysin motif receptor kinase of banana. ● Live cell imaging techniques were used in localization studies. RNAi-silenced transgenic banana plants were generated to analyze the biological role of MaLYK1. The MaLYK1 ectodomain, chitin beads, chitooligosaccharides (COs) and mycorrhizal lipochitooligosaccharides (Myc-LCOs) were used in pull-down assays. Ligand-induced MaLYK1 complex formation was tested in immunoprecipitation experiments. Chimeric receptors were expressed in Lotus japonicus to characterize the function of the MaLYK1 kinase domain. ● MaLYK1 was localized to the plasma membrane. MaLYK1 expression was induced by Foc4 (Fusarium oxysporum f. sp. cubense race 4) and diverse microbe-associated molecular patterns. MaLYK1-silenced banana lines showed reduced chitin-triggered defense responses, increased Foc4-induced disease symptoms and reduced mycorrhization. The MaLYK1 ectodomain was pulled-down by chitin beads and LCOs or COs impaired this process. Ligand treatments induced MaLYK1 complex formation in planta. The kinase domain of MaLYK1 could functionally replace that of the chitin elicitor receptor kinase 1 (AtCERK1) in Arabidopsis thaliana and of a rhizobial LCO (Nod factor) receptor (LjNFR1) in L. japonicus. ● MaLYK1 represents a central molecular switch that controls defense- and symbiosis-related signaling. This article is protected by copyright. All rights reserved.}, } @article {pmid31058335, year = {2019}, author = {Gibelin-Viala, C and Amblard, E and Puech-Pages, V and Bonhomme, M and Garcia, M and Bascaules-Bedin, A and Fliegmann, J and Wen, J and Mysore, KS and le Signor, C and Jacquet, C and Gough, C}, title = {The Medicago truncatula LysM receptor-like kinase LYK9 plays a dual role in immunity and the arbuscular mycorrhizal symbiosis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15891}, pmid = {31058335}, issn = {1469-8137}, abstract = {Plant specific lysin-motif receptor-like kinases (LysM-RLKs) are implicated in the perception of N-acetyl glucosamine-containing compounds, some of which are important signal molecules in plant-microbe interactions. Among these, both lipo-chitooligosaccharides (LCOs) and chitooligosaccharides (COs) are proposed as arbuscular mycorrhizal (AM) fungal symbiotic signals. COs can also activate plant defence, although there is scarce data about CO production by pathogens, especially non-fungal pathogens. We tested Medicago truncatula mutants in the LysM-RLK MtLYK9 for their abilities to interact with the AM fungus Rhizophagus irregularis and the oomycete pathogen Aphanomyces euteiches. This prompted us to analyse whether A. euteiches can produce COs. Compared to wild-type plants, Mtlyk9 mutants had fewer infection events and were less colonised by the AM fungus. In contrast, Mtlyk9 mutants were more heavily infected by A. euteiches and showed more disease symptoms. A. euteiches was also shown to produce short COs, mainly CO II, but also CO III and CO IV, and traces of CO V, both ex planta and in planta. MtLYK9 thus has a dual role in plant immunity and the AM symbiosis, which raises questions about the functioning and the ancestral origins of such a receptor protein. This article is protected by copyright. All rights reserved.}, } @article {pmid31058096, year = {2019}, author = {Moreno-Altamirano, MMB and Kolstoe, SE and Sánchez-García, FJ}, title = {Virus Control of Cell Metabolism for Replication and Evasion of Host Immune Responses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {95}, doi = {10.3389/fcimb.2019.00095}, pmid = {31058096}, issn = {2235-2988}, abstract = {Over the last decade, there has been significant advances in the understanding of the cross-talk between metabolism and immune responses. It is now evident that immune cell effector function strongly depends on the metabolic pathway in which cells are engaged in at a particular point in time, the activation conditions, and the cell microenvironment. It is also clear that some metabolic intermediates have signaling as well as effector properties and, hence, topics such as immunometabolism, metabolic reprograming, and metabolic symbiosis (among others) have emerged. Viruses completely rely on their host's cell energy and molecular machinery to enter, multiply, and exit for a new round of infection. This review explores how viruses mimic, exploit or interfere with host cell metabolic pathways and how, in doing so, they may evade immune responses. It offers a brief outline of key metabolic pathways, mitochondrial function and metabolism-related signaling pathways, followed by examples of the mechanisms by which several viral proteins regulate host cell metabolic activity.}, } @article {pmid31057581, year = {2019}, author = {Hossain, MS and Hoang, NT and Yan, Z and Tóth, K and Meyers, BC and Stacey, G}, title = {Characterization of the Spatial and Temporal Expression of Two Soybean miRNAs Identifies SCL6 as a Novel Regulator of Soybean Nodulation.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {475}, doi = {10.3389/fpls.2019.00475}, pmid = {31057581}, issn = {1664-462X}, abstract = {MicroRNAs (miRNAs) control expression of endogenous target genes through transcript cleavage or translational inhibition. Legume plants can form a specialized organ, the nodule, through interaction with nitrogen fixing soil bacteria. To understand the regulatory roles of miRNAs in the nodulation process, we functionally validated gma-miR171o and gma-miR171q and their target genes in soybean. These two miRNA sequences are identical in sequence but their miRNA genes are divergent and show unique, tissue-specific expression patterns. The expression levels of the two miRNAs are negatively correlated with that of their target genes. Ectopic expression of these miRNAs in transgenic hairy roots resulted in a significant reduction in nodule formation. Both gma-miR171o and gma-miR171q target members of the GRAS transcription factor superfamily, namely GmSCL-6 and GmNSP2. Transient interaction of miRNAs and their target genes in tobacco cells further confirmed their cleavage activity. The results suggest that gma-miR171o and gma-miR171q regulate GmSCL-6 and GmNSP2, which in turn, influence expression of the Nodule inception (NIN), Early Nodulin 40 (ENOD40), and Ethylene Response Factor Required for Nodulation (ERN) genes during the Bradyrhizobium japonicum-soybean nodulation process. Collectively, our data suggest a role for two miRNAs, gma-miR171o and gma-miR171q, in regulating the spatial and temporal aspects of soybean nodulation.}, } @article {pmid31057515, year = {2019}, author = {Methou, P and Hernández-Ávila, I and Aube, J and Cueff-Gauchard, V and Gayet, N and Amand, L and Shillito, B and Pradillon, F and Cambon-Bonavita, MA}, title = {Is It First the Egg or the Shrimp? - Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {808}, doi = {10.3389/fmicb.2019.00808}, pmid = {31057515}, issn = {1664-302X}, abstract = {Rimicaris exoculata is one of the most well-known and emblematic species of endemic vent fauna. Like many other species from these ecosystems, Rimicaris shrimps host important communities of chemosynthetic bacteria living in symbiosis with their host inside the cephalothorax and gut. For many of these symbiotic partners, the mode of transmission remains to be elucidated and the starting point of the symbiotic relationship is not yet defined, but could begin with the egg. In this study, we explored the proliferation of microbial communities on R. exoculata broods through embryonic development using a combination of NGS sequencing and microscopy approaches. Variations in abundance and diversity of egg microbial communities were analyzed in broods at different developmental stages and collected from mothers at two distinct vent fields on the Mid-Atlantic Ridge (TAG and Snake Pit). We also assessed the specificity of the egg microbiome by comparing communities developing on egg surfaces with those developing on the cuticle of pleopods, which are thought to be exposed to similar environmental conditions because the brood is held under the female's abdomen. In terms of abundance, bacterial colonization clearly increases with both egg developmental stage and the position of the egg within the brood: those closest to the exterior having a higher bacterial coverage. Bacterial biomass increase also accompanies an increase of mineral precipitations and thus clearly relates to the degree of exposure to vent fluids. In terms of diversity, most bacterial lineages were found in all samples and were also those found in the cephalothorax of adults. However, significant variation occurs in the relative abundance of these lineages, most of this variation being explained by body surface (egg vs. pleopod), vent field, and developmental stage. The occurrence of symbiont-related lineages of Epsilonbacteraeota, Gammaproteobacteria, Zetaproteobacteria, and Mollicutes provide a basis for discussion on both the acquisition of symbionts and the potential roles of these bacterial communities during egg development.}, } @article {pmid31057502, year = {2019}, author = {Rebollar, EA and Harris, RN}, title = {Editorial: Ecology of Amphibian-Microbial Symbioses.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {766}, doi = {10.3389/fmicb.2019.00766}, pmid = {31057502}, issn = {1664-302X}, } @article {pmid31057424, year = {2019}, author = {Skaljac, M and Vogel, H and Wielsch, N and Mihajlovic, S and Vilcinskas, A}, title = {Transmission of a Protease-Secreting Bacterial Symbiont Among Pea Aphids via Host Plants.}, journal = {Frontiers in physiology}, volume = {10}, number = {}, pages = {438}, doi = {10.3389/fphys.2019.00438}, pmid = {31057424}, issn = {1664-042X}, abstract = {Aphids are economically important pest insects that damage plants by phloem feeding and the transmission of plant viruses. Their ability to feed exclusively on nutritionally poor phloem sap is dependent on the obligatory symbiotic bacterium Buchnera aphidicola, but additional facultative symbionts may also be present, a common example of which is Serratia symbiotica. Many Serratia species secrete extracellular enzymes, so we hypothesised that S. symbiotica may produce proteases that help aphids to feed on plants. Molecular analysis, including fluorescence in situ hybridization (FISH), revealed that S. symbiotica colonises the gut, salivary glands and mouthparts (including the stylet) of the pea aphid Acyrthosiphon pisum, providing a mechanism to transfer the symbiont into host plants. S. symbiotica was also detected in plant tissues wounded by the penetrating stylet and was transferred to naïve aphids feeding on plants containing this symbiont. The maintenance of S. symbiotica by repeated transmission via plants may explain the high frequency of this symbiont in aphid populations. Proteomic analysis of the supernatant from a related but cultivable S. symbiotica strain cultured in liquid medium revealed the presence of known and novel proteases including metalloproteases. The corresponding transcripts encoding these S. symbiotica enzymes were detected in A. pisum and in plants carrying the symbiont, although the mRNA was much more abundant in the aphids. Our data suggest that enzymes from S. symbiotica may facilitate the digestion of plant proteins, thereby helping to suppress plant defense, and that the symbionts are important mediators of aphid-plant interactions.}, } @article {pmid31054574, year = {2019}, author = {Carotenuto, G and Sciascia, I and Oddi, L and Volpe, V and Genre, A}, title = {Size matters: three methods for estimating nuclear size in mycorrhizal roots of Medicago truncatula by image analysis.}, journal = {BMC plant biology}, volume = {19}, number = {1}, pages = {180}, doi = {10.1186/s12870-019-1791-1}, pmid = {31054574}, issn = {1471-2229}, support = {Dottorati di Ricerca XXXI ciclo//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; Ricerca Locale 2016-2017//Università degli Studi di Torino/ ; }, abstract = {BACKGROUND: The intracellular accommodation of arbuscular mycorrhizal (AM) fungi involves a profound molecular reprogramming of the host cell architecture and metabolism, based on the activation of a symbiotic signaling pathway. In analogy with other plant biotrophs, AM fungi are reported to trigger cell cycle reactivation in their host tissues, possibly in support of the enhanced metabolic demand required for the symbiosis.

RESULTS: We here compare the efficiency of three Fiji/ImageJ image analysis plugins in localizing and quantifying the increase in nuclear size - a hallmark of recursive events of endoreduplication - in M. truncatula roots colonized by the AM fungus Gigaspora margarita. All three approaches proved to be versatile and upgradeable, allowing the investigation of nuclear changes in a complex tissue; 3D Object Counter provided more detailed information than both TrackMate and Round Surface Detector plugins. On this base we challenged 3D Object Counter with two case studies: verifying the lack of endoreduplication-triggering responses in Medicago truncatula mutants with a known non-symbiotic phenotype; and analysing the correlation in space and time between the induction of cortical cell division and endoreduplication upon AM colonization. Both case studies revealed important biological aspects. Mutant phenotype analyses have demonstrated that the knock-out mutation of different key genes in the symbiotic signaling pathway block AM-associated endoreduplication. Furthermore, our data show that cell divisions occur during initial stages of root colonization and are followed by recursive activation of the endocycle in preparation for arbuscule accommodation.

CONCLUSIONS: In conclusion, our results indicate 3D Object Counter as the best performing Fiji/ImageJ image analysis script in plant root thick sections and its application highlighted endoreduplication as a major feature of the AM pre-penetration response in root cortical cells.}, } @article {pmid31053805, year = {2019}, author = {Kelsey, R}, title = {Magnetotactic symbiosis in marine sediments.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41579-019-0210-9}, pmid = {31053805}, issn = {1740-1534}, } @article {pmid31053328, year = {2019}, author = {Poinar, G and Vega, FE}, title = {A mid-Cretaceous trichomycete, Priscadvena corymbosa gen. et sp. nov., in Burmese amber.}, journal = {Fungal biology}, volume = {123}, number = {5}, pages = {393-396}, doi = {10.1016/j.funbio.2019.02.007}, pmid = {31053328}, issn = {1878-6146}, abstract = {Priscadvena corymbosa gen. et sp. nov., is described from thalli and sporangia emerging from the oral cavity of a click beetle (Coleoptera: Elateridae) in mid-Cretaceous Burmese amber. The fossil contains several features unknown in extant Trichomycetes including a click beetle (Coleoptera: Elateridae) host, spiny, aerial thalli with the entire thallus bearing numerous small uninucleate globular spores and stalks attached to the oral cavity of its host. Based on these features, P. corymbosa gen. et sp. nov. is placed in a new family, Priscadvenaceae fam. nov., and new order, Priscadvenales ord. nov. The new morphological and behavioral features of the fossil add to the diversity of the trichomycetes as currently defined.}, } @article {pmid31051397, year = {2019}, author = {Moshiri, F and Ebrahimi, H and Ardakani, MR and Rejali, F and Mousavi, SM}, title = {Biogeochemical distribution of Pb and Zn forms in two calcareous soils affected by mycorrhizal symbiosis and alfalfa rhizosphere.}, journal = {Ecotoxicology and environmental safety}, volume = {179}, number = {}, pages = {241-248}, doi = {10.1016/j.ecoenv.2019.04.055}, pmid = {31051397}, issn = {1090-2414}, abstract = {Using of arbuscular mycorrhizal fungi (AMF) has emerged as a new technique to alleviate the toxic metals stress through changing their chemical behavior. The present work was conducted as a factorial arrangement based on a completely randomized design to study the inoculation effects of Glomus intraradices, Glomus mosseae and Glomus etunicatum, on Pb and Zn fractions in the rhizosphere of alfalfa by using rhizobox technique in two agricultural soils with different Zn and Pb concentrations [with low (LH) and high (HH) concentration levels]. The results showed that AMF colonization promoted plant growth and lowered the shoot and root Pb and shoot Zn concentrations in the studied soils compared to uninoculated treatments. Mycorrhizal colonization significantly increased the Ca(NO3)2- extractable Zn and ORG-Zn (respectively 500 and 59.6% more than the uninoculated treatment) and decreased the OXI-Zn (20.32% less than the none inoculated treatment) in the HH soil. By contrast, mycorrhizae slightly increased the CARB, OXI and ORG-Zn forms in the LH soil compared to the uninoculation condition. In the AMF- treated HH soil, an increase was recorded in the Ca(NO3)2- extractable Pb, EXCH-Pb and CARB-Pb (respectively, 17.65, 3.09 and 14.22% compared to the none inoculated treatment) and a decrease in the OXI and ORG-Pb forms (respectively, 28.79 and 13.51% compared to the uninoculated treatment). A reverse status was observed for Pb changes in the LH soil. Depending on the contamination level, the mycorrhizal inoculation differentially affected the Pb and Zn fractions at different distances from the root surface. In the LH soil, at <5 mm distance (i.e. rhizospheric soil), the mycorrhizal inoculation decreased the CARB (about 17.99%) and OXI -Zn (about 29.63%) forms compared to bulk soil (i.e. > 5 mm distance) while ORG-Zn was increased up to 48.63%. However, Ca(NO3)2- extractable, CARB and ORG-Pb was increased in rhizosphere soil (respectively, 89.33, 3.84 and 6.14%) and OXI-Pb was decreased up to 10.36% compared to the bulk soil. In the HH soil, mycorrhizal inoculation increased the CARB and OXI-Zn (respectively, 1.76 and 5.71%) and OXI-Pb fractions (11.56%) compared to the <5 mm distances. Whereas, it reduced the Ca(NO3)2- extractable, EXCH, and ORG-Zn (Respectively, 52.70, 19.19 and 30.16%) and Ca(NO3)2- extractable, CARB and ORG-Pb (respectively, 47.18, 3.70 and 5.79%). These results revealed that depending on the soil contamination level and nature of the element, AMF colonization affects biogeochemical fractions of the metals and their accumulation in the plant tissues.}, } @article {pmid31051335, year = {2019}, author = {Molinero-Rosales, N and Martín-Rodríguez, JÁ and Ho-Plágaro, T and García-Garrido, JM}, title = {Identification and expression analysis of the arbuscular mycorrhiza-inducible Rieske non-heme oxygenase Ptc52 gene from tomato.}, journal = {Journal of plant physiology}, volume = {237}, number = {}, pages = {95-103}, doi = {10.1016/j.jplph.2019.04.009}, pmid = {31051335}, issn = {1618-1328}, abstract = {Arbuscular mycorrhizal (AM) formation enhances plant growth and fitness through improved uptake of water and mineral nutrients in exchange for carbon compounds to the AM fungus. The fungal structure for the reciprocal exchange of nutrients in the symbiosis is the arbuscule, and defence genes expressed in cells containing arbuscules could play a role in the control of hyphal spread and arbuscule formation in the root. We characterized and analyzed the Ptc52 gene from tomato (SlPtc52), a member of the gene family of non-heme oxygenases, whose function has been related to the lethal leaf spot 1 (Lls1) lesion mimic phenotype in plants which is sometimes associated with enhanced disease resistance. Sequence analysis of the SlPTC52 protein revealed conserved typical motifs from non-heme oxygenases, including a Rieske [2Fe-2S] motif, a mononuclear non-heme iron-binding motif and a C-terminal CxxC motif. The level of transcript accumulation was low in stem, flower and green fruits, and high in leaves. Although SlPtc52 expression was perceptible at low levels in roots, its expression increased concomitantly with AM fungus root colonization. Tomato non-mycorrhizal hairy roots expressing the GUS protein under the control of promoter SlPtc52 exhibited GUS activity in the endodermis, the apical meristem of the root tip and in the lateral root primordium. AM fungal colonization also resulted in intensive GUS activity that clearly corresponds to cortical cells containing arbuscules. SlPtc52 gene silencing led to a delay in root colonization and a decrease in arbuscular abundance, suggesting that SlPTC52 plays a regulatory role during AM symbiosis.}, } @article {pmid30979392, year = {2019}, author = {Jaspers, C and Fraune, S and Arnold, AE and Miller, DJ and Bosch, TCG and Voolstra, CR and , }, title = {Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches.}, journal = {Zoology (Jena, Germany)}, volume = {133}, number = {}, pages = {81-87}, doi = {10.1016/j.zool.2019.02.007}, pmid = {30979392}, issn = {1873-2720}, mesh = {Animals ; *Microbiota ; Symbiosis ; }, abstract = {Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of their hosts.}, } @article {pmid30909122, year = {2019}, author = {Cooper, D and Wuebbolt, C and Heryanto, C and Eleftherianos, I}, title = {The prophenoloxidase system in Drosophila participates in the anti-nematode immune response.}, journal = {Molecular immunology}, volume = {109}, number = {}, pages = {88-98}, doi = {10.1016/j.molimm.2019.03.008}, pmid = {30909122}, issn = {1872-9142}, mesh = {Animals ; Catechol Oxidase/genetics/*metabolism ; Cell Differentiation ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/enzymology/genetics/*immunology/*parasitology ; Enzyme Precursors/genetics/*metabolism ; Gene Expression Regulation ; Genes, Insect ; Hemocytes/metabolism ; *Immunity ; Larva ; Nematoda/*physiology ; Survival Analysis ; Symbiosis ; }, abstract = {Drosophila melanogaster relies on an evolutionarily conserved innate immune system to protect itself from potentially deadly pathogens. One of the earliest pathways activated after injury or infection is the melanization pathway, which is responsible for synthesizing and depositing melanin at the site of injury, or onto invading microbes. Three genes, PPO1-3, encoding prophenoloxidase (PPO), an inactive precursor of phenoloxidase (PO), are responsible for the production of melanin after their activation via immune challenge. One pathogen capable of infecting D. melanogaster are entomopathogenic nematodes. Steinernema carpocapsae nematodes exist in a mutualistic relationship with Xenorhabdus nematophila bacteria and are an important biological control agent for controlling insect pests. The nematode-bacteria complex (symbiotic nematodes) can be separated, creating "axenic" nematodes, devoid of their associated bacteria, which are still capable of infecting and killing D. melanogaster. In order to investigate how the D. melanogaster melanization pathway contributes to the anti-nematode immune response, symbiotic and axenic S. carpocapsae were used to study D. melanogaster survival, PPO gene expression, and activation of PPO to PO. Our research suggests that the expression of all three D. melanogaster PPO genes contributes to survival, however only PPO1 or PPO3 appear to be up-regulated during axenic or symbiotic nematode infection. Additionally, we present data suggesting that a complex regulatory system exists between PPOs, potentially allowing for the compensation of PPOs by one another. Further, we found that axenic nematode infection leads to higher levels of PO, suggesting that X. nematophila suppresses this activation. We also report for the first time the differentiation of lamellocytes, a specialized type of hemocytes in D. melanogaster, in response to symbiotic S. carpocapsae nematode infection. Our results suggest an important role played by the melanization pathway in response to nematode infection, and demonstrate how this response can be manipulated by S. carpocapsae nematodes and their mutualistic X. nematophila bacteria.}, } @article {pmid30668658, year = {2019}, author = {Moreira, M and Aguiar, AMF and Bourtzis, K and Latorre, A and Khadem, M}, title = {Wolbachia (Alphaproteobacteria: Rickettsiales) Infections in Isolated Aphid Populations from Oceanic Islands of the Azores Archipelago: Revisiting the Supergroups M and N.}, journal = {Environmental entomology}, volume = {48}, number = {2}, pages = {326-334}, doi = {10.1093/ee/nvy189}, pmid = {30668658}, issn = {1938-2936}, mesh = {Animals ; Aphids/genetics/*microbiology ; Azores ; Symbiosis ; Wolbachia/genetics/*isolation & purification ; }, abstract = {Aphids (Hemiptera: Aphididae) have provided a suitable model to study endosymbionts, their community, and dynamics since the discovery of the obligate endosymbiont Buchnera aphidicola in these organisms. In previous studies, Wolbachia was found in some aphid species. In the present study, we report the prevalence of Wolbachia in aphids sampled from a geographically isolated region (Azores Islands), aiming at a better understanding and characterization of the two newly reported supergroups, M and N. The description of the supergroup M was based on 16S rRNA as well as some protein-coding genes. However, the assignment of the supergroup N was according to 16S rRNA gene sequences of a very few samples. We collected aphid samples and performed phylogenetic analysis of 16S rRNA gene as well as four protein-coding genes (gatB, ftsZ, coxA, and hcpA). The results demonstrate that the 16S rRNA gene data can unambiguously assign the strain supergroup and that the two supergroups, N and M, are equally prevalent in Azorean aphids. The available sequence data for the protein-coding markers can identify supergroup M but the status of supergroup N is inconclusive, requiring further studies. The data suggest that horizontal transmission of Wolbachia (Hertig and Wolbach) between two phylogenetically distant aphid species cohabiting the same plant host.}, } @article {pmid30550591, year = {2018}, author = {Chase, TJ and Pratchett, MS and Frank, GE and Hoogenboom, MO}, title = {Coral-dwelling fish moderate bleaching susceptibility of coral hosts.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208545}, doi = {10.1371/journal.pone.0208545}, pmid = {30550591}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/growth & development/*metabolism ; Chlorophyll/analysis ; *Coral Reefs ; Fishes/*physiology ; Photosynthesis ; Symbiosis ; Temperature ; }, abstract = {Global environmental change has the potential to disrupt well established species interactions, with impacts on nutrient cycling and ecosystem function. On coral reefs, fish living within the branches of coral colonies can promote coral performance, and it has been hypothesized that the enhanced water flow and nutrients provided by fish to corals could ameliorate coral bleaching. The aim of this study was to evaluate the influence of small, aggregating damselfish on the health of their host corals (physiology, recovery, and survival) before, during, and after a thermal-bleaching event. When comparing coral colonies with and without fish, those with resident fish exhibited higher Symbiodinium densities and chlorophyll in both field and experimentally-induced bleaching conditions, and higher protein concentrations in field colonies. Additionally, colonies with damselfish in aquaria exhibited both higher photosynthetic efficiency (FV/FM) during bleaching stress and post-bleaching recovery, compared to uninhabited colonies. These results demonstrate that symbiotic damselfishes, and the services they provide, translate into measureable impacts on coral tissue, and can influence coral bleaching susceptibility/resilience and recovery. By mediating how external abiotic stressors influence coral colony health, damselfish can affect the functional responses of these interspecific interactions in a warming ocean.}, } @article {pmid30496253, year = {2018}, author = {Ikram, M and Ali, N and Jan, G and Jan, FG and Rahman, IU and Iqbal, A and Hamayun, M}, title = {IAA producing fungal endophyte Penicillium roqueforti Thom., enhances stress tolerance and nutrients uptake in wheat plants grown on heavy metal contaminated soils.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0208150}, doi = {10.1371/journal.pone.0208150}, pmid = {30496253}, issn = {1932-6203}, mesh = {Biodegradation, Environmental ; Endophytes/*physiology ; Indoleacetic Acids/*metabolism ; Metals, Heavy/*metabolism ; Nutrients/metabolism ; Penicillium/*physiology ; Seedlings/microbiology/physiology ; Soil Pollutants/*metabolism ; Stress, Physiological ; Symbiosis ; Triticum/*microbiology/physiology ; }, abstract = {Heavy metals contaminated soil is a serious environmental concern that has a negative impact on agriculture and ecosystem. Economical and efficient ways are needed to address this problem worldwide. In this regard, exploration and application of proficient microbial strains that can help the crop plants to thrive in agricultural soils that are greatly contaminated with heavy metals. The present study mainly focused on the effect of IAA producing endophytic fungi Penicillium ruqueforti Thom., on wheat plants cultivated in soil rich in heavy metals (Ni, Cd, Cu, Zn, and Pb). P. ruqueforti has induced great resistance in wheat inoculated plants grown in heavy metal contaminated soil. Application of the isolated strain of P. ruqueforti restricted the transfer of heavy metals from soil to the plants by secreting indole acetic acid (IAA). Furthermore, P. ruqueforti inoculated wheat seedlings watered with waste water had higher plant growth, nutrient uptake and low concentrations of heavy metals in shoot and roots. On the contrary, non-inoculated wheat plants under heavy metal stress had stunted growth with symptoms of chlorosis. From the results, it is concluded that P. ruqueforti inoculation can establish a symbiotic relationship with host plants, which is useful for phytostabilization of heavy metals or in other words helping the host crops to flourish through soil that are highly contaminated with heavy metals.}, } @article {pmid30392387, year = {2019}, author = {Al-Kandari, F and Woodward, MJ}, title = {Genotypic and phenotypic diversity differences of presumptive commensal and avian pathogenic E. coli.}, journal = {British poultry science}, volume = {60}, number = {1}, pages = {79-86}, doi = {10.1080/00071668.2018.1544415}, pmid = {30392387}, issn = {1466-1799}, mesh = {Animals ; *Chickens ; England/epidemiology ; Escherichia coli/*genetics/*pathogenicity/physiology ; Escherichia coli Infections/epidemiology/microbiology/*veterinary ; *Genetic Variation ; Genotype ; Phenotype ; Poultry Diseases/*epidemiology/microbiology ; Symbiosis/genetics ; *Turkeys ; Virulence/genetics ; }, abstract = {1. The objective of the experiment was to characterise the genotypic and phenotypic differences between presumptive commensal E. coli and avian pathogenic E. coli (APEC) of poultry. 2. DNA was extracted from 65 confirmed APEC E. coli from chicken, 100 presumptive commensal E. coli from healthy turkey and 35 from healthy chicken. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and virulence factors genotyping was performed to characterise genetic features. 3. Carbon source utilisation and antimicrobial susceptibility tests were performed to characterise phenotypic features of isolates. 4. The genetic divergence between E. coli strains tested by ERIC-PCR profiles and virulence-associated genes showed a clear genetic separation between E. coli APEC and turkey E. coli strains. 5. The carbon utilisation profile of turkey isolates was different from chicken and APEC strains; whereas antimicrobial susceptibility was highest for turkey isolates (53%), and lowest for APEC strains (33.8%). 6. The study showed a significant negative correlation between utilisation of arabitol and adonitol with different virulence determinants tested, which suggests that the ability to utilise some uncommon carbon sources may be used to discriminate between presumptive commensal E. coli and APEC.}, } @article {pmid29975680, year = {2018}, author = {Pais, IS and Valente, RS and Sporniak, M and Teixeira, L}, title = {Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.}, journal = {PLoS biology}, volume = {16}, number = {7}, pages = {e2005710}, pmid = {29975680}, issn = {1545-7885}, mesh = {Animals ; Bacteria/growth & development/*metabolism ; Biodiversity ; Drosophila melanogaster/*microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Models, Biological ; Species Specificity ; Symbiosis/*physiology ; }, abstract = {Animals live together with diverse bacteria that can impact their biology. In Drosophila melanogaster, gut-associated bacterial communities are relatively simple in composition but also have a strong impact on host development and physiology. It is generally assumed that gut bacteria in D. melanogaster are transient and their constant ingestion with food is required to maintain their presence in the gut. Here, we identify bacterial species from wild-caught D. melanogaster that stably associate with the host independently of continuous inoculation. Moreover, we show that specific Acetobacter wild isolates can proliferate in the gut. We further demonstrate that the interaction between D. melanogaster and the wild isolated Acetobacter thailandicus is mutually beneficial and that the stability of the gut association is key to this mutualism. The stable population in the gut of D. melanogaster allows continuous bacterial spreading into the environment, which is advantageous to the bacterium itself. The bacterial dissemination is in turn advantageous to the host because the next generation of flies develops in the presence of this particularly beneficial bacterium. A. thailandicus leads to a faster host development and higher fertility of emerging adults when compared to other bacteria isolated from wild-caught flies. Furthermore, A. thailandicus is sufficient and advantageous when D. melanogaster develops in axenic or freshly collected figs, respectively. This isolate of A. thailandicus colonizes several genotypes of D. melanogaster but not the closely related D. simulans, indicating that the stable association is host specific. This work establishes a new conceptual model to understand D. melanogaster-gut microbiota interactions in an ecological context; stable interactions can be mutualistic through microbial farming, a common strategy in insects. Moreover, these results develop the use of D. melanogaster as a model to study gut microbiota proliferation and colonization.}, } @article {pmid29852240, year = {2018}, author = {Cording, S and Medvedovic, J and Lecuyer, E and Aychek, T and Eberl, G}, title = {Control of pathogens and microbiota by innate lymphoid cells.}, journal = {Microbes and infection}, volume = {20}, number = {6}, pages = {317-322}, doi = {10.1016/j.micinf.2018.05.003}, pmid = {29852240}, issn = {1769-714X}, mesh = {Animals ; Cytokines/immunology ; Homeostasis/immunology ; Host-Pathogen Interactions/*immunology ; Humans ; *Immunity, Innate ; Intestinal Mucosa/immunology ; Lymphocytes/cytology/*immunology ; Microbiota/*immunology ; Respiratory Mucosa/immunology ; Symbiosis/immunology ; }, abstract = {Innate lymphoid cells (ILCs) are the innate counterpart of T cells. Upon infection or injury, ILCs react promptly to direct the developing immune response to the one most adapted to the threat facing the organism. Therefore, ILCs play an important role early in resistance to infection, but also to maintain homeostasis with the symbiotic microbiota following perturbations induced by diet and pathogens. Such roles of ILCs have been best characterized in the intestine and lung, mucosal sites that are exposed to the environment and are therefore colonized with diverse but specific types of microbes. Understanding the dialogue between pathogens, microbiota and ILCs may lead to new strategies to re-inforce immunity for prevention, vaccination and therapy.}, } @article {pmid29291350, year = {2018}, author = {Smith, TE and Pond, CD and Pierce, E and Harmer, ZP and Kwan, J and Zachariah, MM and Harper, MK and Wyche, TP and Matainaho, TK and Bugni, TS and Barrows, LR and Ireland, CM and Schmidt, EW}, title = {Accessing chemical diversity from the uncultivated symbionts of small marine animals.}, journal = {Nature chemical biology}, volume = {14}, number = {2}, pages = {179-185}, pmid = {29291350}, issn = {1552-4469}, support = {R01 GM102602/GM/NIGMS NIH HHS/United States ; R01 GM107557/GM/NIGMS NIH HHS/United States ; U01 TW006671/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Anti-HIV Agents/*pharmacology ; Bacteria ; Biological Products/*pharmacology ; DNA/analysis ; *Drug Discovery ; Drug Evaluation, Preclinical ; Genomics ; HIV Infections/*drug therapy ; Humans ; Lysinoalanine/chemistry ; Metagenome ; Metagenomics ; *Microbiota ; Multigene Family ; Peptides/pharmacology ; Structure-Activity Relationship ; *Symbiosis ; Synthetic Biology ; T-Lymphocytes/drug effects ; Urochordata ; }, abstract = {Chemistry drives many biological interactions between the microbiota and host animals, yet it is often challenging to identify the chemicals involved. This poses a problem, as such small molecules are excellent sources of potential pharmaceuticals, pretested by nature for animal compatibility. We discovered anti-HIV compounds from small, marine tunicates from the Eastern Fields of Papua New Guinea. Tunicates are a reservoir for new bioactive chemicals, yet their small size often impedes identification or even detection of the chemicals within. We solved this problem by combining chemistry, metagenomics, and synthetic biology to directly identify and synthesize the natural products. We show that these anti-HIV compounds, the divamides, are a novel family of lanthipeptides produced by symbiotic bacteria living in the tunicate. Neighboring animal colonies contain structurally related divamides that differ starkly in their biological properties, suggesting a role for biosynthetic plasticity in a native context wherein biological interactions take place.}, } @article {pmid29255283, year = {2018}, author = {Stappenbeck, TS}, title = {Assigning function to symbionts.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {6-7}, doi = {10.1038/s41564-017-0088-0}, pmid = {29255283}, issn = {2058-5276}, mesh = {Animals ; Bacterial Infections/etiology/*microbiology ; Computational Biology/*methods/trends ; *Disease Models, Animal ; *Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Humans ; Microbiological Techniques/*methods/trends ; *Symbiosis ; }, } @article {pmid31049565, year = {2019}, author = {Samba-Louaka, A and Delafont, V and Rodier, MH and Cateau, E and Héchard, Y}, title = {Free-living amoebae and squatters in the wild: ecological and molecular features.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuz011}, pmid = {31049565}, issn = {1574-6976}, abstract = {Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into 1) the free-living amoeba diversity, assessed with molecular tools 2) the gene functions described to decipher the biology of the amoebae and 3) their interactions with other microorganisms in the environment.}, } @article {pmid31049371, year = {2019}, author = {Rahnama, M and Maclean, P and Fleetwood, DJ and Johnson, RD}, title = {Comparative transcriptomics analysis of compatible wild type and incompatible ΔlaeA mutant strains of Epichloë festucae in association with perennial ryegrass.}, journal = {Data in brief}, volume = {24}, number = {}, pages = {103843}, doi = {10.1016/j.dib.2019.103843}, pmid = {31049371}, issn = {2352-3409}, abstract = {Epichloë festucae fungi form bioprotective endophytic symbioses with perennial ryegrass. Although this interaction is economically important, relatively little is known about the molecular processes and regulatory genes that are involved in establishing a compatible symbiosis. The present study utilised next-generation sequencing to investigate the genes required for establishing a compatible symbiotic interaction between E. festucae and perennial ryegrass. A comparative transcriptomics study, comparing the compatible symbiotic interaction of E. festucae/perennial ryegrass with the incompatible interaction of a ΔlaeA mutant strain of E.festucae/perennial ryegrass, was performed two weeks after inoculation. Differentially expressed genes were identified and classified according to gene ontology and functional annotation analyses. The raw data of this study have been deposited at SRA database with the BioProject ID PRJNA513830.}, } @article {pmid31041384, year = {2019}, author = {Dutta, AK and Choudhary, E and Wang, X and Záhorszka, M and Forbak, M and Lohner, P and Jessen, HJ and Agarwal, N and Korduláková, J and Jessen-Trefzer, C}, title = {Trehalose Conjugation Enhances Toxicity of Photosensitizers against Mycobacteria.}, journal = {ACS central science}, volume = {5}, number = {4}, pages = {644-650}, doi = {10.1021/acscentsci.8b00962}, pmid = {31041384}, issn = {2374-7943}, abstract = {Trehalose is a natural glucose-derived disaccharide found in the cell wall of mycobacteria. It enters the mycobacterial cell through a highly specific trehalose transporter system. Subsequently, trehalose is equipped with mycolic acid species and is incorporated into the cell wall as trehalose monomycolate or dimycolate. Here, we investigate the phototoxicity of several photosensitizer trehalose conjugates and take advantage of the promiscuity of the extracellular Ag85 complex, which catalyzes the attachment of mycolic acids to trehalose and its analogues. We find that processing by Ag85 enriches and tethers photosensitizer trehalose conjugates directly into the mycomembrane. Irradiation of the conjugates triggers singlet oxygen formation, killing mycobacterial cells more efficiently, as compared to photosensitizers without trehalose conjugation. The conjugates are potent antimycobacterial agents that are, per se, affected neither by permeability issues nor by detoxification mechanisms via drug efflux. They could serve as interesting scaffolds for photodynamic therapy of mycobacterial infections.}, } @article {pmid30658519, year = {2019}, author = {Milosevic, I and Vujovic, A and Barac, A and Djelic, M and Korac, M and Radovanovic Spurnic, A and Gmizic, I and Stevanovic, O and Djordjevic, V and Lekic, N and Russo, E and Amedei, A}, title = {Gut-Liver Axis, Gut Microbiota, and Its Modulation in the Management of Liver Diseases: A Review of the Literature.}, journal = {International journal of molecular sciences}, volume = {20}, number = {2}, pages = {}, doi = {10.3390/ijms20020395}, pmid = {30658519}, issn = {1422-0067}, mesh = {Animals ; *Disease Susceptibility ; Dysbiosis ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/immunology/*metabolism/*microbiology ; Humans ; Liver/immunology/*metabolism/pathology ; Liver Diseases/*etiology/*metabolism/pathology/therapy ; Prebiotics ; Probiotics ; Symbiosis ; }, abstract = {The rapid scientific interest in gut microbiota (GM) has coincided with a global increase in the prevalence of infectious and non-infectivous liver diseases. GM, which is also called "the new virtual metabolic organ", makes axis with a number of extraintestinal organs, such as kidneys, brain, cardiovascular, and the bone system. The gut-liver axis has attracted greater attention in recent years. GM communication is bi-directional and involves endocrine and immunological mechanisms. In this way, gut-dysbiosis and composition of "ancient" microbiota could be linked to pathogenesis of numerous chronic liver diseases such as chronic hepatitis B (CHB), chronic hepatitis C (CHC), alcoholic liver disease (ALD), non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), development of liver cirrhosis, and hepatocellular carcinoma (HCC). In this paper, we discuss the current evidence supporting a GM role in the management of different chronic liver diseases and potential new therapeutic GM targets, like fecal transplantation, antibiotics, probiotics, prebiotics, and symbiotics. We conclude that population-level shifts in GM could play a regulatory role in the gut-liver axis and, consequently, etiopathogenesis of chronic liver diseases. This could have a positive impact on future therapeutic strategies.}, } @article {pmid30546098, year = {2019}, author = {Wright, AT}, title = {Gut commensals make choline too.}, journal = {Nature microbiology}, volume = {4}, number = {1}, pages = {4-5}, doi = {10.1038/s41564-018-0325-1}, pmid = {30546098}, issn = {2058-5276}, mesh = {Choline ; *Gastrointestinal Microbiome ; *Phospholipase D ; Phospholipases ; Symbiosis ; }, } @article {pmid30224553, year = {2018}, author = {Chakraborty, R and Lam, V and Kommineni, S and Stromich, J and Hayward, M and Kristich, CJ and Salzman, NH}, title = {Ceftriaxone Administration Disrupts Intestinal Homeostasis, Mediating Noninflammatory Proliferation and Dissemination of Commensal Enterococci.}, journal = {Infection and immunity}, volume = {86}, number = {12}, pages = {}, pmid = {30224553}, issn = {1098-5522}, support = {R01 GM099526/GM/NIGMS NIH HHS/United States ; R01 AI081692/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Bacterial Translocation ; Ceftriaxone/*adverse effects ; Enterococcus faecalis ; Gastrointestinal Microbiome ; Gram-Positive Bacterial Infections ; Homeostasis/*drug effects ; Intestines/*drug effects/microbiology/physiopathology ; Male ; Mice ; Mice, Inbred C57BL ; Symbiosis/*drug effects ; }, abstract = {Enterococci are Gram-positive commensals of the mammalian intestinal tract and harbor intrinsic resistance to broad-spectrum cephalosporins. Disruption of colonization resistance in humans by antibiotics allows enterococci to proliferate in the gut and cause disseminated infections. In this study, we used Enterococcus faecalis (EF)-colonized mice to study the dynamics of enterococci, commensal microbiota, and the host in response to systemic ceftriaxone administration. We found that the mouse model recapitulates intestinal proliferation and dissemination of enterococci seen in humans. Employing a ceftriaxone-sensitive strain of enterococci (E. faecalis JL308), we showed that increased intestinal abundance is critical for the systemic dissemination of enterococci. Investigation of the impact of ceftriaxone on the mucosal barrier defenses and integrity suggested that translocation of enterococci across the intestinal mucosa was not associated with intestinal pathology or increased permeability. Ceftriaxone-induced alteration of intestinal microbial composition was associated with transient increase in the abundance of multiple bacterial operational taxonomic units (OTUs) in addition to enterococci, for example, lactobacilli, which also disseminated to the extraintestinal organs. Collectively, these results emphasize that ceftriaxone-induced disruption of colonization resistance and alteration of mucosal homeostasis facilitate increased intestinal abundance of a limited number of commensals along with enterococci, allowing their translocation and systemic dissemination in a healthy host.}, } @article {pmid30182224, year = {2018}, author = {Baltrus, DA and Spraker, J and Arnold, AE}, title = {Quantifying Re-association of a Facultative Endohyphal Bacterium with a Filamentous Fungus.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1848}, number = {}, pages = {1-11}, doi = {10.1007/978-1-4939-8724-5_1}, pmid = {30182224}, issn = {1940-6029}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacterial Physiological Phenomena/drug effects ; Coculture Techniques ; Fungi/drug effects/*physiology ; Gentamicins/pharmacology ; Phenotype ; *Symbiosis ; }, abstract = {We present here a method to quantify reassociation between facultative endohyphal bacteria and filamentous fungal hosts. Our method takes advantage of the capabilities of fungal cell walls to selectively protect internal bacteria from gentamicin treatment, an assay adapted from studies of internalized bacterial pathogens in cell culture. We report the efficacy of gentamicin to kill planktonic bacteria treated during fungal coculture, and also describe and characterize a sampling scheme to recover and quantify culturable bacteria from the growing edge of fungal mycelium in vitro. This assay enables qualitative and quantitative tests of reassociation capabilities for facultative endohyphal bacteria with host fungi and provides a means to investigate the genetic basis for these associations in a repeatable way.}, } @article {pmid29764656, year = {2018}, author = {Simon, JC and Peccoud, J}, title = {Rapid evolution of aphid pests in agricultural environments.}, journal = {Current opinion in insect science}, volume = {26}, number = {}, pages = {17-24}, doi = {10.1016/j.cois.2017.12.009}, pmid = {29764656}, issn = {2214-5753}, mesh = {*Adaptation, Biological ; Alkenes ; Animals ; Aphids/*genetics/microbiology/physiology ; *Biological Evolution ; Crops, Agricultural ; Insect Control/methods ; Phenotype ; Pyrans ; Symbiosis ; }, abstract = {Aphids constitute a major group of crop pests that inflict serious damages to plants, both directly by ingesting phloem and indirectly as vectors of numerous diseases. In response to intense and repeated human-induced pressures, such as insecticide treatments, the use of resistant plants and biological agents, aphids have developed a series of evolutionary responses relying on adaptation and phenotypic plasticity. In this review, we highlight some remarkable evolutionary responses to anthropogenic pressures in agroecosystems and discuss the mechanisms underlying the ecological and evolutionary success of aphids. We outline the peculiar mode of reproduction, the polyphenism for biologically important traits and the diverse and flexible associations with microbial symbionts as key determinants of adaptive potential and pest status of aphids.}, } @article {pmid29411455, year = {2018}, author = {Ivens, ABF and Gadau, A and Kiers, ET and Kronauer, DJC}, title = {Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1898-1914}, pmid = {29411455}, issn = {1365-294X}, support = {335542//European Research Council/International ; UL1 TR000043/TR/NCATS NIH HHS/United States ; }, mesh = {Acetobacteraceae/genetics/physiology ; Animals ; Ants/genetics/*microbiology ; Aphids/genetics/*microbiology ; Behavior, Animal ; Buchnera/genetics ; Microbiota/*genetics ; Phylogeny ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {Mutualistic interactions with microbes have played a crucial role in the evolution and ecology of animal hosts. However, it is unclear what factors are most important in influencing particular host-microbe associations. While closely related animal species may have more similar microbiota than distantly related species due to phylogenetic contingencies, social partnerships with other organisms, such as those in which one animal farms another, may also influence an organism's symbiotic microbiome. We studied a mutualistic network of Brachymyrmex and Lasius ants farming several honeydew-producing Prociphilus aphids and Rhizoecus mealybugs to test whether the mutualistic microbiomes of these interacting insects are primarily correlated with their phylogeny or with their shared social partnerships. Our results confirm a phylogenetic signal in the microbiomes of aphid and mealybug trophobionts, with each species harbouring species-specific endosymbiont strains of Buchnera (aphids), Tremblaya and Sodalis (mealybugs), and Serratia (both mealybugs and aphids) despite being farmed by the same ants. This is likely explained by strict vertical transmission of trophobiont endosymbionts between generations. In contrast, our results show the ants' microbiome is possibly shaped by their social partnerships, with ants that farm the same trophobionts also sharing strains of sugar-processing Acetobacteraceae bacteria, known from other honeydew-feeding ants and which likely reside extracellularly in the ants' guts. These ant-microbe associations are arguably more "open" and subject to horizontal transmission or social transmission within ant colonies. These findings suggest that the role of social partnerships in shaping a host's symbiotic microbiome can be variable and is likely dependent on how the microbes are transmitted across generations.}, } @article {pmid29411448, year = {2018}, author = {Prest, TL and Kimball, AK and Kueneman, JG and McKenzie, VJ}, title = {Host-associated bacterial community succession during amphibian development.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1992-2006}, doi = {10.1111/mec.14507}, pmid = {29411448}, issn = {1365-294X}, mesh = {Animals ; Bufonidae/genetics/growth & development/*microbiology ; Host Microbial Interactions/*genetics ; Larva/genetics/growth & development/microbiology ; Metamorphosis, Biological/*genetics ; Symbiosis/*genetics ; }, abstract = {Amphibians undergo significant developmental changes during their life cycle, as they typically move from a primarily aquatic environment to a more terrestrial one. Amphibian skin is a mucosal tissue that assembles communities of symbiotic microbiota. However, it is currently not well understood as to where amphibians acquire their skin symbionts, and whether the sources of microbial symbionts change throughout development. In this study, we utilized data collected from four wild boreal toad populations (Anaxyrus boreas); specifically, we sampled the skin bacterial communities during toad development, including eggs, tadpoles, subadults and adults as well as environmental sources of bacteria (water, aquatic sediment and soil). Using 16S rRNA marker gene profiling coupled with SourceTracker, we show that while primary environmental sources remained constant throughout the life cycle, secondary sources of boreal toad symbionts significantly changed with development. We found that toad skin communities changed predictably across development and that two developmental disturbance events (egg hatching and metamorphosis) dictated major changes. Toad skin communities assembled to alternative stable states following each of these developmental disturbances. Using the predicted average rRNA operon copy number of the communities at each life stage, we showed how the skin bacterial communities undergo a successional pattern whereby "fast-growing" (copiotroph) generalist bacteria dominate first before "slow-growing" (oligotroph) specialized bacteria take over. Our study highlights how host-associated bacterial community assembly is tightly coupled to host development and that host-associated communities demonstrate successional patterns akin to those observed in free-living bacteria as well as macrofaunal communities.}, } @article {pmid29290092, year = {2018}, author = {Kessler, RW and Weiss, A and Kuegler, S and Hermes, C and Wichard, T}, title = {Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta).}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1808-1819}, doi = {10.1111/mec.14472}, pmid = {29290092}, issn = {1365-294X}, mesh = {Culture Media/chemistry/metabolism ; Host-Pathogen Interactions/*genetics ; Morphogenesis/drug effects/genetics ; Rhodobacteraceae/*genetics/metabolism ; Sulfhydryl Compounds/metabolism ; Sulfides/metabolism ; Sulfonium Compounds/chemistry/metabolism ; Symbiosis/*genetics ; Ulva/*genetics/growth & development/metabolism/microbiology ; }, abstract = {The marine macroalga Ulva mutabilis (Chlorophyta) develops into callus-like colonies consisting of undifferentiated cells and abnormal cell walls under axenic conditions. Ulva mutabilis is routinely cultured with two bacteria, the Roseovarius sp. MS2 strain and the Maribacter sp. MS6 strain, which release morphogenetic compounds and ensure proper algal morphogenesis. Using this tripartite community as an emerging model system, we tested the hypothesis that the bacterial-algal interactions evolved as a result of mutually taking advantage of signals in the environment. Our study aimed to determine whether cross-kingdom crosstalk is mediated by the attraction of bacteria through algal chemotactic signals. Roseovarius sp. MS2 senses the known osmolyte dimethylsulfoniopropionate (DMSP) released by Ulva into the growth medium. Roseovarius sp. is attracted by DMSP and takes it up rapidly such that DMSP can only be determined in axenic growth media. As DMSP did not promote bacterial growth under the tested conditions, Roseovarius benefited solely from glycerol as the carbon source provided by Ulva. Roseovarius quickly catabolized DMSP into methanethiol (MeSH) and dimethylsulphide (DMS). We conclude that many bacteria can use DMSP as a reliable signal indicating a food source and promote the subsequent development and morphogenesis in Ulva.}, } @article {pmid29230893, year = {2018}, author = {Kohl, KD and Dearing, MD and Bordenstein, SR}, title = {Microbial communities exhibit host species distinguishability and phylosymbiosis along the length of the gastrointestinal tract.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1874-1883}, pmid = {29230893}, issn = {1365-294X}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; T32 DK007673/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Ecology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rodentia/genetics/microbiology ; Ruminococcus/*genetics ; Symbiosis/genetics ; }, abstract = {Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates, it has only been investigated using samples from faeces or the distal colon. Here, we collected the contents of five gut regions from seven rodent species and inventoried the bacterial communities by sequencing the 16S rRNA gene. We investigated how community structures varied across gut regions and whether the pattern of phylosymbiosis was present along the length of the gut. Gut communities varied by host species and gut region, with Oscillospira and Ruminococcus being more abundant in the stomach and hindgut regions. Gut microbial communities were highly distinguishable by host species across all gut regions, with the strength of the discrimination increasing along the length of the gut. Last, the pattern of phylosymbiosis was found in all five gut regions, as well as faeces. Aspects of the gut environment, such as oxygen levels, production of antimicrobials or other factors, may shift microbial communities across gut regions. However, regardless of these differences, host species maintain distinguishable, phylosymbiotic assemblages of microbes that may have functional impacts for the host.}, } @article {pmid29164717, year = {2018}, author = {Raymann, K and Bobay, LM and Moran, NA}, title = {Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {2057-2066}, pmid = {29164717}, issn = {1365-294X}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; R35 GM118038/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bees/drug effects/genetics/*microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Gastrointestinal Tract/drug effects/microbiology ; Genetic Variation/genetics ; Host Microbial Interactions/drug effects/genetics ; Neisseriaceae/drug effects/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; }, abstract = {The gut microbiome plays a key role in animal health, and perturbing it can have detrimental effects. One major source of perturbation to microbiomes, in humans and human-associated animals, is exposure to antibiotics. Most studies of how antibiotics affect the microbiome have used amplicon sequencing of highly conserved 16S rRNA sequences, as in a recent study showing that antibiotic treatment severely alters the species-level composition of the honeybee gut microbiome. But because the standard 16S rRNA-based methods cannot resolve closely related strains, strain-level changes could not be evaluated. To address this gap, we used amplicon sequencing of protein-coding genes to assess effects of antibiotics on fine-scale genetic diversity of the honeybee gut microbiota. We followed the population dynamics of alleles within two dominant core species of the bee gut community, Gilliamella apicola and Snodgrassella alvi, following antibiotic perturbation. Whereas we observed a large reduction in genetic diversity in G. apicola, S. alvi diversity was mostly unaffected. The reduction in G. apicola diversity accompanied an increase in the frequency of several alleles, suggesting resistance to antibiotic treatment. We find that antibiotic perturbation can cause major shifts in diversity and that the extent of these shifts can vary substantially across species. Thus, antibiotics impact not only species composition, but also allelic diversity within species, potentially affecting hosts if variants with particular functions are reduced or eliminated. Overall, we show that amplicon sequencing of protein-coding genes, without clustering into operational taxonomic units, provides an accurate picture of the fine-scale dynamics of microbial communities over time.}, } @article {pmid29134727, year = {2018}, author = {Thairu, MW and Cheng, S and Hansen, AK}, title = {A sRNA in a reduced mutualistic symbiont genome regulates its own gene expression.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1766-1776}, doi = {10.1111/mec.14424}, pmid = {29134727}, issn = {1365-294X}, mesh = {Animals ; Aphids/genetics/microbiology ; Buchnera/*genetics ; *Evolution, Molecular ; Gene Expression Regulation/genetics ; Genome, Bacterial/genetics ; *Proteomics ; RNA/genetics ; RNA, Messenger/genetics ; Symbiosis/*genetics ; }, abstract = {Similar to other nutritional endosymbionts that are obligate for host survival, the mutualistic aphid endosymbiont, Buchnera, has a highly reduced genome with few regulatory elements. Until recently, it was thought that aphid hosts were primarily responsible for regulating their symbiotic relationship. However, we recently revealed that Buchnera displays differential protein regulation, but not mRNA expression. We also identified a number of conserved small RNAs (sRNAs) that are expressed among Buchnera taxa. In this study, we investigate whether differential protein regulation in Buchnera is the result of post-transcriptional gene regulation via sRNAs. We characterize the sRNA profile of two Buchnera life stages: (i) when Buchnera is transitioning from an extracellular proliferating state in aphid embryos and (ii) when Buchnera is in an intracellular nonproliferating state in aphid bacteriocytes (specialized symbiont cells). Overall, we identified 90 differentially expressed sRNAs, 97% of which were upregulated in aphid embryos. Of these sRNAs, the majority were predicted to be involved in the regulation of various metabolic processes, including arginine biosynthesis. Using a heterologous dual expression vector, we reveal for the first time that a Buchnera antisense sRNA can post-transcriptionally interact with its cognate Buchnera coding sequence, carB, a gene involved in arginine biosynthesis. These results corroborate our in vivo RNAseq and proteomic data, where the candidate antisense sRNA carB and the protein CarB are significantly upregulated in aphid embryos. Overall, we demonstrate that Buchnera may regulate gene expression independently from its host by utilizing sRNAs.}, } @article {pmid29124895, year = {2018}, author = {Lawson, CA and Raina, JB and Kahlke, T and Seymour, JR and Suggett, DJ}, title = {Defining the core microbiome of the symbiotic dinoflagellate, Symbiodinium.}, journal = {Environmental microbiology reports}, volume = {10}, number = {1}, pages = {7-11}, doi = {10.1111/1758-2229.12599}, pmid = {29124895}, issn = {1758-2229}, mesh = {Animals ; Anthozoa/parasitology ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; Dinoflagellida/*microbiology ; Genome, Bacterial/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Dinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterized the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome. Similar to other systems, bacteria were nearly two orders of magnitude more numerically abundant than Symbiodinium cells and we identified three operational taxonomic units (OTUs) which were present in all cultures. These represented the α-proteobacterium Labrenzia and the γ-proteobacteria Marinobacter and Chromatiaceae. Based on the abundance and functional potential of bacteria harboured in these cultures, their contribution to Symbiodinium physiology can no longer be ignored.}, } @article {pmid29113026, year = {2018}, author = {Bost, A and Franzenburg, S and Adair, KL and Martinson, VG and Loeb, G and Douglas, AE}, title = {How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1848-1859}, doi = {10.1111/mec.14413}, pmid = {29113026}, issn = {1365-294X}, mesh = {Acetobacteraceae/genetics ; Animals ; Biodiversity ; Drosophila melanogaster/*genetics/microbiology ; Enterobacteriaceae/genetics ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; *Transcription, Genetic ; }, abstract = {Despite evidence from laboratory experiments that perturbation of the gut microbiota affects many traits of the animal host, our understanding of the effect of variation in microbiota composition on animals in natural populations is very limited. The core purpose of this study on the fruit fly Drosophila melanogaster was to identify the impact of natural variation in the taxonomic composition of gut bacterial communities on host traits, with the gut transcriptome as a molecular index of microbiota-responsive host traits. Use of the gut transcriptome was validated by demonstrating significant transcriptional differences between the guts of laboratory flies colonized with bacteria and maintained under axenic conditions. Wild Drosophila from six field collections made over two years had gut bacterial communities of diverse composition, dominated to varying extents by Acetobacteraceae and Enterobacteriaceae. The gut transcriptomes also varied among collections and differed markedly from those of laboratory flies. However, no overall relationship between variation in the wild fly transcriptome and taxonomic composition of the gut microbiota was evident at all taxonomic scales of bacteria tested for both individual fly genes and functional categories in Gene Ontology. We conclude that the interaction between microbiota composition and host functional traits may be confounded by uncontrolled variation in both ecological circumstance and host traits (e.g., genotype, age physiological condition) under natural conditions, and that microbiota effects on host traits identified in the laboratory should, therefore, be extrapolated to field population with great caution.}, } @article {pmid31038750, year = {2019}, author = {Gomes, SI and van Bodegom, PM and Merckx, VS and Soudzilovskaia, NA}, title = {Environmental drivers for cheaters of arbuscular mycorrhizal symbiosis in tropical rainforests.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15876}, pmid = {31038750}, issn = {1469-8137}, abstract = {Hundreds of non-photosynthetic mycoheterotrophic plant species cheat the arbuscular mycorrhizal symbiosis. Their patchy local occurrence suggests constraints by biotic and abiotic factors, among which the role of soil chemistry and nutrient status has not been investigated. Here, we examine the edaphic drivers predicting the local-scale distribution of mycoheterotrophic plants in two lowland rainforests in South America. We compared soil chemistry and nutrient status in plots where mycoheterotrophic plants were present to those without these plants. Soil pH, soil nitrate, and the interaction between soil potassium and nitrate concentrations were the best predictors for the occurrence of mycoheterotrophic plants in these tropical rainforests. Mycoheterotrophic plant occurrences decreased with a rise in each of these predictors. This indicates that these plants are associated with low fertility patches. Such low-fertility conditions coincide with conditions that potentially favor a weak mutualism between plants and arbuscular mycorrhizal fungi according to the trade balance model. Our study points out which soil properties favor the cheating of arbuscular mycorrhizal networks in tropical forests. The patchy occurrence of mycoheterotrophic plants suggests that local soil heterogeneity causes the stability of arbuscular mycorrhizal networks to vary at a very small scale. This article is protected by copyright. All rights reserved.}, } @article {pmid31037067, year = {2019}, author = {Pons, I and Renoz, F and Noël, C and Hance, T}, title = {Circulation of the Cultivable Symbiont Serratia symbiotica in Aphids Is Mediated by Plants.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {764}, doi = {10.3389/fmicb.2019.00764}, pmid = {31037067}, issn = {1664-302X}, abstract = {Symbiosis is a common phenomenon in nature that substantially affects organismal ecology and evolution. Fundamental questions regarding how mutualistic associations arise and evolve in nature remain, however, poorly studied. The aphid-Serratia symbiotica bacterium interaction represents a valuable model to study mechanisms shaping these symbiotic interspecific interactions. S. symbiotica strains capable of living independently of aphid hosts have recently been isolated. These strains probably resulted from horizontal transfers and could be an evolutionary link to an intra-organismal symbiosis. In this context, we used the tripartite interaction between the aphid Aphis fabae, a cultivable S. symbiotica bacterium, and the host plant Vicia faba to evaluate the bacterium ability to circulate in this system, exploring its environmental acquisition by aphids and horizontal transmission between aphids via the host plant. Using molecular analyses and fluorescence techniques, we showed that the cultivable S. symbiotica can enter the plants and induce new bacterial infections in aphids feeding on these new infected plants. Remarkably, we also found that the bacterium can have positive effects on the host plant, mainly at the root level. Furthermore, our results demonstrated that cultivable S. symbiotica can be horizontally transferred from infected to uninfected aphids sharing the same plant, providing first direct evidence that plants can mediate horizontal transmission of certain strains of this symbiont species. These findings highlight the importance of considering symbiotic associations in complex systems where microorganisms can circulate between different compartments. Our study can thus have major implications for understanding the multifaceted interactions between microbes, insects and plants.}, } @article {pmid31036911, year = {2019}, author = {Monteil, CL and Vallenet, D and Menguy, N and Benzerara, K and Barbe, V and Fouteau, S and Cruaud, C and Floriani, M and Viollier, E and Adryanczyk, G and Leonhardt, N and Faivre, D and Pignol, D and López-García, P and Weld, RJ and Lefevre, CT}, title = {Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0432-7}, pmid = {31036911}, issn = {2058-5276}, abstract = {Mutualistic symbioses are often a source of evolutionary innovation and drivers of biological diversification1. Widely distributed in the microbial world, particularly in anoxic settings2,3, they often rely on metabolic exchanges and syntrophy2,4. Here, we report a mutualistic symbiosis observed in marine anoxic sediments between excavate protists (Symbiontida, Euglenozoa)5 and ectosymbiotic Deltaproteobacteria biomineralizing ferrimagnetic nanoparticles. Light and electron microscopy observations as well as genomic data support a multi-layered mutualism based on collective magnetotactic motility with division of labour and interspecies hydrogen-transfer-based syntrophy6. The guided motility of the consortia along the geomagnetic field is allowed by the magnetic moment of the non-motile ectosymbiotic bacteria combined with the protist motor activity, which is a unique example of eukaryotic magnetoreception7 acquired by symbiosis. The nearly complete deltaproteobacterial genome assembled from a single consortium contains a full magnetosome gene set8, but shows signs of reduction, with the probable loss of flagellar genes. Based on the metabolic gene content, the ectosymbiotic bacteria are anaerobic sulfate-reducing chemolithoautotrophs that likely reduce sulfate with hydrogen produced by hydrogenosome-like organelles6 underlying the plasma membrane of the protist. In addition to being necessary hydrogen sinks, ectosymbionts may provide organics to the protist by diffusion and predation, as shown by magnetosome-containing digestive vacuoles. Phylogenetic analyses of 16S and 18S ribosomal RNA genes from magnetotactic consortia in marine sediments across the Northern and Southern hemispheres indicate a host-ectosymbiont specificity and co-evolution. This suggests a historical acquisition of magnetoreception by a euglenozoan ancestor from Deltaproteobacteria followed by subsequent diversification. It also supports the cosmopolitan nature of this type of symbiosis in marine anoxic sediments.}, } @article {pmid31036280, year = {2019}, author = {Shah, NK}, title = {Decision Support in Transfusion Medicine and Blood Banking.}, journal = {Clinics in laboratory medicine}, volume = {39}, number = {2}, pages = {269-279}, doi = {10.1016/j.cll.2019.01.006}, pmid = {31036280}, issn = {1557-9832}, abstract = {Clinical decision support (CDS) can greatly enhance patient blood management through optimizing ordering and providing patient-specific information. At present, modeling and prediction have small roles in inventory management; they will likely have increasing applications to help guide donor center collections based on real-time demand to meet more dispersed needs. Transfusion side-effects management for both donor and recipients is an area ripe for intervention by CDS to enable proactive actions. Last, CDS and broader prediction will 1 day function alongside and seamlessly along many of our major processes to create a human-computer symbiosis.}, } @article {pmid31035831, year = {2019}, author = {Pandey, S}, title = {Heterotrimeric G-Protein Signaling in Plants: Conserved and Novel Mechanisms.}, journal = {Annual review of plant biology}, volume = {70}, number = {}, pages = {213-238}, doi = {10.1146/annurev-arplant-050718-100231}, pmid = {31035831}, issn = {1545-2123}, abstract = {Heterotrimeric GTP-binding proteins are key regulators of a multitude of signaling pathways in all eukaryotes. Although the core G-protein components and their basic biochemistries are broadly conserved throughout evolution, the regulatory mechanisms of G proteins seem to have been rewired in plants to meet specific needs. These proteins are currently the focus of intense research in plants due to their involvement in many agronomically important traits, such as seed yield, organ size regulation, biotic and abiotic stress responses, symbiosis, and nitrogen use efficiency. The availability of massive sequence information from a variety of plant species, extensive biochemical data generated over decades, and impressive genetic resources for plant G proteins have made it possible to examine their role, unique properties, and novel regulation. This review focuses on some recent advances in our understanding of the mechanistic details of this critical signaling pathway to enable the precise manipulation and generation of plants to meet future needs.}, } @article {pmid30459180, year = {2019}, author = {Singh, ND}, title = {Wolbachia Infection Associated with Increased Recombination in Drosophila.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {1}, pages = {229-237}, doi = {10.1534/g3.118.200827}, pmid = {30459180}, issn = {2160-1836}, mesh = {Animals ; Drosophila melanogaster/*genetics/microbiology ; Fertility/genetics ; Genome, Insect/genetics ; Reproduction/*genetics ; Symbiosis/*genetics ; Wolbachia/*genetics/pathogenicity ; }, abstract = {Wolbachia is a maternally-transmitted endosymbiotic bacteria that infects a large diversity of arthropod and nematode hosts. Some strains of Wolbachia are parasitic, manipulating host reproduction to benefit themselves, while other strains of Wolbachia exhibit obligate or facultative mutualisms with their host. The effects of Wolbachia on its host are many, though primarily relate to host immune and reproductive function. Here we test the hypothesis that Wolbachia infection alters the frequency of homologous recombination during meiosis. We use D. melanogaster as a model system, and survey recombination in eight wild-derived Wolbachia-infected (strain wMel) and Wolbachia-uninfected strains, controlling for genotype. We measure recombination in two intervals of the genome. Our results indicate that Wolbachia infection is associated with increased recombination in one genomic interval and not the other. The effect of Wolbachia infection on recombination is thus heterogenous across the genome. Our data also indicate a reproductive benefit of Wolbachia infection; infected females show higher fecundity than their uninfected genotypic controls. Given the prevalence of Wolbachia infection in natural populations, our findings suggest that Wolbachia infection is likely to contribute to recombination rate and fecundity variation among individuals in nature.}, } @article {pmid31034469, year = {2019}, author = {Dietel, AK and Merker, H and Kaltenpoth, M and Kost, C}, title = {Selective advantages favour high genomic AT-contents in intracellular elements.}, journal = {PLoS genetics}, volume = {15}, number = {4}, pages = {e1007778}, doi = {10.1371/journal.pgen.1007778}, pmid = {31034469}, issn = {1553-7404}, abstract = {Extrachromosomal genetic elements such as bacterial endosymbionts and plasmids generally exhibit AT-contents that are increased relative to their hosts' DNA. The AT-bias of endosymbiotic genomes is commonly explained by neutral evolutionary processes such as a mutational bias towards increased A+T. Here we show experimentally that an increased AT-content of host-dependent elements can be selectively favoured. Manipulating the nucleotide composition of bacterial cells by introducing A+T-rich or G+C-rich plasmids, we demonstrate that cells containing GC-rich plasmids are less fit than cells containing AT-rich plasmids. Moreover, the cost of GC-rich elements could be compensated by providing precursors of G+C, but not of A+T, thus linking the observed fitness effects to the cytoplasmic availability of nucleotides. Accordingly, introducing AT-rich and GC-rich plasmids into other bacterial species with different genomic GC-contents revealed that the costs of G+C-rich plasmids decreased with an increasing GC-content of their host's genomic DNA. Taken together, our work identifies selection as a strong evolutionary force that drives the genomes of intracellular genetic elements toward higher A+T contents.}, } @article {pmid31033207, year = {2019}, author = {Horta, A and Alves, C and Pinteus, S and Lopes, C and Fino, N and Silva, J and Ribeiro, J and Rodrigues, D and Francisco, J and Rodrigues, A and Pedrosa, R}, title = {Identification of Asparagopsis armata-associated bacteria and characterization of their bioactive potential.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e00824}, doi = {10.1002/mbo3.824}, pmid = {31033207}, issn = {2045-8827}, support = {265896//FP7 Food, Agriculture and Fisheries, Biotechnology/ ; PTDC/MAR-BIO/6149/2014//Fundação para a Ciência e a Tecnologia/ ; SAICTPAC/0019/2015 - LISBOA-01-0145-FEDER-016405//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/103255/2014//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/120250/2016//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/96203/2013//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/97764/2013//Fundação para a Ciência e a Tecnologia/ ; UID/MAR/04292/2019//Fundação para a Ciência e a Tecnologia/ ; Centro-01-0145-FEDER-000018//Centro 2020 program, Portugal 2020, European Union, European Regional Development Fund/ ; }, abstract = {Macroalgae-associated bacteria have already proved to be an interesting source of compounds with therapeutic potential. Accordingly, the main aim of this study was to characterize Asparagopsis armata-associated bacteria community and evaluate their capacity to produce substances with antitumor and antimicrobial potential. Bacteria were selected according to their phenotype and isolated by the streak plate technique. The identification was carried out by the RNA ribosomal 16s gene amplification through PCR techniques. The antimicrobial activities were evaluated against seven microorganisms (Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Salmonella enteritidis, Staphylococcus aureus, Saccharomyces cerevisiae, Candida albicans) by following their growth through spectrophotometric readings. Antitumor activities were evaluated in vitro on human cell lines derived from hepatocellular (HepG-2) and breast carcinoma (MCF-7) using the MTT method. The present work identified a total of 21 bacteria belonging to the genus Vibrio, Staphylococcus, Shewanella, Alteromonadaceae, Bacillus, Cobetia, and Photobacterium, with Vibrio being the most abundant (42.86%). The extract of Shewanella sp. ASP 26 bacterial strain induced the highest antimicrobial activity, namely against Bacillus subtilis and Staphylococcus aureus with an IC50 of 151.1 and 346.8 μg/mL, respectively. These bacteria (Shewanella sp.) were also the ones with highest antitumor potential, demonstrating antiproliferative activity on HepG-2 cells. Asparagopsis armata-associated bacteria revealed to be a potential source of compounds with antitumor and antibacterial activity.}, } @article {pmid31033101, year = {2019}, author = {Taerum, SJ and Jasso-Selles, DE and Wilson, M and Ware, JL and Sillam-Dussès, D and Šobotník, J and Gile, GH}, title = {Molecular Identity of Holomastigotes (Spirotrichonymphea, Parabasalia) with Descriptions of Holomastigotes flavipes n. sp. and Holomastigotes tibialis n. sp.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12739}, pmid = {31033101}, issn = {1550-7408}, abstract = {Holomastigotes is a protist genus (Parabasalia: Spirotrichonymphea) that resides in the hindguts of "lower" termites. It can be distinguished from other parabasalids by spiral flagellar bands that run along the entire length of the cell, an anterior nucleus, a reduced or absent axostyle, the presence of spherical vesicles inside the cells, and the absence of ingested wood particles. Eight species have been described based on their morphology so far, although no molecular data were available prior to this study. We determined the 18S rRNA gene sequences of Holomastigotes from the hindguts of Hodotermopsis sjostedti, Reticulitermes flavipes, Reticulitermes lucifugus, and Reticulitermes tibialis. Phylogenetic analyses placed all sequences in an exclusive and well-supported clade with the type species, Holomastigotes elongatum from R. lucifugus. However, the phylogenetic position of Holomastigotes within the Spirotrichonymphea was not resolved. We describe two new species, Holomastigotes flavipes n. sp. and Holomastigotes tibialis n. sp., inhabiting the hindguts of R. flavipes and R. tibialis, respectively. This article is protected by copyright. All rights reserved.}, } @article {pmid31031793, year = {2019}, author = {Evelin, H and Devi, TS and Gupta, S and Kapoor, R}, title = {Mitigation of Salinity Stress in Plants by Arbuscular Mycorrhizal Symbiosis: Current Understanding and New Challenges.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {470}, doi = {10.3389/fpls.2019.00470}, pmid = {31031793}, issn = {1664-462X}, abstract = {Modern agriculture is facing twin challenge of ensuring global food security and executing it in a sustainable manner. However, the rapidly expanding salinity stress in cultivable areas poses a major peril to crop yield. Among various biotechnological techniques being used to reduce the negative effects of salinity, the use of arbuscular mycorrhizal fungi (AMF) is considered to be an efficient approach for bio-amelioration of salinity stress. AMF deploy an array of biochemical and physiological mechanisms that act in a concerted manner to provide more salinity tolerance to the host plant. Some of the well-known mechanisms include improved nutrient uptake and maintenance of ionic homeostasis, superior water use efficiency and osmoprotection, enhanced photosynthetic efficiency, preservation of cell ultrastructure, and reinforced antioxidant metabolism. Molecular studies in past one decade have further elucidated the processes involved in amelioration of salt stress in mycorrhizal plants. The participating AMF induce expression of genes involved in Na+ extrusion to the soil solution, K+ acquisition (by phloem loading and unloading) and release into the xylem, therefore maintaining favorable Na+:K+ ratio. Colonization by AMF differentially affects expression of plasma membrane and tonoplast aquaporins (PIPs and TIPs), which consequently improves water status of the plant. Formation of AM (arbuscular mycorrhiza) surges the capacity of plant to mend photosystem-II (PSII) and boosts quantum efficiency of PSII under salt stress conditions by mounting the transcript levels of chloroplast genes encoding antenna proteins involved in transfer of excitation energy. Furthermore, AM-induced interplay of phytohormones, including strigolactones, abscisic acid, gibberellic acid, salicylic acid, and jasmonic acid have also been associated with the salt tolerance mechanism. This review comprehensively covers major research advances on physiological, biochemical, and molecular mechanisms implicated in AM-induced salt stress tolerance in plants. The review identifies the challenges involved in the application of AM in alleviation of salt stress in plants in order to improve crop productivity.}, } @article {pmid31031789, year = {2019}, author = {Hajheidari, M and Koncz, C and Bucher, M}, title = {Chromatin Evolution-Key Innovations Underpinning Morphological Complexity.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {454}, doi = {10.3389/fpls.2019.00454}, pmid = {31031789}, issn = {1664-462X}, abstract = {The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.}, } @article {pmid31031015, year = {2019}, author = {Tounsi-Hammami, S and Le Roux, C and Dhane-Fitouri, S and De Lajudie, P and Duponnois, R and Ben Jeddi, F}, title = {Genetic diversity of rhizobia associated with root nodules of white lupin (Lupinus albus L.) in Tunisian calcareous soils.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2019.04.002}, pmid = {31031015}, issn = {1618-0984}, abstract = {With a view to introducing white lupin (Lupinus albus L.) for cultivation in Tunisian calcareous soils, compatible indigenous rhizobia for nitrogen-fixing symbiosis were investigated and characterized. Two L. albus varieties, Mekna and Lumen, were used to trap rhizobia in soil samples collected from 56 sites with high active lime contents (0-49%). Nodulation occurred in only 15 soils. The local variety, Mekna, developed significantly more root nodules and had a trapping capacity in more soils than the imported variety Lumen. A phylogenetic analysis based on the partial 16S-23S ribosomal RNA internal transcribed spacer region (ITS) and multi-locus sequence analysis (MLSA) of three chromosomal housekeeping genes, recA, atpD and dnaK, showed that strains were affiliated to Agrobacterium, Rhizobium, and Neorhizobium, with large internal diversity, including separate lineages. Infectivity tests highlighted some nodulation specificity at the plant variety level, since the strains originating from Mekna could only nodulate this variety, while strains trapped in Lumen could nodulate both varieties. When inoculated, almost all strains resulted in a significant increase in plant shoot dry weight on L. albus. Although Agrobacterium sp. strains isolated from L. albus could nodulate and had a plant growth promoting effect, no nodA and nodC genes could be amplified. This is discussed together with the absence of bradyrhizobia and the general infrequency of L. albus-nodulating rhizobia in Tunisian soils. The adapted and efficient rhizobial strains reported here were promising candidates for inoculant development and represent a contribution towards successful cultivation of L. albus in Tunisia, especially the most promising Mekna variety.}, } @article {pmid30883545, year = {2019}, author = {Valdano, E and Manrubia, S and Gómez, S and Arenas, A}, title = {Endemicity and prevalence of multipartite viruses under heterogeneous between-host transmission.}, journal = {PLoS computational biology}, volume = {15}, number = {3}, pages = {e1006876}, doi = {10.1371/journal.pcbi.1006876}, pmid = {30883545}, issn = {1553-7358}, mesh = {Animals ; Biological Evolution ; *Host-Pathogen Interactions ; Humans ; Models, Theoretical ; Prevalence ; Symbiosis ; Virus Diseases/*transmission ; Virus Replication ; }, abstract = {Multipartite viruses replicate through a puzzling evolutionary strategy. Their genome is segmented into two or more parts, and encapsidated in separate particles that appear to propagate independently. Completing the replication cycle, however, requires the full genome, so that a systemic infection of a host requires the concurrent presence of several particles. This represents an apparent evolutionary drawback of multipartitism, while its advantages remain unclear. A transition from monopartite to multipartite viral forms has been described in vitro under conditions of high multiplicity of infection, suggesting that cooperation between defective mutants is a plausible evolutionary pathway towards multipartitism. However, it is unknown how the putative advantages that multipartitism might enjoy at the microscopic level affect its epidemiology, or if an explicit advantange is needed to explain its ecological persistence. In order to disentangle which mechanisms might contribute to the rise and fixation of multipartitism, we here investigate the interaction between viral spreading dynamics and host population structure. We set up a compartmental model of the spread of a virus in its different forms and explore its epidemiology using both analytical and numerical techniques. We uncover that the impact of host contact structure on spreading dynamics entails a rich phenomenology of ecological relationships that includes cooperation, competition, and commensality. Furthermore, we find out that multipartitism might rise to fixation even in the absence of explicit microscopic advantages. Multipartitism allows the virus to colonize environments that could not be invaded by the monopartite form, while homogeneous contacts between hosts facilitate its spread. We conjecture that these features might have led to an increase in the diversity and prevalence of multipartite viral forms concomitantly with the expansion of agricultural practices.}, } @article {pmid30873932, year = {2019}, author = {Malke, H}, title = {Genetics and Pathogenicity Factors of Group C and G Streptococci.}, journal = {Microbiology spectrum}, volume = {7}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.GPP3-0002-2017}, pmid = {30873932}, issn = {2165-0497}, mesh = {Animals ; Antigens, Bacterial/classification/genetics ; Antigens, Surface/classification ; Bacterial Proteins/classification/genetics ; Cell Membrane ; Cell Wall ; DNA, Bacterial ; Exotoxins/classification/genetics ; Genes, Bacterial ; Host Specificity ; Humans ; *Phylogeny ; Streptococcal Infections/microbiology ; Streptococcus/*classification/*genetics/pathogenicity ; Streptokinase/genetics ; Symbiosis ; Virulence Factors/*genetics ; }, abstract = {Of the eight phylogenetic groups comprising the genus Streptococcus, Lancefield group C and G streptococci (GCS and GGS, resp.) occupy four of them, including the Pyogenic, Anginosus, and Mitis groups, and one Unnamed group so far. These organisms thrive as opportunistic commensals in both humans and animals but may also be associated with clinically serious infections, often resembling those due to their closest genetic relatives, the group A streptoccci (GAS). Advances in molecular genetics, taxonomic approaches and phylogenomic studies have led to the establishment of at least 12 species, several of which being subdivided into subspecies. This review summarizes these advances, citing 264 early and recent references. It focuses on the molecular structure and genetic regulation of clinically important proteins associated with the cell wall, cytoplasmic membrane and extracellular environment. The article also addresses the question of how, based on the current knowledge, basic research and translational medicine might proceed to further advance our understanding of these multifaceted organisms. Particular emphasis in this respect is placed on streptokinase as the protein determining the host specificity of infection and the Rsh-mediated stringent response with its potential for supporting bacterial survival under nutritional stress conditions.}, } @article {pmid30193959, year = {2018}, author = {Porter, NT and Luis, AS and Martens, EC}, title = {Bacteroides thetaiotaomicron.}, journal = {Trends in microbiology}, volume = {26}, number = {11}, pages = {966-967}, doi = {10.1016/j.tim.2018.08.005}, pmid = {30193959}, issn = {1878-4380}, mesh = {Bacteroides thetaiotaomicron/*physiology ; Dietary Fiber/metabolism ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Host Microbial Interactions/*physiology ; Humans ; Microbial Interactions/physiology ; Plant Cells ; Polysaccharides/metabolism ; Symbiosis ; }, abstract = {This infographic on Bacteroides thetaiotaomicron (Bt) explores the ability of this microbe to digest a broad array of complex carbohydrates, alter its surface features, and its emerging role in gastrointestinal diseases. The infographic of Bacteroides thetaiotaomicron (Bt) illustrates two key facets of its symbiotic lifestyle in the human gut: a broad ability to digest dietary fiber polysaccharides and host glycans, and a dynamic cell-surface architecture that promotes both interactions with and evasion of the host immune system. The starch-utilization system (Sus) is a cell-surface and periplasmic system involved in starch cleavage and transport. Over 80 additional Sus-like systems utilize substrates ranging from host glycans to plant cell wall pectins. Bt has evolved intricate strategies to interact with other microbes or its host, including modification of its surface. Some nutrient utilization pathways select for or directly trigger changes in capsular polysaccharide (CPS) expression. Like other fermentative members of the gut microbiome, Bt produces host absorbable short-chain and organic acids, which can all be absorbed by the host as a source of energy.}, } @article {pmid30120872, year = {2019}, author = {Dello Jacovo, E and Valentine, TA and Maluk, M and Toorop, P and Lopez Del Egido, L and Frachon, N and Kenicer, G and Park, L and Goff, M and Ferro, VA and Bonomi, C and James, EK and Iannetta, PPM}, title = {Towards a characterisation of the wild legume bitter vetch (Lathyrus linifolius L. (Reichard) Bässler): heteromorphic seed germination, root nodule structure and N-fixing rhizobial symbionts.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {21}, number = {3}, pages = {523-532}, doi = {10.1111/plb.12902}, pmid = {30120872}, issn = {1438-8677}, support = {FP7/2007-2013///People Programme (Marie Curie Actions) of the European Union Seventh Framework Programme/ ; //Rural and Environment Science and Analytical Services Division/ ; }, mesh = {Fabaceae/*metabolism/*microbiology ; Germination/*physiology ; RNA, Ribosomal, 16S/genetics ; Rhizobium/*physiology ; Root Nodules, Plant/metabolism/microbiology ; Seeds/metabolism/microbiology ; Symbiosis/physiology ; }, abstract = {Lathyrus linifolius L. (Reichard) Bässler (Fabiaceae, bitter vetch) is a nitrogen (N) fixing species. A coloniser of low nutrient (N) soils, it supports biodiversity such as key moth and butterfly species, and its roots are known for their organoleptic and claimed therapeutic properties. Thus, the species has high potential for restoration, conservation, novel cropping and as a model species. The last because of its genetic synteny with important pulse crops. However, regeneration and functional attributes of L. linifolius remain to be characterised. Seeds of L. linifolius were characterised using physical, colorimetric and chemical data. Ultrastructural and functional characterisation of the N-fixing root nodules included immunolabelling with nifH protein antibodies (recognising the N-fixing enzyme, nitrogenase). Endosymbiotic bacteria were isolated from root nodules and characterised phylogenetically using 16S rRNA, nodA and nodD gene sequences. L. linifolius yielded heteromorphic seed of distinct colour classes: green and brown. Seed morphotypes had similar C:N ratios and were equally germinable (ca. 90%) after scarification at differing optimal temperatures (16 and 20 °C). Brown seeds were larger and comprised a larger proportion of the seed batch (69%). L. linifolius root nodules appeared indeterminate in structure, effective (capable of fixing atmospheric N) and having strains very similar to Rhizobium leguminosarum biovar viciae. The findings and rhizobial isolates have potential application for ecological restoration and horticulture using native seeds. Also, the data and rhizobial resources have potential applications in comparative and functional studies with related and socio-economically important crops such as Pisum, Lens and Vicia.}, } @article {pmid30067212, year = {2018}, author = {Barthole, G}, title = {[Never alone. Microorganism, ecology, evolution].}, journal = {Medecine sciences : M/S}, volume = {34}, number = {6-7}, pages = {604-607}, doi = {10.1051/medsci/20183406023}, pmid = {30067212}, issn = {1958-5381}, mesh = {Animals ; *Biological Evolution ; Civilization ; *Ecosystem ; Endophytes/*physiology ; Host Microbial Interactions/physiology ; Humans ; Microbial Interactions/physiology ; Mitochondria/physiology ; Plants/microbiology ; Symbiosis/*physiology ; }, } @article {pmid29909042, year = {2018}, author = {Keen, EC and Dantas, G}, title = {Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity.}, journal = {Trends in microbiology}, volume = {26}, number = {11}, pages = {943-954}, doi = {10.1016/j.tim.2018.05.009}, pmid = {29909042}, issn = {1878-4380}, support = {R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/*virology ; Bacterial Physiological Phenomena ; Bacteriophages/*physiology ; Host Microbial Interactions/immunology/physiology ; Humans ; Lysogeny ; Microbial Interactions/*immunology/*physiology ; Microbiota/*immunology ; Models, Animal ; Phenotype ; Prophages ; Symbiosis ; }, abstract = {Recent years have witnessed an explosion of interest in the human microbiota. Although commensal bacteria have dominated research efforts to date, mounting evidence suggests that endogenous viral populations (the 'virome') play key roles in basic human physiology. The most numerous constituents of the human virome are not eukaryotic viruses but rather bacteriophages, viruses that infect bacteria. Here, we review phages' interactions with their immediate (prokaryotic) and extended (eukaryotic) hosts and with each other, with a particular emphasis on the temperate phages and prophages which dominate the human virome. We also discuss key outstanding questions in this emerging field and emphasize the urgent need for functional studies in animal models to complement previous in vitro work and current computational approaches.}, } @article {pmid29880910, year = {2018}, author = {Yurchenko, T and Ševčíková, T and Přibyl, P and El Karkouri, K and Klimeš, V and Amaral, R and Zbránková, V and Kim, E and Raoult, D and Santos, LMA and Eliáš, M}, title = {A gene transfer event suggests a long-term partnership between eustigmatophyte algae and a novel lineage of endosymbiotic bacteria.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2163-2175}, pmid = {29880910}, issn = {1751-7370}, mesh = {*Gene Transfer, Horizontal ; Genomics ; Operon ; Rickettsiaceae/*genetics ; Stramenopiles/*microbiology ; Symbiosis ; }, abstract = {Rickettsiales are obligate intracellular bacteria originally found in metazoans, but more recently recognized as widespread endosymbionts of various protists. One genus was detected also in several green algae, but reports on rickettsialean endosymbionts in other algal groups are lacking. Here we show that several distantly related eustigmatophytes (coccoid algae belonging to Ochrophyta, Stramenopiles) are infected by Candidatus Phycorickettsia gen. nov., a new member of the family Rickettsiaceae. The genome sequence of Ca. Phycorickettsia trachydisci sp. nov., an endosymbiont of Trachydiscus minutus CCALA 838, revealed genomic features (size, GC content, number of genes) typical for other Rickettsiales, but some unusual aspects of the gene content were noted. Specifically, Phycorickettsia lacks genes for several components of the respiration chain, haem biosynthesis pathway, or c-di-GMP-based signalling. On the other hand, it uniquely harbours a six-gene operon of enigmatic function that we recently reported from plastid genomes of two distantly related eustigmatophytes and from various non-rickettsialean bacteria. Strikingly, the eustigmatophyte operon is closely related to the one from Phycorickettsia, suggesting a gene transfer event between the endosymbiont and host lineages in early eustigmatophyte evolution. We hypothesize an important role of the operon in the physiology of Phycorickettsia infection and a long-term eustigmatophyte-Phycorickettsia coexistence.}, } @article {pmid29871873, year = {2018}, author = {Hunter, P}, title = {The revival of the extended phenotype: After more than 30 years, Dawkins' Extended Phenotype hypothesis is enriching evolutionary biology and inspiring potential applications.}, journal = {EMBO reports}, volume = {19}, number = {7}, pages = {}, pmid = {29871873}, issn = {1469-3178}, mesh = {*Biological Evolution ; Coral Reefs ; Host-Parasite Interactions/*genetics ; *Phenotype ; Symbiosis/*genetics ; }, } @article {pmid31027729, year = {2019}, author = {Duchatelet, L and Delroisse, J and Flammang, P and Mahillon, J and Mallefet, J}, title = {Etmopterus spinax, the velvet belly lanternshark, does not use bacterial luminescence.}, journal = {Acta histochemica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.acthis.2019.04.010}, pmid = {31027729}, issn = {1618-0372}, abstract = {Marine organisms are able to produce light using either their own luminous system, called intrinsic bioluminescence, or symbiotic luminous bacteria, called extrinsic bioluminescence. Among bioluminescent vertebrates, Osteichthyes are known to harbor both types of bioluminescence, while no study has so far addressed the potential use of intrinsic/extrinsic luminescence in elasmobranchs. In sharks, two families are known to emit light: Etmopteridae and Dalatiidae. The deep-sea bioluminescent Etmopteridae, Etmopterus spinax, has received a particular interest over the past fifteen years and its bioluminescence control was investigated in depth. However, the nature of the shark luminous system still remains enigmatic. The present work was undertaken to assess whether the light of this shark species originates from a bioluminescent bacterial symbiosis. Using fluorescent in situ hybridization (FISH) and transmission electron microscopy (TEM) image analyses, this study supports the conclusion that the bioluminescence in the deep-sea lanternshark, Etmopterus spinax, is not of bacterial origin.}, } @article {pmid31025899, year = {2019}, author = {Smigielski, L and Laubach, EM and Pesch, L and Glock, JML and Albrecht, F and Slusarenko, AJ and Panstruga, R and Kuhn, H}, title = {Nodulation induces systemic resistance of Medicago truncatula and Pisum sativum against Erysiphe pisi and primes for powdery mildew-triggered salicylic acid accumulation.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-11-18-0304-R}, pmid = {31025899}, issn = {0894-0282}, abstract = {Plants encounter beneficial and detrimental microorganisms both above- and below ground and the health status of the plant depends on the composition of this pan-microbiome. Beneficial microorganisms contribute to plant nutrition and/or systemically or locally protect plants against pathogens, thus facilitating adaptation to a variety of environments. Induced systemic resistance, caused by root-associated microbes, manifests as above ground resistance against necrotrophic pathogens and is mediated by jasmonic acid/ethylene- signaling. By contrast, systemic acquired resistance relies on salicylic acid (SA) and confers resistance against secondary infection by (hemi)biotrophic pathogens. To investigate whether symbiotic rhizobia that are ubiquitously found in natural ecosystems are able to modulate resistance against biotrophs, we tested the impact of pre-established nodulation of Medicago truncatula and pea (Pisum sativum) plants against infection by the powdery mildew fungus Erysiphe pisi. We found that root symbiosis interfered with fungal penetration of M. truncatula and reduced asexual spore formation on pea leaves independently of symbiotic nitrogen fixation. Improved resistance of nodulated plants correlated with elevated levels of free SA and SA-dependent marker gene expression upon powdery mildew infection. Our results suggest that nodulation primes the plants systemically for E. pisi-triggered SA accumulation and defense gene expression, resulting in increased resistance.}, } @article {pmid31025880, year = {2019}, author = {Togo, A and Dufour, JC and Lagier, JC and Dubourg, G and Raoult, D and Million, M}, title = {Repertoire of human breast and milk microbiota: a systematic review.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2018-0317}, pmid = {31025880}, issn = {1746-0921}, abstract = {Breastfeeding is a major determinant of human health. Breast milk is not sterile and ecological large-scale sequencing methods have revealed an unsuspected microbial diversity that plays an important role. However, microbiological analysis at the species level has been neglected while it is a prerequisite before understanding which microbe is associated with symbiosis or dysbiosis, and health or disease. We review the currently known bacterial repertoire from the human breast and milk microbiota using a semiautomated strategy. Total 242 articles from 38 countries, 11,124 women and 15,489 samples were included. Total 820 species were identified mainly composed of Proteobacteria and Firmicutes. We report variations according to the analytical method (culture or molecular method), the anatomical site (breast, colostrum or milk) and the infectious status (healthy control, mastitis, breast abscess, neonatal infection). In addition, we compared it with the other human repertoires. Finally, we discuss its putative origin and role in health and disease.}, } @article {pmid31024611, year = {2019}, author = {Janwa, H and Massey, SE and Velev, J and Mishra, B}, title = {On the Origin of Biomolecular Networks.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {240}, doi = {10.3389/fgene.2019.00240}, pmid = {31024611}, issn = {1664-8021}, abstract = {Biomolecular networks have already found great utility in characterizing complex biological systems arising from pairwise interactions amongst biomolecules. Here, we explore the important and hitherto neglected role of information asymmetry in the genesis and evolution of such pairwise biomolecular interactions. Information asymmetry between sender and receiver genes is identified as a key feature distinguishing early biochemical reactions from abiotic chemistry, and a driver of network topology as biomolecular systems become more complex. In this context, we review how graph theoretical approaches can be applied not only for a better understanding of various proximate (mechanistic) relations, but also, ultimate (evolutionary) structures encoded in such networks from among all types of variations they induce. Among many possible variations, we emphasize particularly the essential role of gene duplication in terms of signaling game theory, whereby sender and receiver gene players accrue benefit from gene duplication, leading to a preferential attachment mode of network growth. The study of the resulting dynamics suggests many mathematical/computational problems, the majority of which are intractable yet yield to efficient approximation algorithms, when studied through an algebraic graph theoretic lens. We relegate for future work the role of other possible generalizations, additionally involving horizontal gene transfer, sexual recombination, endo-symbiosis, etc., which enrich the underlying graph theory even further.}, } @article {pmid31024597, year = {2019}, author = {Dolgikh, AV and Kirienko, AN and Tikhonovich, IA and Foo, E and Dolgikh, EA}, title = {The DELLA Proteins Influence the Expression of Cytokinin Biosynthesis and Response Genes During Nodulation.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {432}, doi = {10.3389/fpls.2019.00432}, pmid = {31024597}, issn = {1664-462X}, abstract = {The key event that initiates nodule organogenesis is the perception of bacterial signal molecules, the Nod factors, triggering a complex of responses in epidermal and cortical cells of the root. The Nod factor signaling pathway interacts with plant hormones, including cytokinins and gibberellins. Activation of cytokinin signaling through the homeodomain-containing transcription factors KNOX is essential for nodule formation. The main regulators of gibberellin signaling, the DELLA proteins are also involved in regulation of nodule formation. However, the interaction between the cytokinin and gibberellin signaling pathways is not fully understood. Here, we show in Pisum sativum L. that the DELLA proteins can activate the expression of KNOX and BELL transcription factors involved in regulation of cytokinin metabolic and response genes. Consistently, pea la cry-s (della1 della2) mutant showed reduced ability to upregulate expression of some cytokinin metabolic genes during nodulation. Our results suggest that DELLA proteins may regulate cytokinin metabolism upon nodulation.}, } @article {pmid31024537, year = {2019}, author = {Pantazi, E and Powell, N}, title = {Group 3 ILCs: Peacekeepers or Troublemakers? What's Your Gut Telling You?!.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {676}, doi = {10.3389/fimmu.2019.00676}, pmid = {31024537}, issn = {1664-3224}, abstract = {A complex network of interactions exists between the microbiome, the epithelium, and immune cells that reside along the walls of the gastrointestinal tract. The intestinal immune system has been assigned with the difficult task of discriminating between commensal, harmless bacteria, and invading pathogens that translocate across the epithelial monolayer. Importantly, it is trained to maintain tolerance against commensals, and initiate protective immune responses against pathogens to secure intestinal homeostasis. Breakdown of this fine balance between the host and its intestinal microbiota can lead to intestinal inflammation and subsequently to development of inflammatory bowel disease (IBD). A decade since their discovery, innate lymphoid cells (ILCs) are now recognized as important regulators of intestinal homeostasis. ILC3s have emerged as a critical subset in the gut. They are the most phenotypically diverse ILC population and interact directly with numerous different cell types (haematopoietic and non-haematopoeitic), as well as interface with the bacterial flora. In addition to their contribution to intestinal pathogen immunity, they also mitigate against tissue damage occurring following acute injury, by facilitating tissue repair and regeneration, a key function in the maintenance of intestinal homeostasis. However, in chronic inflammation the tables are turned and ILC3s may acquire a pro-inflammatory phenotype in the gut. Chronic ILC activation can lead to persistent inflammation contributing to IBD and/or colorectal cancer. In this review, we discuss current knowledge of group 3 ILCs and their contributions to intestinal homeostasis and disease leading to novel therapeutic targets and clinical approaches that may inform novel treatment strategies for immune-mediated disorders, including IBD.}, } @article {pmid31022406, year = {2019}, author = {Eckstein, S and Heermann, R}, title = {Regulation of Phenotypic Switching and Heterogeneity in Photorhabdus luminescens Cell Populations.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmb.2019.04.015}, pmid = {31022406}, issn = {1089-8638}, abstract = {Phenotypic heterogeneity in bacterial cell populations allows genetically identical organisms to different behavior under similar environmental conditions. The Gram-negative bacterium Photorhabdus luminescens is an excellent organism to study phenotypic heterogeneity since their life cycle involves a symbiotic interaction with soil nematodes as well as a pathogenic association with insect larvae. Phenotypic heterogeneity is highly distinct in P. luminescens. The bacteria exist in two phenotypic forms that differ in various morphologic and phenotypic traits and are therefore distinguished as primary (1°) and secondary (2°) cells. The 1 ̊ cells are bioluminescent, pigmented, produce several secondary metabolites and exo-enzymes, and support nematode growth and development. The 2° cells lack all these 1° specific phenotypes. The entomopathogenic nematodes carry 1° cells in their upper gut and release them into an insect's body after slipping inside. During insect infection up to the half number of 1° cells undergo phenotypic switching and convert to 2° cells. Since the 2° cells are not able to live in nematode symbiosis any more, they cannot re-associate with their symbiosis partners after the infection and remain in the soil. Phenotypic switching in P. luminescens has to be tightly regulated since a high switching frequency would lead to a complete break-down of the nematode-bacteria life cycle. Here, we present the main regulatory mechanisms known to-date that are important for phenotypic switching in P. luminescens cell populations and discuss the biological reason as well as the fate of the 2° cells in the soil.}, } @article {pmid31021099, year = {2019}, author = {Bhattacharya, A and Paul, A and Chakrabarti, D and DasGupta, M}, title = {Gatekeeper-activation loop cross-talk determine distinct autoactivation states of Symbiosis Receptor Kinase.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.9b00071}, pmid = {31021099}, issn = {1520-4995}, abstract = {Plant receptor-like kinases (RLKs) have Tyr in 'gatekeeper' position adjacent to hinge region. Gatekeeper is phosphorylated in several RLKs including symbiosis receptor kinase (SYMRK) but the significance remains unknown. Gatekeeper substitution did not inactivate Arachis hypogaea SYMRK but affected autophosphorylation on selected sites. Herein we show that nonphosphorylatable gatekeepers (Y670F/A) restrict SYMRK to be a Ser/Thr kinase with a basal level of phosphorylation (~5 P/polypeptide, referred as State-I) whereas phosphorylatable gatekeepers (Y670, Y670T) allowed SYMRK to be dual specific (Ser/Thr/Tyr) with a maximal level of phosphorylation (~10 P/polypeptide, referred as State-II). State-II SYMRKs were phosphorylated on gatekeeper residue and the phosphocode in their activation segment was distinct from State-I. The kcat/Km for substrate phosphorylation was ~10 fold higher for State-II, though for autophosphorylation it was comparable with State-I SYMRKs. To identify other determinants of State-I features we mutagenized all the nine sites where phosphorylation was affected by nonphosphorylatable gatekeepers (Y670F/A). Only two such mutants S754A and S757A located on the activation loop failed to phosphorylate on gatekeeper Tyr and restricted SYMRK in State-I. Double mutants like Y670F/S754A retained the features of State-I, but Y670F/S757A was significantly inactivated indicating nonphosphorylatable gatekeeper can bypass phosphorylation of S754 but not S757 in the activation segment. We propose a working model for the hierarchical phosphorylation of SYMRK on gatekeeper and activation segments for its pS757 mediated activation as a Ser/Thr kinase in selfie mode (autophosphorylation) to a pS754/pY670 mediated activation as a Ser/Thr/Tyr kinase that functions in dual mode (both auto and substrate phosphorylation).}, } @article {pmid31020397, year = {2019}, author = {Tsyganova, AV and Seliverstova, EV and Brewin, NJ and Tsyganov, VE}, title = {Bacterial release is accompanied by ectopic accumulation of cell wall material around the vacuole in nodules of Pisum sativum sym33-3 allele encoding transcription factor PsCYCLOPS/PsIPD3.}, journal = {Protoplasma}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00709-019-01383-1}, pmid = {31020397}, issn = {1615-6102}, support = {16-16-10035//Russian Science Foundation/ ; }, abstract = {Pisum sativum symbiotic mutant SGEFix--2 carries the sym33-3 allele of the gene Sym33, encoding transcription factor PsCYCLOPS/PsIPD3. Previously, strong host cell defence reactions were identified in nodules of this mutant. In the present study, new manifestations of defence reactions were revealed in 28-day-old white nodules in which bacterial release had occurred. These nodules were investigated using histochemical staining of pectin and suberin and by immunogold localisation of three components of pectin: highly methyl-esterified homogalacturonan (HG) recognised by monoclonal antibody JIM7, low methyl-esterified HG recognised by JIM5 and linear (1-4)-β-D-galactan side-chain of rhamnogalacturonan I (RG I) recognised by LM5. In the mutant, but not in the wild-type, cell wall material was deposited around the vacuole in the uninfected cells, in cells containing infection threads and in the infected cells. The deposits around the vacuole were marked with JIM7 and LM5 antibodies but not with JIM5, suggesting that they contain newly formed cell wall material. Deposition was accompanied by suberin accumulation. This is the first report that deposition of cell wall material around the vacuole may be associated with the defence reaction in ineffective nodules. In addition, hypertrophic infection droplets labelled with JIM7 were identified. In the matrix of some infection threads, RG I recognised a pectic gel component. Callose deposits in the cell walls and in the walls of infection threads were occasionally observed. The observations suggest that an important function of transcriptional factor CYCLOPS/IPD3 is the suppression of defence reactions during establishment of the legume-rhizobial symbiosis.}, } @article {pmid31018578, year = {2019}, author = {Mamontova, T and Afonin, AM and Ihling, C and Soboleva, A and Lukasheva, E and Sulima, AS and Shtark, OY and Akhtemova, GA and Povydysh, MN and Sinz, A and Frolov, A and Zhukov, VA and Tikhonovich, IA}, title = {Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {8}, pages = {}, doi = {10.3390/molecules24081603}, pmid = {31018578}, issn = {1420-3049}, support = {16-16-00118//Russian Science Foundation/ ; }, abstract = {Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms-rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions depends on plant genotype. Recently, we have shown that, after simultaneous inoculation with Rh and AM, the productivity gain of pea (Pisum sativum L) line K-8274, characterized by high efficiency of interaction with soil microorganisms (EIBSM), was higher in comparison to a low-EIBSM line K-3358. However, the molecular mechanisms behind this effect are still uncharacterized. Therefore, here, we address the alterations in pea seed proteome, underlying the symbiosis-related productivity gain, and identify 111 differentially expressed proteins in the two lines. The high-EIBSM line K-8274 responded to inoculation by prolongation of seed maturation, manifested by up-regulation of proteins involved in cellular respiration, protein biosynthesis, and down-regulation of late-embryogenesis abundant (LEA) proteins. In contrast, the low-EIBSM line K-3358 demonstrated lower levels of the proteins, related to cell metabolism. Thus, we propose that the EIBSM trait is linked to prolongation of seed filling that needs to be taken into account in pulse crop breeding programs. The raw data have been deposited to the ProteomeXchange with identifier PXD013479.}, } @article {pmid30893296, year = {2019}, author = {Fattouh, N and Cazevieille, C and Landmann, F}, title = {Wolbachia endosymbionts subvert the endoplasmic reticulum to acquire host membranes without triggering ER stress.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {3}, pages = {e0007218}, doi = {10.1371/journal.pntd.0007218}, pmid = {30893296}, issn = {1935-2735}, mesh = {Animals ; Cell Line ; Drosophila melanogaster/cytology/*microbiology ; Endoplasmic Reticulum/metabolism/*microbiology ; Gene Expression Profiling ; Golgi Apparatus/metabolism/microbiology ; Host-Pathogen Interactions ; Intracellular Membranes/metabolism/*microbiology ; Stress, Physiological/genetics/*physiology ; Symbiosis/genetics/*physiology ; Vacuoles/microbiology ; Wolbachia/pathogenicity/*physiology ; }, abstract = {The reproductive parasites Wolbachia are the most common endosymbionts on earth, present in a plethora of arthropod species. They have been introduced into mosquitos to successfully prevent the spread of vector-borne diseases, yet the strategies of host cell subversion underlying their obligate intracellular lifestyle remain to be explored in depth in order to gain insights into the mechanisms of pathogen-blocking. Like some other intracellular bacteria, Wolbachia reside in a host-derived vacuole in order to replicate and escape the immune surveillance. Using here the pathogen-blocking Wolbachia strain from Drosophila melanogaster, introduced into two different Drosophila cell lines, we show that Wolbachia subvert the endoplasmic reticulum to acquire their vacuolar membrane and colonize the host cell at high density. Wolbachia redistribute the endoplasmic reticulum, and time lapse experiments reveal tight coupled dynamics suggesting important signalling events or nutrient uptake. Wolbachia infection however does not affect the tubular or cisternal morphologies. A fraction of endoplasmic reticulum becomes clustered, allowing the endosymbionts to reside in between the endoplasmic reticulum and the Golgi apparatus, possibly modulating the traffic between these two organelles. Gene expression analyses and immunostaining studies suggest that Wolbachia achieve persistent infections at very high titers without triggering endoplasmic reticulum stress or enhanced ERAD-driven proteolysis, suggesting that amino acid salvage is achieved through modulation of other signalling pathways.}, } @article {pmid30070649, year = {2019}, author = {Schierstaedt, J and Bziuk, N and Kuzmanović, N and Blau, K and Smalla, K and Jechalke, S}, title = {Role of Plasmids in Plant-Bacteria Interactions.}, journal = {Current issues in molecular biology}, volume = {30}, number = {}, pages = {17-38}, doi = {10.21775/cimb.030.017}, pmid = {30070649}, issn = {1467-3045}, mesh = {*Bacterial Physiological Phenomena ; Endophytes ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Microbiota ; Plant Diseases/microbiology ; *Plant Physiological Phenomena ; Plasmids/*genetics ; Rhizosphere ; *Symbiosis ; }, abstract = {Plants are colonized by diverse microorganisms, which may positively or negatively influence the plant fitness. The positive impact includes nutrient acquisition, enhancement of resistance to biotic and abiotic stresses, both important factors for plant growth and survival, while plant pathogenic bacteria can cause diseases. Plant pathogens are adapted to negate or evade plant defense mechanisms, e.g. by the injection of effector proteins into the host cells or by avoiding the recognition by the host. Plasmids play an important role in the rapid bacterial adaptation to stresses and changing environmental conditions. In the plant environment, plasmids can further provide a selective advantage for the host bacteria, e.g. by carrying genes encoding metabolic pathways, metal and antibiotic resistances, or pathogenicity-related genes. However, we are only beginning to understand the role of mobile genetic elements and horizontal gene transfer for plant-associated bacteria. In this review, we aim to provide a short update on what is known about plasmids and horizontal gene transfer of plant associated bacteria and their role in plant-bacteria interactions. Furthermore, we discuss tools available to study the plant-associated mobilome, its transferability, and its bacterial hosts.}, } @article {pmid30070648, year = {2019}, author = {Holden, N}, title = {You Are What You Can Find to Eat: Bacterial Metabolism in the Rhizosphere.}, journal = {Current issues in molecular biology}, volume = {30}, number = {}, pages = {1-16}, doi = {10.21775/cimb.030.001}, pmid = {30070648}, issn = {1467-3045}, mesh = {Bacteria/*metabolism ; *Bacterial Physiological Phenomena ; *Energy Metabolism ; Metabolic Networks and Pathways ; *Plant Physiological Phenomena ; Plant Roots/*microbiology ; *Rhizosphere ; Symbiosis ; }, abstract = {Metabolism is the underpinning force that sustains life. Within the rhizosphere it is a cyclic process, with substrates flowing between different compartments of the complete soil-plant-microbe system. The physiochemical and structural environment of the rhizosphere is shaped by a combination of plant genotype and soil type, both of which strongly impact the microbial community structure. External influences such as seasonality, the degree of water saturation and anthropomorphic inputs also play a role. Together these factors influence the flux of metabolites through the rhizosphere community, which in turn impacts on plant growth, development and disease. In this review, the focus is on metabolism within the bacterial population of the rhizosphere, since this group covers every type of plant-microbe interaction: from obligately symbiotic to destructively pathogenic, and includes those have little or no direct impact on plant hosts. The focus of the review is on metabolic functions that occur in the rhizosphere either during bacteria-plant interactions or bacteria-bacteria interactions and mainly covers heterotrophic metabolism of organic substrates. As such, many of the autotrophic (and phototrophic) reactions of inorganic compounds are not included.}, } @article {pmid29925618, year = {2018}, author = {Caves, EM and Green, PA and Johnsen, S}, title = {Mutual visual signalling between the cleaner shrimp Ancylomenes pedersoni and its client fish.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1881}, pages = {}, pmid = {29925618}, issn = {1471-2954}, mesh = {*Animal Communication ; Animals ; Cues ; Curacao ; Fishes/*physiology ; Palaemonidae/*physiology ; Photic Stimulation ; *Symbiosis ; *Visual Perception ; }, abstract = {Cleaner shrimp and their reef fish clients are an interspecific mutualistic interaction that is thought to be mediated by signals, and a useful system for studying the dynamics of interspecific signalling. To demonstrate signalling, one must show that purported signals at minimum (a) result in a consistent state change in the receiver and (b) contain reliable information about the sender's intrinsic state or future behaviour. Additionally, signals must be perceptible by receivers. Here, we document fundamental attributes of the signalling system between the cleaner shrimp Ancylomenes pedersoni and its clients. First, we use sequential analysis of in situ behavioural interactions to show that cleaner antenna whipping reliably predicts subsequent cleaning. If shrimp do not signal via antenna whipping, clients triple their likelihood of being cleaned by adopting darker coloration over a matter of seconds, consistent with dark colour change signalling that clients want cleaning. Using experimental manipulations, we found that visual stimuli are sufficient to elicit antenna whipping, and that shrimp are more likely to 'clean' dark than light visual stimuli. Lastly, we show that antenna whipping and colour change are perceptible when accounting for the intended receiver's visual acuity and spectral sensitivity, which differ markedly between cleaners and clients. Our results show that signalling by both cleaners and clients can initiate and mediate their mutualistic interaction.}, } @article {pmid31018159, year = {2019}, author = {Bethencourt, L and Boubakri, H and Taib, N and Normand, P and Armengaud, J and Fournier, P and Brochier-Armanet, C and Herrera-Belaroussi, A}, title = {Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.resmic.2019.04.002}, pmid = {31018159}, issn = {1769-7123}, abstract = {Sporulation is a microbial adaptive strategy to resist inhospitable conditions for vegetative growth and to disperse to colonise more favourable environments. This microbial trait is widespread in Actinobacteria. Among them, Frankia strains are able to differentiate sporangia in pure culture, while others can sporulate even when in symbiosis with sporulation occurring within host cells. The molecular determinants controlling Frankia sporulation have not been yet described. In order to highlight, for the first time, the molecular players potentially involved in Frankia sporulation, we conducted (i) a comparison of protein contents between Frankia spores and hyphae and (ii) a comparative genomic analysis of Frankia proteomes with sporulating and non-sporulating Actinobacteria. Among the main results, glycogen-metabolism related proteins, as well as oxidative stress response and protease-like proteins were overdetected in hyphae, recalling lytic processes that allow Streptomyces cells to erect sporogenic hyphae. Several genes encoding transcriptional regulators, including GntR-like, appeared up-regulated in spores, as well as tyrosinase, suggesting their potential role in mature spore metabolism. Finally, our results highlighted new proteins potentially involved in Frankia sporulation, including a pyrophosphate-energized proton pump and YaaT, described as involved in the phosphorelay allowing sporulation in Bacillus subtilis, leading us to discuss the role of a phosphorelay in Frankia sporulation.}, } @article {pmid31016002, year = {2019}, author = {Pogoda, CS and Keepers, KG and Nadiadi, AY and Bailey, DW and Lendemer, JC and Tripp, EA and Kane, NC}, title = {Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria.}, journal = {Ecology and evolution}, volume = {9}, number = {7}, pages = {4245-4263}, doi = {10.1002/ece3.5056}, pmid = {31016002}, issn = {2045-7758}, abstract = {Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensisand Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.}, } @article {pmid30627568, year = {2018}, author = {Ismail, and Hamayun, M and Hussain, A and Iqbal, A and Khan, SA and Lee, IJ}, title = {Endophytic Fungus Aspergillus japonicus Mediates Host Plant Growth under Normal and Heat Stress Conditions.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {7696831}, doi = {10.1155/2018/7696831}, pmid = {30627568}, issn = {2314-6141}, mesh = {Aspergillus/metabolism/*physiology ; DNA, Ribosomal/genetics ; Endophytes/metabolism/*physiology ; Flavonoids/metabolism ; Heat-Shock Response/*physiology ; Helianthus/metabolism/physiology ; Indoleacetic Acids/metabolism ; Phenol/metabolism ; Phylogeny ; Plant Growth Regulators/*metabolism ; Salicylic Acid/metabolism ; Soybeans/metabolism/physiology ; Stress, Physiological/*physiology ; Symbiosis/*physiology ; }, abstract = {We have isolated an endophytic fungus with heat stress alleviation potential from wild plant Euphorbia indica L. The phylogenetic analysis and 18S rDNA sequence homology revealed that the designated isolate was Aspergillus japonicus EuR-26. Analysis of A. japonicus culture filtrate displayed higher concentrations of salicylic acid (SA), indoleacetic acid (IAA), flavonoids, and phenolics. Furthermore, A. japonicus association with soybean and sunflower had improved plant biomass and other growth features under high temperature stress (40°C) in comparison to endophyte-free plants. In fact, endophytic association mitigated heat stress by negotiating the activities of abscisic acid, catalase, and ascorbic acid oxidase in both soybean and sunflower. The nutritional quality (phenolic, flavonoids, soluble sugars, proteins, and lipids) of the A. japonicus-associated seedlings has also improved under heat stress in comparison to endophyte-free plants. From the results, it is concluded that A. japonicus can modulate host plants growth under heat stress and can be used as thermal stress alleviator in arid and semiarid regions of the globe (where mean summer temperature exceeds 40°C) to sustain agriculture.}, } @article {pmid31011810, year = {2019}, author = {Shitole, AA and Raut, PW and Sharma, N and Giram, P and Khandwekar, AP and Garnaik, B}, title = {Electrospun polycaprolactone/hydroxyapatite/ZnO nanofibers as potential biomaterials for bone tissue regeneration.}, journal = {Journal of materials science. Materials in medicine}, volume = {30}, number = {5}, pages = {51}, doi = {10.1007/s10856-019-6255-5}, pmid = {31011810}, issn = {1573-4838}, abstract = {Fabricating a bioartificial bone graft possessing structural, mechanical and biological properties mimicking the real bone matrix is a major challenge in bone tissue engineering. Moreover, the developed materials are prone to microbial invasion leading to biomaterial centered infections which might limit their clinical translation. In the present study, biomimetic nanofibrous scaffolds of Poly ɛ-caprolactone (PCL)/nano-hydroxyapatite (nHA) were electrospun with 1wt%, 5wt%, 10wt%, 15wt% and 30wt% of zinc oxide (ZnO) nanoparticles in order to understand the optimal concentration range of (ZnO) nanoparticles balancing both biocompatibility and osteoregeneration. The developed nanofibrous scaffolds were successfully characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray analysis (EDAX), contact angle, fourier transform infrared spectroscopy (FTIR), wide-angle X-Ray diffraction (WAXD), brunaueremmett Teller (BET) surface area and tensile testing. Biocompatibility of the developed scaffolds at in vitro level was evaluated by culturing MG-63 cells and investigating the impact on cell viability, proliferation, protein adsorption, alkaline phosphatase (ALP) activity and biomineralization. The PCL/nHA scaffolds exhibited a 1.2-fold increase in cell viability and proliferation, while incorporation of ZnO nanoparticles to PCL/nHA imparted antimicrobial activity to the scaffolds with a progressive increase in the antimicrobial efficacy with increasing ZnO concentration. The results of cell viability were supported by ALP activity and mineralization assay, wherein, PCL/nHA/ZnO scaffolds showed higher ALP activity and better mineralization capacity as compared to pristine PCL. Although, the PCL/nHA/ZnO scaffolds with 10, 15 and 30wt% of ZnO particles exhibited superior antimicrobial efficacy against both gram-negative (E. coli) and gram-positive (S. aureus) bacteria, a significant decrease in the cell viability and mechanical properties was observed at higher concentrations of ZnO namely 15 and 30%. Amongst the various ZnO concentrations studied optimal cell viability, antimicrobial effect and mechanical strength were observed at 10wt.% ZnO concentration. Thus, the present study revealed that the biomimetic tri-component PCL/nHA/ZnO scaffolds with ZnO concentration range of ≤ 10% could be ideal for achieving optimal biocompatibility (cell proliferation, biomineralization, and antimicrobial capacity) and mechanical stability thus making it a promising biomaterial substrate for bone tissue regeneration.}, } @article {pmid31011805, year = {2019}, author = {Guerrero-Galán, C and Calvo-Polanco, M and Zimmermann, SD}, title = {Ectomycorrhizal symbiosis helps plants to challenge salt stress conditions.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-019-00894-2}, pmid = {31011805}, issn = {1432-1890}, abstract = {Soil salinity is an environmental condition that is currently increasing worldwide. Plant growth under salinity induces osmotic stress and ion toxicity impairing root water and nutrient absorption, but the association with beneficial soil microorganisms has been linked to an improved adaptation to this constraint. The ectomycorrhizal (ECM) symbiosis has been proposed as a key factor for a better tolerance of woody species to salt stress, thanks to the reduction of sodium (Na+) uptake towards photosynthetic organs. Although no precise mechanisms for this enhanced plant salt tolerance have been described yet, in this review, we summarize the knowledge accumulated so far on the role of ECM symbiosis. Moreover, we propose several strategies by which ECM fungi might help plants, including restriction of Na+ entrance into plant tissues and improvement of mineral nutrition and water balances. This positive effect of ECM fungi has been proven in field assays and the results obtained point to a promising application in forestry cultures and reforestation.}, } @article {pmid31011585, year = {2019}, author = {Wang, S and Ye, Q and Zeng, X and Qiao, S}, title = {Functions of Macrophages in the Maintenance of Intestinal Homeostasis.}, journal = {Journal of immunology research}, volume = {2019}, number = {}, pages = {1512969}, doi = {10.1155/2019/1512969}, pmid = {31011585}, issn = {2314-7156}, abstract = {Intestinal macrophages constitute the largest pool of macrophages in the body and have emerged as crucial sentinels for pathogen recognition and elimination. The source and development of intestinal macrophages, as well as their distinct properties have been well documented. Intestinal macrophages exert their functions in the maintenance of intestinal homeostasis by shaping host-microbiota symbiosis, managing gut inflammation, crosstalking with T cells, and facilitating wound repair. Recently, nutritional regulation of intestinal macrophages has attracted substantial attention and is becoming a promising approach to disease prevention and control. Understanding the mechanisms employed by intestinal macrophages in mediating intestinal immune homeostasis and inflammation, as well as the mode of action of dietary nutrients in the modulating functions of intestinal macrophages, represents an opportunity to prevent and control inflammatory bowel diseases.}, } @article {pmid30446385, year = {2018}, author = {Iatsenko, I and Boquete, JP and Lemaitre, B}, title = {Microbiota-Derived Lactate Activates Production of Reactive Oxygen Species by the Intestinal NADPH Oxidase Nox and Shortens Drosophila Lifespan.}, journal = {Immunity}, volume = {49}, number = {5}, pages = {929-942.e5}, doi = {10.1016/j.immuni.2018.09.017}, pmid = {30446385}, issn = {1097-4180}, mesh = {Animals ; Carrier Proteins/genetics/metabolism ; Drosophila/*physiology ; Dysbiosis ; Gene Expression ; Intestinal Mucosa/immunology/metabolism/microbiology ; L-Lactate Dehydrogenase/genetics/metabolism ; Lactic Acid/*metabolism ; *Longevity ; *Microbiota ; Mutation ; NADPH Oxidases/genetics/*metabolism ; Reactive Oxygen Species/*metabolism ; Signal Transduction ; Symbiosis ; }, abstract = {Commensal microbes colonize the gut epithelia of virtually all animals and provide several benefits to their hosts. Changes in commensal populations can lead to dysbiosis, which is associated with numerous pathologies and decreased lifespan. Peptidoglycan recognition proteins (PGRPs) are important regulators of the commensal microbiota and intestinal homeostasis. Here, we found that a null mutation in Drosophila PGRP-SD was associated with overgrowth of Lactobacillus plantarum in the fly gut and a shortened lifespan. L. plantarum-derived lactic acid triggered the activation of the intestinal NADPH oxidase Nox and the generation of reactive oxygen species (ROS). In turn, ROS production promoted intestinal damage, increased proliferation of intestinal stem cells, and dysplasia. Nox-mediated ROS production required lactate oxidation by the host intestinal lactate dehydrogenase, revealing a host-commensal metabolic crosstalk that is probably broadly conserved. Our findings outline a mechanism whereby host immune dysfunction leads to commensal dysbiosis that in turn promotes age-related pathologies.}, } @article {pmid29970413, year = {2018}, author = {Matamoros, MA and Kim, A and Peñuelas, M and Ihling, C and Griesser, E and Hoffmann, R and Fedorova, M and Frolov, A and Becana, M}, title = {Protein Carbonylation and Glycation in Legume Nodules.}, journal = {Plant physiology}, volume = {177}, number = {4}, pages = {1510-1528}, pmid = {29970413}, issn = {1532-2548}, mesh = {Amino Acids/metabolism ; Chromatography, Liquid/methods ; Leghemoglobin/metabolism ; Malate Dehydrogenase/genetics/metabolism ; Nuclear Proteins/metabolism ; Phaseolus/*metabolism ; Plant Proteins/analysis/genetics/*metabolism ; Protein Carbonylation ; Root Nodules, Plant/*metabolism/microbiology ; Symbiosis ; Tandem Mass Spectrometry/methods ; }, abstract = {Nitrogen fixation is an agronomically and environmentally important process catalyzed by bacterial nitrogenase within legume root nodules. These unique symbiotic organs have high metabolic rates and produce large amounts of reactive oxygen species that may modify proteins irreversibly. Here, we examined two types of oxidative posttranslational modifications of nodule proteins: carbonylation, which occurs by direct oxidation of certain amino acids or by interaction with reactive aldehydes arising from cell membrane lipid peroxides; and glycation, which results from the reaction of lysine and arginine residues with reducing sugars or their autooxidation products. We used a strategy based on the enrichment of carbonylated peptides by affinity chromatography followed by liquid chromatography-tandem mass spectrometry to identify 369 oxidized proteins in bean (Phaseolus vulgaris) nodules. Of these, 238 corresponded to plant proteins and 131 to bacterial proteins. Lipid peroxidation products induced most carbonylation sites. This study also revealed that carbonylation has major effects on two key nodule proteins. Metal-catalyzed oxidation caused the inactivation of malate dehydrogenase and the aggregation of leghemoglobin. In addition, numerous glycated proteins were identified in vivo, including three key nodule proteins: sucrose synthase, glutamine synthetase, and glutamate synthase. Label-free quantification identified 10 plant proteins and 18 bacterial proteins as age-specifically glycated. Overall, our results suggest that the selective carbonylation or glycation of crucial proteins involved in nitrogen metabolism, transcriptional regulation, and signaling may constitute a mechanism to control cell metabolism and nodule senescence.}, } @article {pmid29182785, year = {2018}, author = {Fjalstad, JW and Esaiassen, E and Juvet, LK and van den Anker, JN and Klingenberg, C}, title = {Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {73}, number = {3}, pages = {569-580}, doi = {10.1093/jac/dkx426}, pmid = {29182785}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/adverse effects/*therapeutic use ; *Drug Resistance, Multiple, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Gram-Negative Bacteria/drug effects ; Gram-Negative Bacterial Infections/drug therapy ; Humans ; Infant, Newborn ; Observational Studies as Topic ; Randomized Controlled Trials as Topic ; Symbiosis/drug effects ; }, abstract = {Objectives: To systematically review the impact of antibiotic therapy in the neonatal period on changes in the gut microbiota and/or antibiotic resistance development.

Methods: Data sources were PubMed, Embase, Medline and the Cochrane Database, supplemented by manual searches of reference lists. Randomized controlled trials (RCTs) and observational studies were included if they provided data on different categories of antibiotic treatment (yes versus no, long versus short duration and/or broad- versus narrow-spectrum regimens) and subsequent changes in the gut microbiota and/or antibiotic resistance development. We evaluated risk of bias using the Cochrane Handbook, adapted to include observational studies. When appropriate, we used the vote-counting method to perform semi-quantitative meta-analyses. We applied the Grades of Recommendation, Assessment, Development and Evaluation approach to rate the quality of evidence (QoE). Study protocol registration: PROSPERO CRD42015026743.

Results: We included 48 studies, comprising 3 RCTs and 45 observational studies. Prolonged antibiotic treatment was associated with reduced gut microbial diversity in all three studies investigating this outcome (very low QoE). Antibiotic treatment was associated with reduced colonization rates of protective commensal anaerobic bacteria in four of five studies (very low QoE). However, all three categories of antibiotic treatment were associated with an increased risk of antibiotic resistance development, in particular MDR in Gram-negative bacteria, and we graded the QoE for these outcomes as moderate.

Conclusions: We are moderately confident that antibiotic treatment leads to antibiotic resistance development in neonates and it may also induce potentially disease-promoting gut microbiota alterations. Our findings emphasize the need to reduce unnecessary antibiotic treatment in neonates.}, } @article {pmid28855618, year = {2017}, author = {Smith, H and Epstein, H and Torda, G}, title = {The molecular basis of differential morphology and bleaching thresholds in two morphs of the coral Pocillopora acuta.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10066}, pmid = {28855618}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/classification/*genetics ; Coral Reefs ; DNA, Intergenic/genetics ; Dinoflagellida/physiology ; *Genetic Speciation ; Genetics, Population ; *Genome ; Pacific Ocean ; *Phylogeny ; Symbiosis/physiology ; Whole Genome Sequencing ; }, abstract = {Processes of cnidarian evolution, including hybridization and phenotypic plasticity, have complicated the clear diagnosis of species boundaries within the phylum. Pocillopora acuta, a species of scleractinian coral that was recently split from the widespread Pocillopora damicornis species complex, occurs in at least two distinct morphs on the Great Barrier Reef. Contrasting morphology combined with evidence of differential bleaching thresholds among sympatrically distributed colonies suggest that the taxonomy of this recently described species is not fully resolved and may represent its own species complex. To examine the basis of sympatric differentiation between the two morphs, we combined analyses of micro- and macro-skeletal morphology with genome wide sequencing of the coral host, as well as ITS2 genotyping of the associated Symbiodinium communities. We found consistent differences between morphs on both the macro- and micro-skeletal scale. In addition, we identified 18 candidate functional genes that relate to skeletal formation and morphology that may explain how the two morphs regulate growth to achieve their distinct growth forms. With inconclusive results in endosymbiotic algal community diversity between the two morphs, we propose that colony morphology may be linked to bleaching susceptibility. We conclude that cryptic speciation may be in the early stages within the species P. acuta.}, } @article {pmid31008572, year = {2019}, author = {Green, KA and Eaton, CJ and Savoian, MS and Scott, B}, title = {A homologue of the fungal tetraspanin Pls1 is required for Epichloë festucae expressorium formation and establishment of a mutualistic interaction with Lolium perenne.}, journal = {Molecular plant pathology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mpp.12805}, pmid = {31008572}, issn = {1364-3703}, support = {MAU1301//Tertiary Education Commission/ ; }, abstract = {Epichloë festucae is an endophytic fungus that forms a mutualistic symbiotic association with the grass host Lolium perenne. Endophytic hyphae exit the host by an appressorium-like structure known as an expressorium. In plant-pathogenic fungi, the tetraspanin Pls1 and the NADPH oxidase component Nox2 are required for appressorium development. Previously we showed that the homologue of Nox2, NoxB, is required for E. festucae expressorium development and establishment of a mutualistic symbiotic interaction with the grass host. Here we used a reverse genetics approach to functionally characterize the role of the E. festucae homologue of Pls1, PlsA. The morphology and growth of ΔplsA in axenic culture was comparable to wild-type. The tiller length of plants infected with ΔplsA was significantly reduced. Hyphae of ΔplsA had a proliferative pattern of growth within the leaves of L. perenne with increased colonization of the intercellular spaces and the vascular bundles. The ΔplsA mutant was also defective in expressorium development although the phenotype was not as severe as for ΔnoxB, highlighting potentially distinct roles for PlsA and NoxB in signalling through the NoxB complex. Hyphae of ΔplsA proliferate below the cuticle surface but still occasionally form an expressorium-like structure that enables the mutant hyphae to exit the leaf to grow on the surface. These expressoria still form a septin ring-like structure at the point of cuticle exit as found in the wild-type strain. These results establish that E. festucae PlsA has an important, but distinct, role to NoxB in expressorium development and plant symbiosis.}, } @article {pmid30902623, year = {2019}, author = {Maal-Bared, R and Dixon, B and Axelsson-Olsson, D}, title = {Fate of internalized Campylobacter jejuni and Mycobacterium avium from encysted and excysted Acanthamoeba polyphaga.}, journal = {Experimental parasitology}, volume = {199}, number = {}, pages = {104-110}, doi = {10.1016/j.exppara.2019.03.011}, pmid = {30902623}, issn = {1090-2449}, mesh = {Acanthamoeba/genetics/growth & development/*microbiology ; Bacterial Load ; Campylobacter jejuni/*physiology ; Coculture Techniques ; Culture Media/chemistry ; DNA, Protozoan/isolation & purification ; Mycobacterium avium/*physiology ; Nucleic Acid Amplification Techniques ; Refrigeration ; Symbiosis ; Trophozoites ; }, abstract = {Association of the water- and foodborne pathogen Campylobacter jejuni with free-living Acanthamoeba spp. trophozoites enhances C. jejuni survival and resistance to biocides and starvation. When facing less than optimal environmental conditions, however, the Acanthamoeba spp. host can temporarily transform from trophozoite to cyst and back to trophozoite, calling the survival of the internalized symbiont and resulting public health risk into question. Studies investigating internalized C. jejuni survival after A. castellanii trophozoite transformation have neither been able to detect its presence inside the Acanthamoeba cyst after encystation nor to confirm its presence upon excystation of trophozoites through culture-based techniques. The purpose of this study was to detect C. jejuni and Mycobacterium avium recovered from A. polyphaga trophozoites after co-culture and induction of trophozoite encystation using three different encystation methods (Neff's medium, McMillen's medium and refrigeration), as well as after cyst excystation. Internalized M. avium was used as a positive control, since studies have consistently detected the organism after co-culture and after host excystation. Concentrations of C. jejuni in A. polyphaga trophozoites were 4.5 × 105 CFU/ml, but it was not detected by PCR or culture post-encystation. This supports the hypothesis that C. jejuni may be digested during encystation of the amoebae. M. avium was recovered at a mean concentration of 1.9 × 104 from co-cultured trophozoites and 4.4 × 101 CFU/ml after excystation. The results also suggest that M. avium recovery post-excystation was statistically significantly different based on which encystation method was used, ranging from 1.3 × 101 for Neff's medium to 5.4 × 101 CFU/ml for refrigeration. No M. avium was recovered from A. polyphaga cysts when trophozoites were encysted by McMillen's medium. Since C. jejuni internalized in cysts would be more likely to survive harsh environmental conditions and disinfection, a better understanding of potential symbioses between free-living amoebae and campylobacters in drinking water distribution systems and food processing environments is needed to protect public health. Future co-culture experiments examining survival of internalized C. jejuni should carefully consider the encystation media used, and include molecular detection tools to falsify the hypothesis that C. jejuni may be present in a viable but not culturable state.}, } @article {pmid30773514, year = {2019}, author = {Ramírez, MDA and España, M and Aguirre, C and Kojima, K and Ohkama-Ohtsu, N and Sekimoto, H and Yokoyama, T}, title = {Burkholderia and Paraburkholderia are Predominant Soybean Rhizobial Genera in Venezuelan Soils in Different Climatic and Topographical Regions.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {43-58}, doi = {10.1264/jsme2.ME18076}, pmid = {30773514}, issn = {1347-4405}, mesh = {Aluminum Compounds/metabolism ; Bradyrhizobium/classification/genetics/isolation & purification/physiology ; Burkholderia/classification/genetics/isolation & purification/physiology ; Burkholderiaceae/*classification/genetics/*isolation & purification/physiology ; Climate ; Genes, Bacterial/genetics ; Geography ; Multilocus Sequence Typing ; Nitrogen Fixation/genetics ; *Phylogeny ; Plant Root Nodulation ; Rhizobium/classification/genetics/isolation & purification/physiology ; Root Nodules, Plant/microbiology ; Sodium Chloride/metabolism ; *Soil Microbiology ; Soybeans/*microbiology ; Stress, Physiological ; Symbiosis ; Venezuela ; }, abstract = {The climate, topography, fauna, and flora of Venezuela are highly diverse. However, limited information is currently available on the characterization of soybean rhizobia in Venezuela. To clarify the physiological and genetic diversities of soybean rhizobia in Venezuela, soybean root nodules were collected from 11 soil types located in different topographical regions. A total of 395 root nodules were collected and 120 isolates were obtained. All isolates were classified in terms of stress tolerance under different concentrations of NaCl and Al3+. The tolerance levels of isolates to NaCl and Al3+ varied. Based on sampling origins and stress tolerance levels, 44 isolates were selected for further characterization. An inoculation test indicated that all isolates showed the capacity for root nodulation on soybean. Based on multilocus sequence typing (MLST), 20 isolates were classified into the genera Rhizobium and Bradyrhizobium. The remaining 24 isolates were classified into the genus Burkholderia or Paraburkholderia. There is currently no evidence to demonstrate that the genera Burkholderia and Paraburkholderia are the predominant soybean rhizobia in agricultural fields. Of the 24 isolates classified in (Para) Burkholderia, the nodD-nodB intergenic spacer regions of 10 isolates and the nifH gene sequences of 17 isolates were closely related to the genera Rhizobium and Bradyrhizobium, respectively. The root nodulation numbers of five (Para) Burkholderia isolates were higher than those of the 20 α-rhizobia. Furthermore, among the 44 isolates tested, one Paraburkholderia isolate exhibited the highest nitrogen-fixation activity in root nodules.}, } @article {pmid30760664, year = {2019}, author = {Girard, L and Blanchet, E and Stien, D and Baudart, J and Suzuki, M and Lami, R}, title = {Evidence of a Large Diversity of N-acyl-Homoserine Lactones in Symbiotic Vibrio fischeri Strains Associated with the Squid Euprymna scolopes.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {99-103}, doi = {10.1264/jsme2.ME18145}, pmid = {30760664}, issn = {1347-4405}, mesh = {Acyl-Butyrolactones/*chemistry/metabolism ; Aliivibrio fischeri/*chemistry/genetics ; Animals ; Bacterial Proteins/genetics/metabolism ; Decapodiformes/*microbiology ; Gene Expression Regulation, Bacterial ; Genetic Variation ; Phenotype ; *Quorum Sensing ; Species Specificity ; Symbiosis ; }, abstract = {Vibrio fischeri possesses a complex AHL-mediated Quorum-sensing (QS) system including two pathways, LuxI/R (3-oxo-C6-HSL and C6-HSL) and AinS/R (C8-HSL), which are important for the regulation of physiological traits. Diverse QS-dependent functional phenotypes have been described in V. fischeri; however, AHL diversity is still underestimated. In the present study, we investigated AHL diversity in five symbiotic V. fischeri strains with distinct phenotypic properties using UHPLC-HRMS/MS. The results obtained (1) revealed an unexpectedly high diversity of signaling molecules, (2) emphasized the complexity of QS in V. fischeri, and (3) highlight the importance of understanding the specificity of AHL-mediated QS.}, } @article {pmid30584188, year = {2019}, author = {Akyol, TY and Niwa, R and Hirakawa, H and Maruyama, H and Sato, T and Suzuki, T and Fukunaga, A and Sato, T and Yoshida, S and Tawaraya, K and Saito, M and Ezawa, T and Sato, S}, title = {Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {23-32}, doi = {10.1264/jsme2.ME18109}, pmid = {30584188}, issn = {1347-4405}, mesh = {*Agriculture ; Bacteria/classification/genetics/growth & development/isolation & purification ; Fungi/classification/genetics/growth & development/isolation & purification ; *Microbiota ; Mycorrhizae/classification/*physiology ; Onions/growth & development/microbiology ; Phosphorus/chemistry ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.}, } @article {pmid29255260, year = {2017}, author = {Levy, A and Salas Gonzalez, I and Mittelviefhaus, M and Clingenpeel, S and Herrera Paredes, S and Miao, J and Wang, K and Devescovi, G and Stillman, K and Monteiro, F and Rangel Alvarez, B and Lundberg, DS and Lu, TY and Lebeis, S and Jin, Z and McDonald, M and Klein, AP and Feltcher, ME and Rio, TG and Grant, SR and Doty, SL and Ley, RE and Zhao, B and Venturi, V and Pelletier, DA and Vorholt, JA and Tringe, SG and Woyke, T and Dangl, JL}, title = {Genomic features of bacterial adaptation to plants.}, journal = {Nature genetics}, volume = {50}, number = {1}, pages = {138-150}, pmid = {29255260}, issn = {1546-1718}, support = {/HHMI/Howard Hughes Medical Institute/United States ; F32 GM112345/GM/NIGMS NIH HHS/United States ; T32 GM007092/GM/NIGMS NIH HHS/United States ; T32 GM067553/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Bacteria/*genetics/growth & development ; *Genome, Bacterial ; *Genomics ; Host-Pathogen Interactions/*genetics ; Plant Roots/genetics/microbiology ; Plants/*microbiology ; Symbiosis ; }, abstract = {Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.}, } @article {pmid28805645, year = {2017}, author = {Biedermann, PH and Rohlfs, M}, title = {Evolutionary feedbacks between insect sociality and microbial management.}, journal = {Current opinion in insect science}, volume = {22}, number = {}, pages = {92-100}, doi = {10.1016/j.cois.2017.06.003}, pmid = {28805645}, issn = {2214-5753}, mesh = {Animals ; Behavior, Animal/physiology ; *Biological Evolution ; Ecosystem ; Feeding Behavior ; Insecta/*microbiology ; Microbiota ; Social Behavior ; Symbiosis ; }, abstract = {Fitness-determining interactions with microbes-in particular fungi-have often been considered a by-product of social evolution in insects. Here, we take the view that both beneficial and harmful microbial consortia are major drivers of social behaviours in many insect systems-ranging from aggregation to eusociality. We propose evolutionary feedbacks between the insect sociality and microbial communities that strengthen mutualistic interactions with beneficial (dietary or defensive) microbes and simultaneously increase the capacity to defend against pathogens (i.e. social immunity). We identified variation in habitat stability-as determined by breeding site predictability and ephemerality-as a main ecological factor that constrains these feedbacks. To test this hypothesis we suggest following the evolution of insect social traits upon experimental manipulation of habitat stability and microbial consortia.}, } @article {pmid31006112, year = {2019}, author = {Kazenel, MR and Kivlin, SN and Taylor, DL and Lynn, JS and Rudgers, JA}, title = {Altitudinal gradients fail to predict fungal symbiont responses to warming.}, journal = {Ecology}, volume = {}, number = {}, pages = {e02740}, doi = {10.1002/ecy.2740}, pmid = {31006112}, issn = {1939-9170}, abstract = {Climate change is shifting altitudinal species ranges, with potential to disrupt species interactions. Altitudinal gradient studies and warming experiments can both increase understanding of climate effects on species interactions, but few studies have used both together to improve predictions. We examined whether plant-fungal symbioses responded similarly to altitude and 23 years of experimental warming. Root- and leaf-associated fungi, which can mediate plants' climate sensitivity, responded divergently to elevation versus warming. Fungal colonization, diversity, and composition varied with altitude, but climate variables were generally weak predictors; other factors such as host plant identity, plant community composition, or edaphic variables likely drive fungal altitudinal distributions. Manipulated warming altered fungal colonization, but not composition or diversity. Leaf symbionts were more sensitive to climate and experimental warming than root symbionts. Altitudinal patterns and responses to warming differed among host plant species and fungal groups, indicating that predicting climate effects on symbioses will require tracking both host and symbiont identities. Combining experimental and observational methods can yield valuable insight into how climate change may alter plant-symbiont interactions, but our results indicate that altitude does not always serve as an adequate proxy for warming effects on fungal symbionts of plants. This article is protected by copyright. All rights reserved.}, } @article {pmid31006045, year = {2019}, author = {Prasad, S and Shah, A and Bhalsing, KS and Ingalhalikar, M and Saini, J and Pal, PK}, title = {Clinical correlates of abnormal subcortical volumes in Essential Tremor.}, journal = {Journal of neural transmission (Vienna, Austria : 1996)}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00702-019-02004-0}, pmid = {31006045}, issn = {1435-1463}, support = {ECR/2016/000808//Science and Engineering Research Board/ ; }, abstract = {Essential tremor (ET) is considered to be a neurodegenerative disorder and it is plausible that the observed motor and non-motor symptoms may be attributable to functional alterations secondary to abnormalities of subcortical nuclei. This study aims to compare the volumes of subcortical nuclei in patients with ET to ascertain neuroimaging correlates of motor and non-motor features of ET. Forty patients of ET and 40 age- and gender-matched healthy controls (HC) were enrolled in this study. Tremor severity was quantified with the Fahn-Tolosa-Marin tremor rating scale. Patients of ET with and without a rest tremor were also compared. Structural imaging was performed on a 3T scanner, and volumes of subcortical structures were obtained using Freesurfer. There was no difference in total brain volume between ET and HC. However, compared to HC, significantly lower volumes of bilateral thalamus, hippocampus, and ventral diencephalon were observed in patients with ET. A significantly higher volume was observed in the right caudate nucleus, pallidum, amygdala, and bilateral putamen, and nucleus accumbens. No difference was observed between patients of ET with and without a rest tremor. Patients with ET have significant alterations in volumes of subcortical nuclei, which are not limited to the motor domain and include structures involved in cognitive and behavioral functions. These results add to the growing concept of a neurodegenerative pathophysiology of ET with abnormalities extending beyond the cerebellum.}, } @article {pmid31005641, year = {2019}, author = {Zhu, S and Feng, S and Xu, Z and Qin, L and Shang, C and Feng, P and Wang, Z and Yuan, Z}, title = {Cultivation of Chlorella vulgaris on unsterilized dairy-derived liquid digestate for simultaneous biofuels feedstock production and pollutant removal.}, journal = {Bioresource technology}, volume = {285}, number = {}, pages = {121353}, doi = {10.1016/j.biortech.2019.121353}, pmid = {31005641}, issn = {1873-2976}, abstract = {In order to assess viability of microalgae cultivation using unsterilized dairy-derived liquid digestate (DLD) for simultaneous biofuels feedstock production and contaminant removal, four DLD concentrations (25%, 50%, 75% and 100%) were used to grow Chlorella vulgaris in batch photobioreactors (PBRs). The 25% DLD was an ideal alternative medium in that high growth rate (0.69 d-1), high lipid productivity (112.9 mg L-1 d-1) as well as high nutrient removal were attained. The high DLD concentration caused inhibition of microalgal growth, where COD was more inhibitive than ammonium. The presence of bacteria did not influence microalgae production because of limited growth. Microalgal growth reduced the richness and diversity of bacterial community. Furthermore, the species of Bacteroidetes, Candidatus Saccharibacteria, and Chlamydiae rather than Proteobacteria benefited microalgal-bacterial symbiosis. These findings contribute to better application of microalgal-bacterial system for large-scale microalgae cultivation as well as environmental sustainability.}, } @article {pmid31003984, year = {2019}, author = {Ogran, A and Yardeni, EH and Keren-Paz, A and Bucher, T and Jain, R and Gilhar, O and Kolodkin-Gal, I}, title = {The plant host induces antibiotic production to select the most beneficial colonizers.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00512-19}, pmid = {31003984}, issn = {1098-5336}, abstract = {Microbial ecosystems tightly associated with a eukaryotic host are wide-spread in nature. The genetic and metabolic networks of the eukaryotic hosts and the associated microbes have co-evolved to form a symbiotic relationship. Both the Gram-positive Bacillus subtilis and the Gram-negative Serratia plymuthica can form biofilms on plant roots, and thus can serve as a model system for the study of interspecies interactions in a host-associated ecosystem. We found that B. subtilis biofilms expand collectively and asymmetrically towards Serratia plymuthica, while expressing a non-ribosomal antibiotic bacillaene and an extracellular protease. As a result, B. subtilis biofilms out-competed S. plymuthica for a successful colonization of the host. Strikingly, the plant host could enhance the efficiency of this killing by inducing bacillaene synthesis. In turn, B. subtilis biofilms increased the resistance of the plant host to pathogens. These results provide an example of how plant-bacterium symbiosis promotes the immune response of the plant host and the fitness of the associated bacteria.Importance Our study sheds a mechanistic light on how multicellular biofilm units compete and successfully colonize a eukaryote host, using B. subtilis microbial communities as our lens. The microbiota and its interactions with its host play various roles in the development and prevention of diseases. Using competing beneficial biofilms that are essential microbiota members on the plant host, we found that B. subtilis biofilms activate collective migration to capture their prey followed by non-ribosomal antibiotic synthesis. Plant hosts increase the efficiency of antibiotic production by B. subtilis biofilms as they activate the synthesis of polyketides, therefore our study provides a first evidence to a mechanism by which the host can indirectly select for beneficial microbiota members.}, } @article {pmid31001301, year = {2019}, author = {Lamouche, F and Bonadé-Bottino, N and Mergaert, P and Alunni, B}, title = {Symbiotic Efficiency of Spherical and Elongated Bacteroids in the Aeschynomene-Bradyrhizobium Symbiosis.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {377}, doi = {10.3389/fpls.2019.00377}, pmid = {31001301}, issn = {1664-462X}, abstract = {The legume-rhizobium symbiosis is a major supplier of fixed nitrogen in the biosphere and constitutes a key step of the nitrogen biogeochemical cycle. In some legume species belonging to the Inverted Repeat Lacking Clade (IRLC) and the Dalbergioids, the differentiation of rhizobia into intracellular nitrogen-fixing bacteroids is terminal and involves pronounced cell enlargement and genome endoreduplication, in addition to a strong loss of viability. In the Medicago truncatula-Sinorhizobium spp. system, the extent of bacteroid differentiation correlates with the level of symbiotic efficiency. Here, we used different physiological measurements to compare the symbiotic efficiency of photosynthetic bradyrhizobia in different Aeschynomene spp. (Dalbergioids) hosts inducing different bacteroid morphotypes associated with increasing ploidy levels. The strongly differentiated spherical bacteroids were more efficient than the less strongly differentiated elongated ones, providing a higher mass gain to their hosts. However, symbiotic efficiency is not solely correlated with the extent of bacteroid differentiation especially in spherical bacteroid-inducing plants, suggesting the existence of other factors controlling symbiotic efficiency.}, } @article {pmid31001272, year = {2019}, author = {Khare, SP and Shetty, A and Biradar, R and Patta, I and Chen, ZJ and Sathe, AV and Reddy, PC and Lahesmaa, R and Galande, S}, title = {NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {667}, doi = {10.3389/fimmu.2019.00667}, pmid = {31001272}, issn = {1664-3224}, abstract = {SATB1 is a genome organizer protein that is expressed in a lineage specific manner in CD4+ T-cells. SATB1 plays a crucial role in expression of multiple genes throughout the thymic development and peripheral differentiation of T cells. Although SATB1 function has been subjected to intense investigation, regulation of SATB1 gene expression remains poorly understood. Analysis of RNA-seq data revealed multiple transcription start sites at the upstream regulatory region of SATB1. We further demonstrated that SATB1 gene is expressed via alternative promoters during T-helper (Th) cell differentiation. The proximal promoter "P1" is used more by the naïve and activated CD4+ T-cells whereas the middle "P2" and the distal "P3" promoters are used at a significantly higher level by polarized T-helper cells. Cytokine and TCR signaling play crucial roles toward SATB1 alternative promoter usage. Under Th2 polarization conditions, transcription factor STAT6, which operates downstream of the cytokine signaling binds to the P2 and P3 promoters. Genetic perturbation by knockout and chemical inhibition of STAT6 activation resulted in the loss of P2 and P3 promoter activity. Moreover, chemical inhibition of activation of NF-κB, a transcription factor that operates downstream of the TCR signaling, also resulted in reduced P2 and P3 promoter usage. Furthermore, usage of the P1 promoter correlated with lower SATB1 protein expression whereas P2 and P3 promoter usage correlated with higher SATB1 protein expression. Thus, the promoter switch might play a crucial role in fine-tuning of SATB1 protein expression in a cell type specific manner.}, } @article {pmid31001223, year = {2019}, author = {Sun, Y and Xie, Z and Sui, F and Liu, X and Cheng, W}, title = {Identification of Cbp1, a c-di-GMP Binding Chemoreceptor in Azorhizobium caulinodans ORS571 Involved in Chemotaxis and Nodulation of the Host Plant.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {638}, doi = {10.3389/fmicb.2019.00638}, pmid = {31001223}, issn = {1664-302X}, abstract = {Cbp1, a chemoreceptor containing a PilZ domain was identified in Azorhizobium caulinodans ORS571, a nitrogen-fixing free-living soil bacterium that induces nodule formation in both the roots and stems of the host legume Sesbania rostrata. Chemoreceptors are responsible for sensing signals in the chemotaxis pathway, which guides motile bacteria to beneficial niches and plays an important role in the establishment of rhizobia-legume symbiosis. PilZ domain proteins are known to bind the second messenger c-di-GMP, an important regulator of motility, biofilm formation and virulence. Cbp1 was shown to bind c-di-GMP through the conserved RxxxR motif of its PilZ domain. A mutant strain carrying a cbp1 deletion was impaired in chemotaxis, a feature that could be restored by genetic complementation. Compared with the wild type strain, the Δcbp1 mutant displayed enhanced aggregation and biofilm formation. The Δcbp1 mutant induced functional nodules when inoculated individually. However, the Δcbp1 mutant was less competitive than the wild type in competitive root colonization and nodulation. These data are in agreement with the hypothesis that the c-di-GMP binding chemoreceptor Cbp1 in A. caulinodans is involved in chemotaxis and nodulation.}, } @article {pmid31001143, year = {2019}, author = {Zhou, Z and Zhao, S and Tang, J and Liu, Z and Wu, Y and Wang, Y and Lin, S}, title = {Altered Immune Landscape and Disrupted Coral-Symbiodinium Symbiosis in the Scleractinian Coral Pocillopora damicornis by Vibrio coralliilyticus Challenge.}, journal = {Frontiers in physiology}, volume = {10}, number = {}, pages = {366}, doi = {10.3389/fphys.2019.00366}, pmid = {31001143}, issn = {1664-042X}, abstract = {Vibrio coralliilyticus is known to cause coral diseases, especially under environmental perturbation, but its impact on coral physiology and underpinning mechanism is poorly understood. In the present study, we investigated cytological, immunological, and metatranscriptomic responses of the scleractinian coral Pocillopora damicornis to V. coralliilyticus infection. The density and chlorophyll content of symbiotic zooxanthellae decreased significantly at 12 and 24 h after Vibrio challenge. The activities of antioxidant enzymes such as superoxide dismutase and catalase, nitric oxide synthase, phenoloxidase (PO), and the activation level of caspase3 all rose significantly in P. damicornis after Vibrio challenge. In the metatranscriptomic analysis, we found 10 significantly upregulated genes in the symbionts at 24 h after the challenge, which were mostly involved in the metabolism of nucleic acid and polysaccharide, and 133 significantly down-regulated symbiont genes, which were mainly related to amino acid catabolism and transport. Meanwhile, 1432 significantly upregulated coral genes were revealed, highly overrepresented in GO terms that are mostly related to the regulation of immune response, the regulation of cytokine production, and innate immune response. Furthermore, at 24 h after Vibrio challenge, 890 coral genes were significantly downregulated, highly overrepresented in four GO terms implicated in defense response. These results in concert suggest that V. coralliilyticus infection triggered the innate immune response including the redox, PO, and apoptosis systems, but repressed the response of the complement system in the scleractinian coral P. damicornis, accompanied by symbiont density decrease and symbiosis collapse through disordering the metabolism of the symbionts. These findings shed light on the molecular regulatory processes underlying bleaching and degradation of P. damicornis resulting from the infection of V. coralliilyticus.}, } @article {pmid31000761, year = {2019}, author = {Fortier, J and Truax, B and Gagnon, D and Lambert, F}, title = {Abiotic and biotic factors controlling fine root biomass, carbon and nutrients in closed-canopy hybrid poplar stands on post-agricultural land.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6296}, doi = {10.1038/s41598-019-42709-6}, pmid = {31000761}, issn = {2045-2322}, abstract = {Fine roots (diameter <2 mm) have a pivotal role in resource acquisition, symbiosis development, and for elemental cycling in forests. Various abiotic and biotic factors affect their biomass and nutrient content. Understanding the effect of these factors on root traits could improve biogeochemical modelling, nutrient management and ecosystem services provision in planted forests. Data from 14-year old poplars planted along a fertility/climatic gradient in Southeastern Canada, show that live fine root biomass varied with genotype and environment, was negatively correlated to soil fertility, and uncorrelated to tree size. Dead fine root biomass varied with genotype and peaked during fall and in colder environments with slower element cycling. Root chemistry also varied with environment, genotype and season. The genotype producing recalcitrant leaf litter had the highest root biomass, suggesting a compensation strategy. Along the studied gradient, plasticity level observed for some root traits (biomass, element contents) was genotype-specific and high for some genotypes. Regionally, such plasticity patterns should be considered in elemental budgets, for nutrient management and ecosystem services provision in plantations (carbon storage, nutrient retention). The small inter-site aboveground productivity differences observed suggest that plasticity in fine root growth may contribute to overcome nutrient limitations on less fertile marginal lands.}, } @article {pmid31000545, year = {2019}, author = {Alai, S and Ghattargi, VC and Gautam, M and Dhotre, DP and Patel, K and Pawar, SP and Kumar, R and Shaligram, U and Deobagkar, D and Gairola, S}, title = {Genome Sequence of Bordetella pertussis Vaccine Strain BP 165.}, journal = {Microbiology resource announcements}, volume = {8}, number = {16}, pages = {}, doi = {10.1128/MRA.00150-19}, pmid = {31000545}, issn = {2576-098X}, abstract = {Whole-cell and acellular pertussis vaccines are used globally against Bordetella pertussis Various vaccine reference strains are used globally for the production of such vaccines. We report here a draft genome sequence for Bordetella pertussis strain BP 165, which is used by the Serum Institute of India in the production of acellular pertussis vaccine.}, } @article {pmid29875304, year = {2018}, author = {Koski, MH and Ison, JL and Padilla, A and Pham, AQ and Galloway, LF}, title = {Linking pollinator efficiency to patterns of pollen limitation: small bees exploit the plant-pollinator mutualism.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1880}, pages = {}, pmid = {29875304}, issn = {1471-2954}, mesh = {Animals ; Bees/*physiology ; Body Size ; Campanulaceae/*physiology ; Flowers/physiology ; *Pollen ; *Pollination ; Species Specificity ; *Symbiosis ; }, abstract = {Seemingly mutualistic relationships can be exploited, in some cases reducing fitness of the exploited species. In plants, the insufficient receipt of pollen limits reproduction. While infrequent pollination commonly underlies pollen limitation (PL), frequent interactions with low-efficiency, exploitative pollinators may also cause PL. In the widespread protandrous herb Campanula americana, visitation by three pollinators explained 63% of the variation in PL among populations spanning the range. Bumblebees and the medium-sized Megachile campanulae enhanced reproductive success, but small solitary bees exacerbated PL. To dissect mechanisms behind these relationships, we scored sex-specific floral visitation, and the contributions of each pollinator to plant fitness using single flower visits. Small bees and M. campanulae overvisited male-phase flowers, but bumblebees frequently visited female-phase flowers. Fewer bumblebee visits were required to saturate seed set compared to other bees. Scaling pollinator efficiency metrics to populations, small bees deplete large amounts of pollen due to highly male-biased flower visitation and infrequent pollen deposition. Thus, small bees reduce plant reproduction by limiting pollen available for transfer by efficient pollinators, and appear to exploit the plant-pollinator mutualism, acting as functional parasites to C. americana It is therefore unlikely that small bees will compensate for reproductive failure in C. americana when bumblebees are scarce.}, } @article {pmid30999182, year = {2019}, author = {Bharti, A and Garg, N}, title = {SA and AM symbiosis modulate antioxidant defense mechanisms and asada pathway in chickpea genotypes under salt stress.}, journal = {Ecotoxicology and environmental safety}, volume = {178}, number = {}, pages = {66-78}, doi = {10.1016/j.ecoenv.2019.04.025}, pmid = {30999182}, issn = {1090-2414}, abstract = {Salt stress disturbs redox homeostasis by perturbing equilibrium between generation and removal of reactive oxygen species (ROS), which alters the normal metabolism of plants through membrane damage, lipid peroxidation and denaturation of proteins. Salicylic acid (SA) seed priming and arbuscular mycorrhizal (AM) fungi impart salt tolerance in legumes by maintaining redox balance. The present investigation focused on the relative and combined applications of SA and Rhizoglomus intraradices in scavenging ROS in Cicer arietinum L. (chickpea) genotypes (salt tolerant-PBG 5, relatively sensitive-BG 256) subjected to salt stress. Despite the enhanced antioxidant mechanisms under salt stress, ROS (superoxide, O2- and hydrogen peroxide, H2O2) accumulation increased significantly and induced lipid peroxidation and lipoxygenase (LOX) activities, which disrupted membrane stability, more in BG 256 than PBG 5. Salt stress also caused redox imbalance by lowering ascorbate/dehydroascorbate (ASA/DHA) and reduced glutathione/oxidized glutathione (GSH/GSSG) ratios, indicating that redox-homeostasis was crucial for salt-tolerance. Exogenous SA was more promising in reducing ROS-generation and lipid-peroxidation, which provided higher membrane stability as compared to AM inoculation. Although, the enzymatic antioxidants were more active in SA treated plants, yet, AM inoculation outperformed in increasing reformative enzyme activities of Foyer-Halliwell-Asada cycle, which resulted in higher plant biomass in a genotype-dependent manner. SA increased AM root colonization and provided functional complementarity to R. intraradices and thereby strengthening antioxidant defense mechanisms through their cumulative contribution. The study suggested the use of +SA+AM as an eco-friendly tool in imparting salt tolerance in chickpea genotypes subjected to long-term salinity.}, } @article {pmid30802772, year = {2019}, author = {Liu, P and Hou, J and Zou, Y and Stephenson, SL and Huo, X and Hu, X and Li, Y}, title = {Developmental features and associated symbiont bacterial diversity in essential life cycle stages of Heterostelium colligatum.}, journal = {European journal of protistology}, volume = {68}, number = {}, pages = {99-107}, doi = {10.1016/j.ejop.2019.02.003}, pmid = {30802772}, issn = {1618-0429}, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Dictyostelium/*growth & development/*microbiology ; Life Cycle Stages/*physiology ; Symbiosis/*physiology ; }, abstract = {Dictyostelium discoideum is a specialized amoebozoan protist that can feed on, carry and disperse bacteria. However, the symbiont bacterial diversity in other species of dictyostelids and the diversity associated with essential life cycle stages are still unknown until now. Here, another species of dictyostelids, Heterostelium colligatum, a new record for tropical China, was isolated from the soil collected in Xishuangbanna Tropical Botanical Garden, Yunnan Province, China. We describe the complete life cycle of this species and illustrate details of spore-to-spore development. The symbiont bacterial diversity and relative abundance associated with life cycle stages of H. colligatum, including the aggregation, pseudoplasmodium, and sorocarp stages, were investigated by high throughput metagenomic techniques. H. colligatum appears to be capable of carrying different types of bacteria during its life history in addition to those used as a food resource. The dominant groups of those three stages in its life cycle were the Proteobacteria, Actinobacteria and Firmicutes. The relative abundance of the dominant phyla and shared OTUs were different for the aggregation, pseudoplasmodium, and sorocarp stages. A comparison of the symbiont bacterial assemblages associated with D. discoideum and H. colligatum indicated that different dictyostelid species carried different species of symbiont associated bacteria.}, } @article {pmid30353644, year = {2019}, author = {Liu, JF and Zhang, ZQ and Beggs, JR}, title = {Tri-partite complexity: odour from a psyllid's mutualist ant increased predation by a predatory mite on the psyllid.}, journal = {Pest management science}, volume = {75}, number = {5}, pages = {1317-1327}, doi = {10.1002/ps.5246}, pmid = {30353644}, issn = {1526-4998}, support = {//University of Auckland/ ; //Core Funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group/ ; }, mesh = {Animals ; Ants/*metabolism/physiology ; *Hemiptera ; Longevity/drug effects ; Mites/*drug effects/physiology ; *Odorants ; Predatory Behavior/*drug effects ; Reproduction/drug effects ; Survival Analysis ; *Symbiosis ; }, abstract = {BACKGROUND: Predator-prey interactions consist of direct consumption of prey by predators and indirect non-consumptive effects on prey. Predator cues can induce predation stress in prey that negatively influences the survival, development, reproduction, and feeding behaviour of the prey. This study evaluated the effects of hemipteran-tending ant (Technomyrmex albipes) odour on the development, survival, reproduction, and predation rates of the predatory mite Amblydromalus limonicus when feeding on an invasive pest of solanaceous crops, Bactericera cockerelli. The age-stage, two-sex life table theory was used to compare the demographic characteristics and predation rates of A. limonicus in the presence and absence of ant odour.

RESULTS: We show that exposure to ant odour did not alter the development, survival rate, and fecundity of A. limonicus, but induced a sexually dimorphic response in its longevity; consumption rates also showed that dimorphic response-predation rates increased in female A. limonicus, but not in males.

CONCLUSION: To our knowledge, this is the first report indicating increased consumption rates by natural enemies exposed to odour from a mutualist of pest (ant). This finding may provide new insights into understanding tri-partite interaction involving a pest, its predator, and a mutulist of the pest. © 2018 Society of Chemical Industry.}, } @article {pmid30995278, year = {2019}, author = {Leinonen, PH and Helander, M and Vázquez-de-Aldana, BR and Zabalgogeazcoa, I and Saikkonen, K}, title = {Local adaptation in natural European host grass populations with asymmetric symbiosis.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0215510}, doi = {10.1371/journal.pone.0215510}, pmid = {30995278}, issn = {1932-6203}, abstract = {Recent work on microbiomes is revealing the wealth and importance of plant-microbe interactions. Microbial symbionts are proposed to have profound effects on fitness of their host plants and vice versa, especially when their fitness is tightly linked. Here we studied local adaptation of host plants and possible fitness contribution of such symbiosis in the context of abiotic environmental factors. We conducted a four-way multi-year reciprocal transplant experiment with natural populations of the perennial grass Festuca rubra s.l. from northern and southern Finland, Faroe Islands and Spain. We included F. rubra with and without transmitted symbiotic fungus Epichloë that is vertically transmitted via host seed. We found local adaptation across the European range, as evidenced by higher host fitness of the local geographic origin compared with nonlocals at three of the four studied sites, suggesting that selection pressures are driving evolution in different directions. Abiotic factors did not result in strong fitness effects related to Epichloë symbiosis, indicating that other factors such as herbivory are more likely to contribute to fitness differences between plants naturally occurring with or without Epichloë. Nevertheless, in the case of asymmetric symbiosis that is obligatory for the symbiont, abiotic conditions that affect performance of the host, may also cause selective pressure for the symbiont.}, } @article {pmid30993446, year = {2019}, author = {Singh, AN and Sharma, N}, title = {Epigenetic Modulators as Potential Multi-targeted Drugs Against Hedgehog Pathway for Treatment of Cancer.}, journal = {The protein journal}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10930-019-09832-9}, pmid = {30993446}, issn = {1875-8355}, abstract = {The Sonic hedgehog signalling is known to play a crucial role in regulating embryonic development, cancer stem cell maintenance and tissue patterning. Dysregulated hedgehog signalling has been reported to affect tumorigenesis and drug response in various human malignancies. Epigenetic therapy relying on DNA methyltransferase and Histone deacetylase inhibitors are being proposed as potential drug candidates considering their efficiency in preventing development of cancer progenitor cells, killing drug resistant cells and also dictating "on/off" switch of tumor suppressor genes and oncogenes. In this docking approach, epigenetic modulators were virtually screened for their efficiency in inhibiting key regulators of SHH pathway viz., sonic hedgehog, Smoothened and Gli using polypharmacological approach. The control drugs and epigenetic modulators were docked with PDB protein structures using AutoDock vina and further checked for their drug-likeness properties. Further molecular dynamics simulation using VMD and NAMD, and MMP/GBSA energy calculation were employed for verifying the stability and entropy of the ligand-receptor complex. EPZ-6438 and GSK 343 (EZH2 inhibitors), CHR 3996 and Mocetinostat (HDAC inhibitors), GSK 126 (HKMT inhibitor) and UNC 1215 (L3MBTL3 antagonist) exhibited multiple-targeted approach in modulating HH signalling. This is the first study to report these epigenetic drugs as potential multi-targeted hedgehog pathway inhibitors. Thus, epigenetic polypharmacology approach can be explored as a better alternative to challenges of acute long term toxicity and drug resistance occurring due to traditional single targeted chemotherapy in the future.}, } @article {pmid30991927, year = {2019}, author = {Dixon, GB and Kenkel, CD}, title = {Molecular convergence and positive selection associated with the evolution of symbiont transmission mode in stony corals.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1901}, pages = {20190111}, doi = {10.1098/rspb.2019.0111}, pmid = {30991927}, issn = {1471-2954}, abstract = {Heritable symbioses have been critical for the evolution of life. The genetic consequences of evolving a heritable symbiosis from the perspective of the symbiont are well established, but concomitant changes in the host remain unresolved. In stony corals, heritable, vertical transmission has evolved repeatedly, providing a unique opportunity to investigate the genomic basis of this complex trait. We conducted a comparative analysis of 25 coral transcriptomes to identify orthologous genes exhibiting signatures of positive selection and convergent amino acid substitutions in vertically transmitting lineages. The frequency of convergence events tends to be higher among vertically transmitting lineages, consistent with the proposed role of selection in driving the evolution of convergent transmission mode phenotypes. Of 10 774 orthologous genes, 403 exhibited at least one molecular convergence event and evidence of positive selection in at least one vertically transmitting lineage. Functional enrichments among these top candidate genes include processes previously implicated in symbiosis including endocytosis, immune response, cytoskeletal protein binding and cytoplasmic membrane-bounded vesicles. Finally, several novel candidates were identified among 100 genes showing evidence of positive selection at the particular convergence event, highlighting the value of our approach for generating new insight into host mechanisms associated with the evolution of heritable symbioses.}, } @article {pmid30991290, year = {2019}, author = {Ezra, H}, title = {On the relationship between road safety research and the practice of road design and operation.}, journal = {Accident; analysis and prevention}, volume = {128}, number = {}, pages = {114-131}, doi = {10.1016/j.aap.2019.03.016}, pmid = {30991290}, issn = {1879-2057}, abstract = {How do the findings of road safety research affect the practice by which the road infrastructure is built and operated? The question is seldom asked. I discuss the complexities of the research-practice symbiosis in the light of two historical anecdotes. These allow me to point out several issues of concern. My general conclusion is that the relationship, as it evolved over time, is unpremeditated and occasionally dysfunctional. Issues of concern are the lightness with which decisions affecting road-user safety can be based on opinion that is unsupported by evidence, that such opinions can trump inconvenient evidence, that research findings can be willfully distorted or disregarded, that questionable results can be given a ring of consensual truth, and that the questions which research asks and what findings get published are at times influenced by external interest. In sum, the concern is that practice is not sufficiently evidence-based. Road users have a right to expect that decisions substantially affecting their safety take into account fact-based expectation of safety consequences. It is therefore time to endow the research-practice relationship with a premeditated and purposeful structure.}, } @article {pmid30990223, year = {2019}, author = {Hugo, MH and Kaech, H and Ganesanandamoorthy, P and Vorburger, C}, title = {Evolutionary costs and benefits of infection with diverse strains of Spiroplasma in pea aphids.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1111/evo.13740}, pmid = {30990223}, issn = {1558-5646}, abstract = {The heritable endosymbiont Spiroplasma infects many insects and has repeatedly evolved the ability to protect its hosts against different parasites. Defenses do not come for free to the host, and theory predicts that more costly symbionts need to provide stronger benefits to persist in host populations. We investigated the costs and benefits of Spiroplasma infections in pea aphids (Acyrthosiphon pisum), testing 12 bacterial strains from three different clades. Virtually all strains decreased aphid lifespan and reproduction, but only two had a (weak) protective effect against the parasitoid Aphidius ervi, an important natural enemy of pea aphids. Spiroplasma induced fitness costs were variable, with strains from the most slowly evolving clade reaching higher titers and curtailing aphid lifespan more strongly than other strains. Some Spiroplasma strains shared their host with a second endosymbiont, Regiella insecticola. Although the result of an unfortunate handling error, these co-infections proved instructive, because they showed that the cost of infection with Spiroplasma may be attenuated in the presence of Regiella. These results suggest that mechanisms other than protection against A. ervi maintain pea aphid infections with diverse strains of Spiroplasma, and that studying them in isolation will not provide a complete picture of their effects on host fitness. This article is protected by copyright. All rights reserved.}, } @article {pmid30990167, year = {2019}, author = {Zhou, YL and Ślipiński, A and Ren, D and Parker, J}, title = {A Mesozoic clown beetle myrmecophile (Coleoptera: Histeridae).}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.44985}, pmid = {30990167}, issn = {2050-084X}, support = {31402008//National Natural Science Foundation of China/ ; 20150064//International Postdoctoral Exchange Fellowship/ ; }, abstract = {Complex interspecies relationships are widespread among metazoans, but the evolutionary history of these lifestyles is poorly understood. We describe a fossil beetle in 99-million-year-old Burmese amber that we infer to have been a social impostor of the earliest-known ant colonies. Promyrmister kistneri gen. et sp. nov. belongs to the haeteriine clown beetles (Coleoptera: Histeridae), a major clade of 'myrmecophiles'-specialized nest intruders with dramatic anatomical, chemical and behavioral adaptations for colony infiltration. Promyrmister reveals that myrmecophiles evolved close to the emergence of ant eusociality, in colonies of stem-group ants that predominate Burmese amber, or with cryptic crown-group ants that remain largely unknown at this time. The clown beetle-ant relationship has been maintained ever since by the beetles host-switching to numerous modern ant genera, ultimately diversifying into one of the largest radiations of symbiotic animals. We infer that obligate behavioral symbioses can evolve relatively rapidly, and be sustained over deep time.}, } @article {pmid30990122, year = {2019}, author = {Shah, S and Thapa, BB and Chand, K and Pradhan, S and Maharjan, A and Verma, A and Sen Thakuri, L and Joshi, P and Pant, B}, title = {Piriformospora indica promotes the growth of the in-vitro-raised Cymbidium aloifolium plantlet and their acclimatization.}, journal = {Plant signaling & behavior}, volume = {}, number = {}, pages = {1-7}, doi = {10.1080/15592324.2019.1596716}, pmid = {30990122}, issn = {1559-2324}, abstract = {Cymbidium aloifolium is known for its ornamental and medicinal values. It has been listed as threatened orchid species. In this study, in vitro propagated C. aloifolium plantlets were interacted with the Piriformospora indica. The growth assay was performed for 45 days; the plant growth pattern such as number and length of roots and shoots were measured. Microscopic study of the root section stained by trypan blue was done to detect the peloton formation. The methanol extracts of the fungal colonized plant as well as uncolonized (control) plant were prepared and various metabolites were identified by gas chromatography mass spectroscopy. Acclimatization was done in a substrate composition of coco peat: gravel: charcoal in ratio 2:2:1. P. indica-colonized plantlet showed the highest growth with the formation of clamdospore in the root section. The growth regulator such as auxin, ascorbic acid, andrographolide, hexadecanoic acid, and DL-proline were identified. After three months of field transfer, plantlet colonized by P. indica survived and remained healthy as compared to uncolonized control plantlet.}, } @article {pmid30989804, year = {2019}, author = {Mediavilla, O and Geml, J and Olaizola, J and Oria-de-Rueda, JA and Baldrian, P and Martín-Pinto, P}, title = {Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13395}, pmid = {30989804}, issn = {1751-7915}, support = {VA050P17//Junta de Castilla y León/ ; //University of Valladolid programme 'Ayudas para estancias breves en el desarrollo de Tesis Doctorales. Convocatoria 2016'/ ; 2018//Naturalis Biodiversity Center/ ; //European Social Fund/ ; }, abstract = {Cistus ladanifer scrublands, traditionally considered as unproductive, have nonetheless been observed to produce large quantities of king bolete (Boletus edulis) fruitbodies. These pyrophytic scrublands are prone to wildfires, which severely affect fungi, hence the need for fire prevention in producing C. ladanifer scrublands. In addition, B. edulis productions have severely decreased in the last years. A deeper understanding of the B. edulis life cycle and of biotic and abiotic factors influencing sporocarp formation is needed to implement management practices that facilitate B. edulis production. For example, some bacteria likely are involved in sporocarp production, representing a key part in the triple symbiosis (plant-fungus-bacteria). In this study, we used soil DNA metabarcoding in C. ladanifer scrublands to (i) assess the effect of site history and fire prevention treatment on bacterial richness and community composition; (ii) test if there was any correlation between various taxonomic groups of bacteria and mycelial biomass and sporocarp production of B. edulis; and to (iii) identify indicator bacteria associated with the most productive B. edulis sites. Our results show that site history drives bacterial richness and community composition, while fire prevention treatments have a weaker, but still detectable effect, particularly in the senescent plots. Sporocarp production correlated positively with genera in Verrucomicrobia. Several genera, e.g. Azospirillum and Gemmatimonas, were identified as indicators of the most productive sites, suggesting a potential biological role in B. edulis fructification. This study provides a better understanding of the triple symbiosis (plant-fungus-bacteria) involved in C. ladanifer-B. edulis systems.}, } @article {pmid30989446, year = {2019}, author = {Zhang, Z and Ke, D and Hu, M and Zhang, C and Deng, L and Li, Y and Li, J and Zhao, H and Cheng, L and Wang, L and Yuan, H}, title = {Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia-legume symbiosis.}, journal = {Plant molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11103-019-00857-3}, pmid = {30989446}, issn = {1573-5028}, support = {182300410063//Natural Science Foundation of Henan Provincial Science and Technology/ ; 18A180031//key scientific research projects of Henan higher education institutions/ ; 31400213//National Natural Science Foundation of China/ ; 2015, 2016//Funding scheme for young core teachers of Xinyang Normal University/ ; 2017//Nanhu Scholars Program for Young Scholars of XYNU/ ; }, abstract = {KEY MESSAGE: Symbiotic nitrogen fixation in root nodules of grain legumes is essential for high yielding. Protein phosphorylation/dephosphorylation plays important role in root nodule development. Differences in the phosphoproteomes may either be developmental specific and related to nitrogen fixation activity. An iTRAQ-based quantitative phosphoproteomic analyses during nodule development enables identification of specific phosphorylation signaling in the Lotus-rhizobia symbiosis. During evolution, legumes (Fabaceae) have evolved a symbiotic relationship with rhizobia, which fix atmospheric nitrogen and produce ammonia that host plants can then absorb. Root nodule development depends on the activation of protein phosphorylation-mediated signal transduction cascades. To investigate possible molecular mechanisms of protein modulation during nodule development, we used iTRAQ-based quantitative proteomic analyses to identify root phosphoproteins during rhizobial colonization and infection of Lotus japonicus. 1154 phosphoproteins with 2957 high-confidence phosphorylation sites were identified. Gene ontology enrichment analysis of functional groups of these genes revealed that the biological processes mediated by these proteins included cellular processes, signal transduction, and transporter activity. Quantitative data highlighted the dynamics of protein phosphorylation during nodule development and, based on regulatory trends, seven groups were identified. RNA splicing and brassinosteroid (BR) signaling pathways were extensively affected by phosphorylation, and most Ser/Arg-rich (SR) proteins were multiply phosphorylated. In addition, many proposed kinase-substrate pairs were predicted, and in these MAPK6 substrates were found to be highly enriched. This study offers insights into the regulatory processes underlying nodule development, provides an accessible resource cataloging the phosphorylation status of thousands of Lotus proteins during nodule development, and develops our understanding of post-translational regulatory mechanisms in the Lotus-rhizobia symbiosis.}, } @article {pmid30989396, year = {2019}, author = {Deveau, A and Clowez, P and Petit, F and Maurice, JP and Todesco, F and Murat, C and Harroué, M and Ruelle, J and Le Tacon, F}, title = {New insights into black truffle biology: discovery of the potential connecting structure between a Tuber aestivum ascocarp and its host root.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-019-00892-4}, pmid = {30989396}, issn = {1432-1890}, support = {ANR-11-LABX 0002 01//ANR/ ; }, abstract = {According to isotopic labeling experiments, most of the carbon used by truffle (Tuber sp.) fruiting bodies to develop underground is provided by host trees, suggesting that trees and truffles are physically connected. However, such physical link between trees and truffle fruiting bodies has never been observed. We discovered fruiting bodies of Tuber aestivum adhering to the walls of a belowground quarry and we took advantage of this unique situation to analyze the physical structure that supported these fruiting bodies in the open air. Observation of transversal sections of the attachment structure indicated that it was organized in ducts made of gleba-like tissue and connected to a network of hyphae traveling across soil particles. Only one mating type was detected by PCR in the gleba and in the attachment structure, suggesting that these two organs are from maternal origin, leaving open the question of the location of the opposite paternal mating type.}, } @article {pmid30989224, year = {2019}, author = {Chong, RA and Park, H and Moran, NA}, title = {Genome evolution of the obligate endosymbiont Buchnera aphidicola.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msz082}, pmid = {30989224}, issn = {1537-1719}, abstract = {An evolutionary consequence of uniparentally transmitted symbiosis is degradation of symbiont genomes. We use the system of aphids and their maternally inherited obligate endosymbiont, Buchnera aphidicola, to explore the evolutionary process of genome degradation. We compared complete genome sequences for 39 Buchnera strains, including 23 newly sequenced symbiont genomes from diverse aphid hosts. We reconstructed the genome of the most recent shared Buchnera ancestor, which contained 616 protein-coding genes, and 39 RNA genes. The extent of subsequent gene loss varied across lineages, resulting in modern genomes ranging from 412 to 646 kilobases and containing 354 to 587 protein-coding genes. Loss events were highly non-random across loci. Genes involved in replication, transcription, translation, and amino acid biosynthesis are largely retained, whereas genes underlying ornithine biosynthesis, stress responses and transcriptional regulation were lost repeatedly. Aside from losses, gene order is almost completely stable. The main exceptions involve movement between plasmid and chromosome locations of genes underlying tryptophan and leucine biosynthesis and supporting nutrition of aphid hosts. This set of complete genomes enabled tests for signatures of positive diversifying selection. Of 371 Buchnera genes tested, 29 genes show strong support for ongoing positive selection. These include genes encoding outer membrane porins that are expected to be involved in direct interactions with hosts. Collectively, these results indicate that extensive genome reduction occurred in the ancestral Buchnera prior to aphid diversification and that reduction has continued since, with losses greater in some lineages and for some loci.}, } @article {pmid30987816, year = {2019}, author = {Morris, LA and Voolstra, CR and Quigley, KM and Bourne, DG and Bay, LK}, title = {Nutrient Availability and Metabolism Affect the Stability of Coral-Symbiodiniaceae Symbioses.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2019.03.004}, pmid = {30987816}, issn = {1878-4380}, abstract = {Coral reefs rely upon the highly optimized coral-Symbiodiniaceae symbiosis, making them sensitive to environmental change and susceptible to anthropogenic stress. Coral bleaching is predominantly attributed to photo-oxidative stress, yet nutrient availability and metabolism underpin the stability of symbioses. Recent studies link symbiont proliferation under nutrient enrichment to bleaching; however, the interactions between nutrients and symbiotic stability are nuanced. Here, we demonstrate how bleaching is regulated by the forms and ratios of available nutrients and their impacts on autotrophic carbon metabolism, rather than algal symbiont growth. By extension, historical nutrient conditions mediate host-symbiont compatibility and bleaching tolerance over proximate and evolutionary timescales. Renewed investigations into the coral nutrient metabolism will be required to truly elucidate the cellular mechanisms leading to coral bleaching.}, } @article {pmid30670649, year = {2019}, author = {Brunetti, AE and Lyra, ML and Melo, WGP and Andrade, LE and Palacios-Rodríguez, P and Prado, BM and Haddad, CFB and Pupo, MT and Lopes, NP}, title = {Symbiotic skin bacteria as a source for sex-specific scents in frogs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {6}, pages = {2124-2129}, doi = {10.1073/pnas.1806834116}, pmid = {30670649}, issn = {1091-6490}, mesh = {Animals ; Anura ; *Bacteria/classification ; Biodiversity ; Female ; Male ; Sex Factors ; Skin/*microbiology ; *Symbiosis ; Volatile Organic Compounds ; }, abstract = {Amphibians are known to possess a wide variety of compounds stored in their skin glands. While significant progress has been made in understanding the chemical diversity and biological relevance of alkaloids, amines, steroids, and peptides, most aspects of the odorous secretions are completely unknown. In this study, we examined sexual variations in the volatile profile from the skin of the tree frog Boana prasina and combined culture and culture-independent methods to investigate if microorganisms might be a source of these compounds. We found that sesquiterpenes, thioethers, and methoxypyrazines are major contributors to the observed sex differences. We also observed that each sex has a distinct profile of methoxypyrazines, and that the chemical origin of these compounds can be traced to a Pseudomonas sp. strain isolated from the frog's skin. This symbiotic bacterium was present in almost all individuals examined from different sites and was maintained in captive conditions, supporting its significance as the source of methoxypyrazines in these frogs. Our results highlight the potential relevance of bacteria as a source of chemical signals in amphibians and contribute to increasing our understanding of the role that symbiotic associations have in animals.}, } @article {pmid30456532, year = {2019}, author = {Schneider, DI and Ehrman, L and Engl, T and Kaltenpoth, M and Hua-Van, A and Le Rouzic, A and Miller, WJ}, title = {Symbiont-Driven Male Mating Success in the Neotropical Drosophila paulistorum Superspecies.}, journal = {Behavior genetics}, volume = {49}, number = {1}, pages = {83-98}, doi = {10.1007/s10519-018-9937-8}, pmid = {30456532}, issn = {1573-3297}, mesh = {Animals ; Behavior, Animal ; Biological Evolution ; Drosophila/*microbiology ; Drosophila Proteins/metabolism ; Female ; Male ; Reproduction/*physiology ; Reproductive Isolation ; Sex Attractants/metabolism/physiology ; Sexual Behavior, Animal/physiology ; Species Specificity ; Symbiosis/*genetics ; Wolbachia/physiology ; }, abstract = {Microbial symbionts are ubiquitous associates of living organisms but their role in mediating reproductive isolation (RI) remains controversial. We addressed this knowledge gap by employing the Drosophila paulistorum-Wolbachia model system. Semispecies in the D. paulistorum species complex exhibit strong RI between each other and knockdown of obligate mutualistic Wolbachia bacteria in female D. paulistorum flies triggers loss of assortative mating behavior against males carrying incompatible Wolbachia strains. Here we set out to determine whether de novo RI can be introduced by Wolbachia-knockdown in D. paulistorum males. We show that Wolbachia-knockdown D. paulistorum males (i) are rejected as mates by wild type females, (ii) express altered sexual pheromone profiles, and (iii) are devoid of the endosymbiont in pheromone producing cells. Our findings suggest that changes in Wolbachia titer and tissue tropism can induce de novo premating isolation by directly or indirectly modulating sexual behavior of their native D. paulistorum hosts.}, } @article {pmid30440037, year = {2018}, author = {Castillo, M and Sanfuentes, E and Angulo, A and Becerra, J and Romero-Romero, JL and Arce-Johnson, P}, title = {Biocontrol of Sirex noctilio by the parasitic nematode Deladenus siricidicola: A five season field study in southern Chile.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0207529}, pmid = {30440037}, issn = {1932-6203}, mesh = {Animals ; Chile ; Hymenoptera/*physiology ; Nematoda/*pathogenicity ; Pest Control, Biological/*methods ; Pinus/parasitology ; Seasons ; Symbiosis/*physiology ; }, abstract = {In 2001, the woodwasp Sirex noctilio was detected in Pinus radiata plantations in the Biobio region of southern Chile. Subsequently, an intense biological control program using the female sterilizing nematode Deladenus siricidicola was implemented in 2010. During five seasons between 2012 and 2017, we studied the parasitism of D. siricidicola nematode and its effect on woodwasp populations and infestation of P. radiata in different locations within the Biobio region. Parasitism was assessed by dissecting adult females of S. noctilio obtained from infested P. radiata logs. The total population of S. noctilio was determined by the emergence of individuals from the same logs. The level of damage caused by the S. noctilio pest was determined by establishing plots in stands of P. radiata at an intensity of 1 plot every 5 ha-1. During the study period, parasitism of S. noctilio by the nematode D. siricidicola increased from 29.6% in 2012 to 93.1% in 2016, while pest population decreased 3.4% in the same time period. Infestation increased from 0.3 to 11,6% of trees between 2012 and 2015, but subsequently decreased to 5.9% by 2017. We confirmed establishment of the nematode in the region under study and its natural dispersion to non-inoculated areas. Finally, we determined that the effect of inoculation age (antiquity) on parasitism levels reached 90% after three years of inoculation.}, } @article {pmid29258070, year = {2018}, author = {Huang, X and Browngardt, CM and Jiang, M and Ahn, SJ and Burne, RA and Nascimento, MM}, title = {Diversity in Antagonistic Interactions between Commensal Oral Streptococci and Streptococcus mutans.}, journal = {Caries research}, volume = {52}, number = {1-2}, pages = {88-101}, pmid = {29258070}, issn = {1421-976X}, support = {K23 DE023579/DE/NIDCR NIH HHS/United States ; R01 DE025832/DE/NIDCR NIH HHS/United States ; R90 DE022530/DE/NIDCR NIH HHS/United States ; T90 DE021990/DE/NIDCR NIH HHS/United States ; }, mesh = {Arginine/metabolism ; Biofilms/growth & development ; Hydrogen Peroxide/metabolism ; Hydrogen-Ion Concentration ; Streptococcus/*growth & development/metabolism ; Streptococcus mutans/*growth & development/metabolism ; Streptococcus sanguis/growth & development ; *Symbiosis ; }, abstract = {Arginine metabolism via the arginine deiminase system (ADS) of oral bacteria generates ammonia, which can increase the pH of oral biofilms and decrease the risk for dental caries. Antagonistic interactions between ADS-positive and cariogenic bacteria in oral biofilms may be an important ecological determinant of caries. This study investigated the antagonistic potential and mechanisms of clinical isolates of arginolytic streptococci on and by Streptococcus mutans UA159, a well-characterized cariogenic human isolate. Low-passage isolates of Streptococcus gordonii, Streptococcus sanguinis, Streptococcus parasanguinis, Streptococcus australis, and Streptococcus cristatus inhibited the growth of S. mutans to various degrees when they were inoculated on growth media first or simultaneously with S. mutans. The antagonistic effects of arginolytic strains against S. mutans and the production of H2O2 by these strains were enhanced during growth in a less-rich medium or when galactose was substituted for glucose as the primary carbohydrate source. Pyruvate oxidase was the dominant pathway for H2O2 production by arginolytic strains, but lactate oxidase activity was also detected in some strains of S. gordonii and S. cristatus. UA159 inhibited the growth of all tested arginolytic strains when inoculated first, especially in aerobic conditions. However, the antagonistic effects of S. mutans on certain strains of S. gordonii and S. australis were not observed during anaerobic growth in the presence of arginine. Thus, arginolytic commensal streptococci may have a synergistically positive impact on the ecology of oral biofilms by moderating biofilm pH while antagonizing the growth and virulence of caries pathogens.}, } @article {pmid29124868, year = {2018}, author = {Fadhlaoui, K and Ben Hania, W and Armougom, F and Bartoli, M and Fardeau, ML and Erauso, G and Brasseur, G and Aubert, C and Hamdi, M and Brochier-Armanet, C and Dolla, A and Ollivier, B}, title = {Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae, in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor.}, journal = {Environmental microbiology}, volume = {20}, number = {1}, pages = {281-292}, doi = {10.1111/1462-2920.13995}, pmid = {29124868}, issn = {1462-2920}, mesh = {Carbohydrate Metabolism/*physiology ; Coculture Techniques ; Desulfotomaculum/*metabolism ; Desulfovibrio vulgaris/*metabolism ; Fermentation/physiology ; Gram-Negative Anaerobic Straight, Curved, and Helical Rods/growth & development/*metabolism ; Hydrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sugars/*metabolism ; Sulfates/metabolism ; Sulfur/metabolism ; Symbiosis/*physiology ; }, abstract = {Mesotoga prima strain PhosAc3 is a mesophilic representative of the phylum Thermotogae comprising only fermentative bacteria so far. We show that while unable to ferment glucose, this bacterium is able to couple its oxidation to reduction of elemental sulfur. We demonstrate furthermore that M. prima strain PhosAc3 as well as M. prima strain MesG1 and Mesotoga infera are able to grow in syntrophic association with sulfate-reducing bacteria (SRB) acting as hydrogen scavengers through interspecies hydrogen transfer. Hydrogen production was higher in M. prima strain PhosAc3 cells co-cultured with SRB than in cells cultured alone in the presence of elemental sulfur. We propose that the efficient sugar-oxidizing metabolism by M. prima strain PhosAc3 in syntrophic association with a hydrogenotrophic sulfate-reducing bacterium can be extrapolated to all members of the Mesotoga genus. Genome comparison of Thermotogae members suggests that the metabolic difference between Mesotoga and Thermotoga species (sugar oxidation versus fermentation) is mainly due to the absence of the bifurcating [FeFe]-hydrogenase in the former. Such an obligate oxidative process for using sugars, unusual within prokaryotes, is the first reported within the Thermotogae. It is hypothesized to be of primary ecological importance for growth of Mesotoga spp. in the environments that they inhabit.}, } @article {pmid30986120, year = {2019}, author = {Si, Z and Yang, Q and Liang, R and Chen, L and Chen, DS and Li, Y}, title = {Digalactosyldiacylglycerol synthase gene MtDGD1 plays an essential role in nodule development and nitrogen fixation.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-11-18-0322-R}, pmid = {30986120}, issn = {0894-0282}, abstract = {Little is known about the genes participating in digalactosyldiacylglycerol (DGDG) synthesis during nodule symbiosis. Here, we identified full-length MtDGD1, a synthase of DGDG, and characterized its effect on symbiotic nitrogen fixation in Medicago truncatula. Immunofluorescence and immunoelectron microscopy showed that MtDGD1 was located on the symbiosome membranes in the infected cells. GUS histochemical staining revealed that MtDGD1 was highly expressed in the infection zone of young nodules as well as in the whole mature nodules. Compared with the control, MtDGD1-RNAi transgenic plants exhibited significant decreases in nodule number, symbiotic nitrogen fixation activity and DGDG abundance in the nodules, as well as abnormal nodule and symbiosome development. Overexpression of MtDGD1 resulted in enhancement of nodule number and nitrogen fixation activity. In response to phosphorus starvation, the MtDGD1 expression level was substantially up-regulated and the abundance of non-phospholipid DGDG was significantly increased in the roots and nodules, accompanied by corresponding decreases in the abundance of phospholipids such as phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol. Overall, our results indicate that DGD1 contributes to effective nodule organogenesis and nitrogen fixation by affecting the synthesis and content of DGDG during symbiosis. Keywords: DGDG; Medicago truncatula; MtDGD1; phospholipids; RNAi; symbiotic phenotype.}, } @article {pmid30984121, year = {2019}, author = {Deja-Sikora, E and Mercy, L and Baum, C and Hrynkiewicz, K}, title = {The Contribution of Endomycorrhiza to the Performance of Potato Virus Y-Infected Solanaceous Plants: Disease Alleviation or Exacerbation?.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {516}, doi = {10.3389/fmicb.2019.00516}, pmid = {30984121}, issn = {1664-302X}, abstract = {Solanaceae, comprising meaningful crops (as potato, tomato, pepper, eggplant, and tobacco), can benefit from a symbiosis with arbuscular mycorrhizal fungi (AMF), which improve plant fitness and support plant defense against pathogens. Currently, those crops are likely the most impacted by Potato virus Y (PVY). Unfortunately, the effects of AM symbiosis on the severity of disease induced by PVY in solanaceous crops remain uncertain, partly because the interplay between AMF and PVY is poorly characterized. To shed some light on this issue, available studies on interactions in tripartite association between the host plant, its fungal colonizer, and viral pathogen were analyzed and discussed. Although the best-documented PVY transmission pathway is aphid-dependent, PVY infections are also observed in the absence of insect vector. We hypothesize the existence of an additional pathway for virus transmission involving AMF, in which the common mycorrhizal network (CMN) may act as a potential bridge. Therefore, we reviewed (1) the significance of AM colonization for the course of disease, (2) the potential of AMF networks to act as vectors for PVY, and (3) the consequences for crop breeding and production of AM biofertilizers.}, } @article {pmid30984118, year = {2019}, author = {Ek-Ramos, MJ and Gomez-Flores, R and Orozco-Flores, AA and Rodríguez-Padilla, C and González-Ochoa, G and Tamez-Guerra, P}, title = {Bioactive Products From Plant-Endophytic Gram-Positive Bacteria.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {463}, doi = {10.3389/fmicb.2019.00463}, pmid = {30984118}, issn = {1664-302X}, abstract = {Endophytes constitute plant-colonizing microorganisms in a mutualistic symbiosis relationship. They are found in most ecosystems reducing plant crops' biotic and abiotic stressors by stimulating immune responses, excluding plant pathogens by niche competition, and participating in antioxidant activities and phenylpropanoid metabolism, whose activation produces plant defense, structural support, and survival molecules. In fact, metabolomic studies have demonstrated that endophyte genes associated to specific metabolites are involved in plant growth promotion (PGP) by stimulating plant hormones production such as auxins and gibberellins or as plant protective agents against microbial pathogens, cancer, and insect pests, but eco-friendly and eco-safe. A number of metabolites of Gram-positive endophytes isolated from agriculture, forest, mangrove, and medicinal plants, mainly related to the Firmicutes phyla, possess distinctive biocontrol and plant growth-promoting activities. In general, Actinobacteria and Bacillus endophytes produce aromatic compounds, lipopeptides, plant hormones, polysaccharides, and several enzymes linked to phenylpropanoid metabolism, thus representing high potential for PGP and crop management strategies. Furthermore, Actinobacteria have been shown to produce metabolites with antimicrobial and antitumor activities, useful in agriculture, medicine, and veterinary areas. The great endophytes diversity, their metabolites production, and their adaptation to stress conditions make them a suitable and unlimited source of novel metabolites, whose application could reduce agrochemicals usage in food and drugs production.}, } @article {pmid30561050, year = {2019}, author = {Speare, DJ}, title = {Cleaner fish diseases.}, journal = {Journal of fish diseases}, volume = {42}, number = {2}, pages = {155-156}, doi = {10.1111/jfd.12937}, pmid = {30561050}, issn = {1365-2761}, mesh = {Animals ; Fish Diseases/*etiology ; Fishes/*physiology ; *Symbiosis ; }, } @article {pmid30440041, year = {2018}, author = {Kawaka, F and Makonde, H and Dida, M and Opala, P and Ombori, O and Maingi, J and Muoma, J}, title = {Genetic diversity of symbiotic bacteria nodulating common bean (Phaseolus vulgaris) in western Kenya.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0207403}, pmid = {30440041}, issn = {1932-6203}, mesh = {*Bacteria/classification/genetics ; Kenya ; Nitrogen Fixation/physiology ; Phaseolus/growth & development/*microbiology ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Root Nodules, Plant/*microbiology ; Symbiosis/*physiology ; }, abstract = {Biological nitrogen fixation (BNF) in legumes plays a critical role in improving soil fertility. Despite this vital role, there is limited information on the genetic diversity and BNF of bacteria nodulating common bean (Phaseolus vulgaris L.). This study evaluated the genetic diversity and symbiotic nitrogen fixation of bacteria nodulating common bean in soils of Western Kenya. The genetic diversity was determined using 16S rRNA gene partial sequences while BNF was estimated in a greenhouse experiment. The sequences of the native isolates were closely affiliated with members from the genera Pantoea, Klebsiella, Rhizobium, Enterobacter and Bacillus. These results show that apart from rhizobia, there are non-rhizobial strains in the nodules of common bean. The symbiotic efficiency (SE) of native isolates varied and exhibited comparable or superior BNF compared to the local commercial inoculants (CIAT 899 and Strain 446). Isolates (MMUST 003 [KP027691], MMUST 004 [KP027687], MMUST 005 [KP027688], KSM 001 [KP027682], KSM 002 [KP027680], KSM 003 [KP027683] and KSM 005 [KP027685]) recorded equal or significantly higher SE (p < 0.05) compared to N supplemented treatments. The results demonstrate the presence of genetic diversity of native bacteria nodulating bean that are effective in N fixation. These elite bacterial strains should be exploited as candidates for the development of Phaseolus vulgaris inoculants.}, } @article {pmid30408087, year = {2018}, author = {Elias, LG and Silva, DB and Silva, R and Peng, YQ and Yang, DR and Lopes, NP and Pereira, RAS}, title = {A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0207051}, pmid = {30408087}, issn = {1932-6203}, mesh = {Animals ; Ficus/*physiology ; Molecular Weight ; Pollination ; *Symbiosis ; Venoms/chemistry/*metabolism ; Wasps/*metabolism/physiology ; }, abstract = {The galling habit represents a complex type of interaction between insects and plants, ranging from antagonism to mutualism. The obligate pollination mutualism between Ficus and fig wasps relies strongly on the induction of galls in Ficus flowers, where wasps' offspring develop. Even though gall induction plays an important role in many insect-plant interactions, the mechanisms that trigger gall formation are still not completely known. Using a fingerprinting approach, we show here that venom protein profiles from galling fig wasps differ from the venom profiles of non-galling species, suggesting the secretion plays different roles according to the type of interaction it is involved in. Each studied cleptoparasitic species had a distinct venom profile, suggesting that cleptoparasitism in fig wasps covers a vast diversity of molecular interactions. Fig wasp venoms are mainly composed of peptides. No low molecular weight compounds were detected by UPLC-DAD-MS, suggesting that such compounds (e.g., IAA and cytokinines) are not involved in gall induction. The differences in venom composition observed between galling and non-galling fig wasp species bring new perspectives to the study of gall induction processes and the role of insect secretions.}, } @article {pmid29535364, year = {2018}, author = {Séne, S and Selosse, MA and Forget, M and Lambourdière, J and Cissé, K and Diédhiou, AG and Rivera-Ocasio, E and Kodja, H and Kameyama, N and Nara, K and Vincenot, L and Mansot, JL and Weber, J and Roy, M and Sylla, SN and Bâ, A}, title = {A pantropically introduced tree is followed by specific ectomycorrhizal symbionts due to pseudo-vertical transmission.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1806-1816}, pmid = {29535364}, issn = {1751-7370}, mesh = {Basidiomycota/classification/genetics/isolation & purification/*physiology ; Brazil ; Caribbean Region ; Japan ; Mycorrhizae/genetics/growth & development/isolation & purification/*physiology ; Polygonaceae/*microbiology ; Seedlings/microbiology/physiology ; Soil ; Spores, Fungal/classification/genetics/isolation & purification/physiology ; *Symbiosis ; Trees/*microbiology/physiology ; }, abstract = {Global trade increases plant introductions, but joint introduction of associated microbes is overlooked. We analyzed the ectomycorrhizal fungi of a Caribbean beach tree, seagrape (Coccoloba uvifera, Polygonacaeae), introduced pantropically to stabilize coastal soils and produce edible fruits. Seagrape displays a limited symbiont diversity in the Caribbean. In five regions of introduction (Brazil, Japan, Malaysia, Réunion and Senegal), molecular barcoding showed that seagrape mostly or exclusively associates with Scleroderma species (Basidiomycota) that were hitherto only known from Caribbean seagrape stands. An unknown Scleroderma species dominates in Brazil, Japan and Malaysia, while Scleroderma bermudense exclusively occurs in Réunion and Senegal. Population genetics analysis of S. bermudense did not detect any demographic bottleneck associated with a possible founder effect, but fungal populations from regions where seagrape is introduced are little differentiated from the Caribbean ones, separated by thousands of kilometers, consistently with relatively recent introduction. Moreover, dry seagrape fruits carry Scleroderma spores, probably because, when drying on beach sand, they aggregate spores from the spore bank accumulated by semi-hypogeous Scleroderma sporocarps. Aggregated spores inoculate seedlings, and their abundance may limit the founder effect after seagrape introduction. This rare pseudo-vertical transmission of mycorrhizal fungi likely contributed to efficient and repeated seagrape/Scleroderma co-introductions.}, } @article {pmid29476142, year = {2018}, author = {Desirò, A and Hao, Z and Liber, JA and Benucci, GMN and Lowry, D and Roberson, R and Bonito, G}, title = {Mycoplasma-related endobacteria within Mortierellomycotina fungi: diversity, distribution and functional insights into their lifestyle.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1743-1757}, pmid = {29476142}, issn = {1751-7370}, mesh = {Biodiversity ; Burkholderia/classification/genetics/isolation & purification/*physiology ; Fungi/chemistry/*physiology ; Mycoplasma/classification/genetics/isolation & purification/*physiology ; Phylogeny ; *Symbiosis ; }, abstract = {Bacterial interactions with animals and plants have been examined for over a century; by contrast, the study of bacterial-fungal interactions has received less attention. Bacteria interact with fungi in diverse ways, and endobacteria that reside inside fungal cells represent the most intimate interaction. The most significant bacterial endosymbionts that have been studied are associated with Mucoromycota and include two main groups: Burkholderia-related and Mycoplasma-related endobacteria (MRE). Examples of Burkholderia-related endobacteria have been reported in the three Mucoromycota subphyla. By contrast, MRE have only been identified in Glomeromycotina and Mucoromycotina. This study aims to understand whether MRE dwell in Mortierellomycotina and, if so, to determine their impact on the fungal host. We carried out a large-scale screening of 394 Mortierellomycotina strains and employed a combination of microscopy, molecular phylogeny, next-generation sequencing and qPCR. We detected MRE in 12 strains. These endosymbionts represent novel bacterial phylotypes and show evidence of recombination. Their presence in Mortierellomycotina demonstrates that MRE occur within fungi across Mucoromycota and they may have lived in their common ancestor. We cured the fungus of its endosymbionts with antibiotics and observed improved biomass production in isogenic lines lacking MRE, demonstrating that these endobacteria impose some fitness costs to their fungal host. Here we provided the first functional insights into the lifestyle of MRE. Our findings indicate that MRE may be antagonistic to their fungal hosts, and adapted to a non-lethal parasitic lifestyle in the mycelium of Mucoromycota. However, context-dependent adaptive benefits to their host at minimal cost cannot not be excluded. Finally, we conclude that Mortierellomycotina represent attractive model organisms for exploring interactions between MRE and fungi.}, } @article {pmid30978547, year = {2019}, author = {Munzi, S and Cruz, C and Corrêa, A}, title = {When the exception becomes the rule: An integrative approach to symbiosis.}, journal = {The Science of the total environment}, volume = {672}, number = {}, pages = {855-861}, doi = {10.1016/j.scitotenv.2019.04.038}, pmid = {30978547}, issn = {1879-1026}, abstract = {Symbiosis, mainly due to the advances in -omics technology and to the microbiome revolution, is being increasingly acknowledged as fundamental to explain any aspect of life existence. Previously considered an exception, a peculiar characteristic of few systems like lichens, corals and mycorrhizas, symbiosis is nowadays recognized as the rule, with the microbiome being part of all living entities and systems. However, our knowledge of the ecological meaning and functioning of many symbiotic systems is still limited. Here, we discuss a new, integrative approach based on current findings that looks at commonalities among symbiotic systems to produce theoretical models and conceptual knowledge that would allow a more efficient exploitation of symbiosis-based biotechnologies. The microbiome recruitment and assemblage processes are indicated as one of the potential targets where a holistic approach could bring advantages. Finally, we reflect on the potential socio-economic and environmental consequences of a symbiotic view of the world, where co-dependence is the matrix of life.}, } @article {pmid30977796, year = {2019}, author = {Salinero-Lanzarote, A and Pacheco-Moreno, A and Domingo-Serrano, L and Durán, D and Ormeño-Orrillo, E and Martínez-Romero, E and Albareda, M and Palacios, JM and Rey, L}, title = {The type VI secretion system of Rhizobium etli Mim1 has a positive effect in symbiosis.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz054}, pmid = {30977796}, issn = {1574-6941}, abstract = {The type six secretion systems (T6SSs) allow bacteria to translocate effector proteins to other bacteria or to eukaryotic cells. However, little is known about the role of T6SS in endosymbiotic bacteria. In this work we describe the T6SS of Rhizobium etli Mim1, a bacteria able to effectively nodulate common beans. Structural genes and those encoding possible effectors have been identified in a 28-gene DNA region of R. etli Mim1 pRetMIM1f plasmid. Immunodetection of Hcp protein, a conserved key structural component of T6SS systems, indicates that this secretion system is active at high cell densities, in the presence of root exudates, and in bean nodules. R. etli mutants affected in T6SS structural genes produced plants with lower dry weight and smaller nodules than the wild-type strain, indicating for the first time that the T6SS plays a positive role in Rhizobium-legume symbiosis.}, } @article {pmid30977533, year = {2019}, author = {Wu, Z and Wang, M and Yang, S and Chen, S and Chen, X and Liu, C and Wang, S and Wang, H and Zhang, B and Liu, H and Qin, R and Wang, X}, title = {A global coexpression network of soybean genes gives insight into the evolution of nodulation in non-legumes and legumes.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15845}, pmid = {30977533}, issn = {1469-8137}, abstract = {A coexpression network is a powerful tool for revealing genes' relationship with many biological processes. Mass transcriptomic and genomic data from different plant species provide the foundation for understanding the evolution of nodulation across the Viridiplantae at a systematic level. We used weighted coexpression network analysis (WGCNA) to mine a nodule-related module (NRM) in Glycine max. Comparative genomic analysis of 78 green plant species revealed that NRM genes are recruited from different evolutionary nodes along with gene duplication events. A set of core coexpressed genes within legumes that may play vital roles in regulating nodule environments essential for nitrogen fixation, including oxygen concentrations, sulfur transport, and iron homeostasis (such as GmCHY). The regulation of these genes occurred mainly at the transcription level, although some of them, such as sulfate transporters, may also undergo positive selection at protein level. We revealed that ancient orthologs and duplication events prior to the origin of legumes were preadapted for symbiosis. Conserved coregulated genes found within legumes paved the way for nodule formation and nitrogen fixation. These findings provide significant insights into the evolution of nodulation and indicate promising candidates for identifying other key components of legume nodulation and nitrogen fixation. This article is protected by copyright. All rights reserved.}, } @article {pmid30976084, year = {2019}, author = {Kim, GB and Son, SU and Yu, HJ and Mun, JH}, title = {MtGA2ox10 encoding C20-GA2-oxidase regulates rhizobial infection and nodule development in Medicago truncatula.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5952}, doi = {10.1038/s41598-019-42407-3}, pmid = {30976084}, issn = {2045-2322}, support = {PJ012251//Rural Development Administration (RDA)/ ; PJ012421//Rural Development Administration (RDA)/ ; }, abstract = {Gibberellin (GA) plays a controversial role in the legume-rhizobium symbiosis. Recent studies have shown that the GA level in legumes must be precisely controlled for successful rhizobial infection and nodule organogenesis. However, regulation of the GA level via catabolism in legume roots has not been reported to date. Here, we investigate a novel GA inactivating C20-GA2-oxidase gene MtGA2ox10 in Medicago truncatula. RNA sequencing analysis and quantitative polymerase chain reaction revealed that MtGA2ox10 was induced as early as 6 h post-inoculation (hpi) of rhizobia and reached peak transcript abundance at 12 hpi. Promoter::β-glucuronidase fusion showed that the promoter activity was localized in the root infection/differentiation zone during the early stage of rhizobial infection and in the vascular bundle of the mature nodule. The CRISPR/Cas9-mediated deletion mutation of MtGA2ox10 suppressed infection thread formation, which resulted in reduced development and retarded growth of nodules on the Agrobacterium rhizogenes-transformed roots. Over-expression of MtGA2ox10 in the stable transgenic plants caused dwarfism, which was rescued by GA3 application, and increased infection thread formation but inhibition of nodule development. We conclude that MtGA2ox10 plays an important role in the rhizobial infection and the development of root nodules through fine catabolic tuning of GA in M. truncatula.}, } @article {pmid30976027, year = {2019}, author = {Lefoulon, E and Vaisman, N and Frydman, HM and Sun, L and Foster, JM and Slatko, BE}, title = {Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5939}, doi = {10.1038/s41598-019-42454-w}, pmid = {30976027}, issn = {2045-2322}, abstract = {Symbiosis is a major force of evolutionary change, influencing virtually all aspects of biology, from population ecology and evolution to genomics and molecular/biochemical mechanisms of development and reproduction. A remarkable example is Wolbachia endobacteria, present in some parasitic nematodes and many arthropod species. Acquisition of genomic data from diverse Wolbachia clades will aid in the elucidation of the different symbiotic mechanisms(s). However, challenges of de novo assembly of Wolbachia genomes include the presence in the sample of host DNA: nematode/vertebrate or insect. We designed biotinylated probes to capture large fragments of Wolbachia DNA for sequencing using PacBio technology (LEFT-SEQ: Large Enriched Fragment Targeted Sequencing). LEFT-SEQ was used to capture and sequence four Wolbachia genomes: the filarial nematode Brugia malayi, wBm, (21-fold enrichment), Drosophila mauritiana flies (2 isolates), wMau (11-fold enrichment), and Aedes albopictus mosquitoes, wAlbB (200-fold enrichment). LEFT-SEQ resulted in complete genomes for wBm and for wMau. For wBm, 18 single-nucleotide polymorphisms (SNPs), relative to the wBm reference, were identified and confirmed by PCR. A limit of LEFT-SEQ is illustrated by the wAlbB genome, characterized by a very high level of insertion sequences elements (ISs) and DNA repeats, for which only a 20-contig draft assembly was achieved.}, } @article {pmid30975812, year = {2019}, author = {Gogoleva, NE and Nikolaichik, YA and Ismailov, TT and Khlopko, YA and Dmitrieva, SA and Konnova, TA and Ermekkaliev, TS and Safronova, VI and Belimov, AA and Gogolev, YV}, title = {Complete Genome Sequence of Abscisic Acid-Metabolizing Rhizobacterium Rhodococcus sp. Strain P1Y.}, journal = {Microbiology resource announcements}, volume = {8}, number = {15}, pages = {}, doi = {10.1128/MRA.01591-18}, pmid = {30975812}, issn = {2576-098X}, abstract = {Mechanisms of microbial catabolism of phytohormone abscisic acid (ABA) are still unknown. Here, we report the complete genome sequence of ABA-utilizing Rhodococcus sp. strain P1Y, isolated from the rice (Oryza sativa L.) rhizosphere. The sequence was obtained using an approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequence data.}, } @article {pmid30825301, year = {2019}, author = {Coyne, MJ and Comstock, LE}, title = {Type VI Secretion Systems and the Gut Microbiota.}, journal = {Microbiology spectrum}, volume = {7}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.PSIB-0009-2018}, pmid = {30825301}, issn = {2165-0497}, support = {R01 AI093771/AI/NIAID NIH HHS/United States ; R01 AI120633/AI/NIAID NIH HHS/United States ; }, mesh = {Antibiosis ; Bacteria/*metabolism/pathogenicity ; Bacterial Proteins ; Colon/microbiology ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Proteobacteria/metabolism ; Symbiosis ; *Type VI Secretion Systems/antagonists & inhibitors/genetics/immunology ; }, abstract = {The human colonic microbiota is a dense ecosystem comprised of numerous microbes, including bacteria, phage, fungi, archaea, and protozoa, that compete for nutrients and space. Studies are beginning to reveal the antagonistic mechanisms that gut bacteria use to compete with other members of this ecosystem. In the healthy human colon, the majority of the Gram-negative bacteria are of the order Bacteroidales. Proteobacteria, such as Escherichia coli, are numerically fewer but confer important properties to the host, such as colonization resistance. Several enteric pathogens use type VI secretion systems (T6SSs) to antagonize symbiotic gut E. coli, facilitating colonization and disease progression. T6SS loci are also widely distributed in human gut Bacteroidales, which includes three predominant genera: Bacteroides, Parabacteroides, and Prevotella. There are three distinct genetic architectures of T6SS loci among the gut Bacteroidales, termed GA1, GA2, and GA3. GA1 and GA2 T6SS loci are contained on integrative and conjugative elements and are the first T6SS loci shown to be readily transferred in the human gut between numerous species and families of Bacteroidales. In contrast, the GA3 T6SSs are present exclusively in Bacteroides fragilis. There are divergent regions in all three T6SS GAs that contain genes encoding effector and immunity proteins, many of which function by unknown mechanisms. To date, only the GA3 T6SSs have been shown to antagonize bacteria, and they target nearly all gut Bacteroidales species analyzed. This review delves more deeply into properties of the T6SSs of these human gut bacteria and the ecological outcomes of their synthesis in vivo.}, } @article {pmid30588764, year = {2019}, author = {Woyke, T and Schulz, F}, title = {Entities inside one another - a matryoshka doll in biology?.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {26-28}, doi = {10.1111/1758-2229.12716}, pmid = {30588764}, issn = {1758-2229}, mesh = {*Biological Evolution ; Eukaryota/physiology ; Giant Viruses/physiology ; Metagenomics ; Microbial Consortia ; Organelles/physiology ; *Symbiosis ; Thiothrix/physiology ; }, } @article {pmid30516032, year = {2019}, author = {Danchin, A}, title = {Conceptual sequel to biological expeditions at the time of global changes.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {38-40}, doi = {10.1111/1758-2229.12722}, pmid = {30516032}, issn = {1758-2229}, mesh = {Adaptation, Physiological ; Biological Evolution ; *Climate Change ; *Expeditions ; Humans ; Intrinsically Disordered Proteins/chemistry/metabolism ; Pacific Ocean ; Symbiosis ; }, } @article {pmid29514991, year = {2018}, author = {Lam, WN and Lim, RJY and Wong, SH and Tan, HTW}, title = {Predatory dipteran larva contributes to nutrient sequestration in a carnivorous pitcher plant.}, journal = {Biology letters}, volume = {14}, number = {3}, pages = {}, pmid = {29514991}, issn = {1744-957X}, mesh = {Ammonium Compounds/*metabolism ; Animals ; Diptera/growth & development/*physiology ; Food Chain ; Larva/growth & development/physiology ; Nutrients/metabolism ; *Predatory Behavior ; Sarraceniaceae/*physiology ; Singapore ; *Symbiosis ; }, abstract = {The fluids of Nepenthes pitcher plants are habitats to many specialized animals known as inquilines, which facilitate the conversion of prey protein into pitcher-absorbable nitrogen forms such as ammonium. Xenoplatyura beaveri (Diptera: Mycetophilidae) is a predatory dipteran inquiline that inhabits the pitchers of Nepenthes ampullaria Larvae of X. beaveri construct sticky webs over the fluid surface of N. ampullaria to ensnare emerging adult dipteran inquilines. However, the interaction between X. beaveri and its host has never been examined before, and it is not known if X. beaveri can contribute to nutrient sequestration in N. ampullaria. Xenoplatyura beaveri individuals were reared in artificial pitchers in the laboratory on a diet of emergent Tripteroides tenax mosquitoes, and the ammonium concentration of the pitcher fluids was measured over time. Fluid ammonium concentration in tubes containing X. beaveri was significantly greater than those of the controls. Furthermore, fluid ammonium concentrations increased greatly after X. beaveri larvae metamorphosed, although the cause of this increase could not be identified. Our results show that a terrestrial, inquiline predator can contribute significantly to nutrient sequestration in the phytotelma it inhabits, and suggest that this interaction has a net mutualistic outcome for both species.}, } @article {pmid30972304, year = {2019}, author = {Choudhary, E and Sharma, R and Kumar, Y and Agarwal, N}, title = {Conditional Silencing by CRISPRi Reveals the Role of DNA Gyrase in Formation of Drug-Tolerant Persister Population in Mycobacterium tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {70}, doi = {10.3389/fcimb.2019.00070}, pmid = {30972304}, issn = {2235-2988}, abstract = {Drug tolerance in mycobacterial pathogens is a global concern. Fluoroquinolone (FQ) treatment is widely used for induction of persisters in bacteria. Although FQs that target DNA gyrase are currently used as second-line anti-tuberculosis (TB) drugs, little is known about their impact on Mycobacterium tuberculosis (Mtb) persister formation. Here we explored the CRISPRi-based genetic repression for better understanding the effect of DNA gyrase depletion on Mtb physiology and response to anti-TB drugs. We find that suppression of DNA gyrase drastically affects intra- and extracellular growth of Mtb. Interestingly, gyrase depletion in Mtb leads to activation of RecA/LexA-mediated SOS response and drug tolerance via induction of persister subpopulation. Chemical inhibition of RecA in gyrase-depleted bacteria results in reversion of persister phenotype and better killing by antibiotics. This study provides evidence that inhibition of SOS response can be advantageous in improving the efficacy of anti-TB drugs and shortening the duration of current TB treatment.}, } @article {pmid30972043, year = {2019}, author = {Mills, JG and Brookes, JD and Gellie, NJC and Liddicoat, C and Lowe, AJ and Sydnor, HR and Thomas, T and Weinstein, P and Weyrich, LS and Breed, MF}, title = {Relating Urban Biodiversity to Human Health With the 'Holobiont' Concept.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {550}, doi = {10.3389/fmicb.2019.00550}, pmid = {30972043}, issn = {1664-302X}, abstract = {A relatively unaccounted ecosystem service from biodiversity is the benefit to human health via symbiotic microbiota from our environment. This benefit occurs because humans evolved alongside microbes and have been constantly exposed to diverse microbiota. Plants and animals, including humans, are organised as a host with symbiotic microbiota, whose collective genome and life history form a single holobiont. As such, there are interdependencies between biodiversity, holobionts, and public health which lead us to argue that human health outcomes could be improved by increasing contact with biodiversity in an urban context. We propose that humans, like all holobionts, likely require a diverse microbial habitat to appropriate resources for living healthy, long lives. We discuss how industrial urbanisation likely disrupts the symbiosis between microbiota and their hosts, leading to negative health outcomes. The industrialised urban habitat is low in macro and microbial biodiversity and discourages contact with beneficial environmental microbiota. These habitat factors, alongside diet, antibiotics, and others, are associated with the epidemic of non-communicable diseases in these societies. We suggest that restoration of urban microbial biodiversity and micro-ecological processes through microbiome rewilding can benefit holobiont health and aid in treating the urban non-communicable disease epidemic. Further, we identify research gaps and some solutions to economic and strategic hurdles in applying microbiome rewilding into daily urban life.}, } @article {pmid30971198, year = {2019}, author = {Malinich, EA and Wang, K and Mukherjee, PK and Kolomiets, M and Kenerley, CM}, title = {Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {280}, doi = {10.1186/s12864-019-5651-z}, pmid = {30971198}, issn = {1471-2164}, support = {2016-67013-24730//National Institute of Food and Agriculture/ ; }, abstract = {BACKGROUND: Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-industrial products. To better take advantage of this fungal-plant symbiosis it is necessary to obtain detailed knowledge of which genes Trichoderma utilizes during interaction with its plant host. In this study, we explored the transcriptional activity undergone by T. virens during two phases of symbiosis with maize; recognition of roots and after ingress into the root cortex.

RESULTS: We present a model of T. virens - maize interaction wherein T. virens experiences global repression of transcription upon recognition of maize roots and then induces expression of a broad spectrum of genes during colonization of maize roots. The genes expressed indicate that, during colonization of maize roots, T. virens modulates biosynthesis of phytohormone-like compounds, secretes a plant-environment specific array of cell wall degrading enzymes and secondary metabolites, remodels both actin-based and cell membrane structures, and shifts metabolic activity. We also highlight transcription factors and signal transduction genes important in future research seeking to unravel the molecular mechanisms of T. virens activity in maize roots.

CONCLUSIONS: T. virens displays distinctly different transcriptional profiles between recognizing the presence of maize roots and active colonization of these roots. A though understanding of these processes will allow development of T. virens as a bio-control agent. Further, the publication of these datasets will target future research endeavors specifically to genes of interest when considering T. virens - maize symbiosis.}, } @article {pmid30603945, year = {2018}, author = {Pavlova, LV}, title = {First Finding of Representatives of the Eccrinida Order in the Digestive Tract of King Crab Specie from the Barents Sea.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {483}, number = {1}, pages = {231-234}, doi = {10.1134/S0012496618060066}, pmid = {30603945}, issn = {1608-3105}, mesh = {Animals ; Anomura/*anatomy & histology ; Gastrointestinal Tract/*anatomy & histology ; *Symbiosis ; }, abstract = {This is the first report on the finding of large intra-intestinal symbionts belonging to the order Eccrinida in crab-like decapod crustaceans of the family Lithodidae, Paralithodes camtschaticus and Lithodes maja, inhabiting the Barents Sea. Studies have been regularly conducted since the early 2000s in Kola Bay and in one of the inlets of the Eastern Murman Coast. Since 2005, Eccrinida representatives (presumably, a new species of the genus Arundinula) have been found in the guts of the red king crab. A brief description of the endosymbionts and data on their frequency of occurrence are presented. The possible reasons for the distribution of eccrinids in the crab-like decapod crustaceans of the Barents Sea are discussed.}, } @article {pmid30598000, year = {2018}, author = {Mannaa, M and Park, I and Seo, YS}, title = {Genomic Features and Insights into the Taxonomy, Virulence, and Benevolence of Plant-Associated Burkholderia Species.}, journal = {International journal of molecular sciences}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijms20010121}, pmid = {30598000}, issn = {1422-0067}, support = {918019-04-1-HD030//Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture, Food and Rural Affairs, Republic of Korea/ ; }, mesh = {Burkholderia/classification/*genetics/pathogenicity ; Crops, Agricultural/*microbiology ; *Genome, Bacterial ; *Host-Pathogen Interactions ; Phylogeny ; Symbiosis ; }, abstract = {The members of the Burkholderia genus are characterized by high versatility and adaptability to various ecological niches. With the availability of the genome sequences of numerous species of Burkholderia, many studies have been conducted to elucidate the unique features of this exceptional group of bacteria. Genomic and metabolic plasticity are common among Burkholderia species, as evidenced by their relatively large multi-replicon genomes that are rich in insertion sequences and genomic islands and contain a high proportion of coding regions. Such unique features could explain their adaptability to various habitats and their versatile lifestyles, which are reflected in a multiplicity of species including free-living rhizospheric bacteria, plant endosymbionts, legume nodulators, and plant pathogens. The phytopathogenic Burkholderia group encompasses several pathogens representing threats to important agriculture crops such as rice. Contrarily, plant-beneficial Burkholderia have also been reported, which have symbiotic and growth-promoting roles. In this review, the taxonomy of Burkholderia is discussed emphasizing the recent updates and the contributions of genomic studies to precise taxonomic positioning. Moreover, genomic and functional studies on Burkholderia are reviewed and insights are provided into the mechanisms underlying the virulence and benevolence of phytopathogenic and plant-beneficial Burkholderia, respectively, on the basis of cutting-edge knowledge.}, } @article {pmid30552831, year = {2019}, author = {Manzello, DP and Matz, MV and Enochs, IC and Valentino, L and Carlton, RD and Kolodziej, G and Serrano, X and Towle, EK and Jankulak, M}, title = {Role of host genetics and heat-tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida Keys with ocean warming.}, journal = {Global change biology}, volume = {25}, number = {3}, pages = {1016-1031}, doi = {10.1111/gcb.14545}, pmid = {30552831}, issn = {1365-2486}, mesh = {Alveolata/genetics/*physiology ; Animals ; Anthozoa/genetics/*parasitology/*physiology ; Coral Reefs ; Florida ; Genetic Variation ; *Hot Temperature ; Oceans and Seas ; *Symbiosis ; Thermotolerance/genetics/*physiology ; }, abstract = {Identifying which factors lead to coral bleaching resistance is a priority given the global decline of coral reefs with ocean warming. During the second year of back-to-back bleaching events in the Florida Keys in 2014 and 2015, we characterized key environmental and biological factors associated with bleaching resilience in the threatened reef-building coral Orbicella faveolata. Ten reefs (five inshore, five offshore, 179 corals total) were sampled during bleaching (September 2015) and recovery (May 2016). Corals were genotyped with 2bRAD and profiled for algal symbiont abundance and type. O. faveolata at the inshore sites, despite higher temperatures, demonstrated significantly higher bleaching resistance and better recovery compared to offshore. The thermotolerant Durusdinium trenchii (formerly Symbiondinium trenchii) was the dominant endosymbiont type region-wide during initial (78.0% of corals sampled) and final (77.2%) sampling; >90% of the nonbleached corals were dominated by D. trenchii. 2bRAD host genotyping found no genetic structure among reefs, but inshore sites showed a high level of clonality. While none of the measured environmental parameters were correlated with bleaching, 71% of variation in bleaching resistance and 73% of variation in the proportion of D. trenchii was attributable to differences between genets, highlighting the leading role of genetics in shaping natural bleaching patterns. Notably, D. trenchii was rarely dominant in O. faveolata from the Florida Keys in previous studies, even during bleaching. The region-wide high abundance of D. trenchii was likely driven by repeated bleaching associated with the two warmest years on record for the Florida Keys (2014 and 2015). On inshore reefs in the Upper Florida Keys, O. faveolata was most abundant, had the highest bleaching resistance, and contained the most corals dominated by D. trenchii, illustrating a causal link between heat tolerance and ecosystem resilience with global change.}, } @article {pmid29584555, year = {2019}, author = {Garcia-Gutierrez, E and Mayer, MJ and Cotter, PD and Narbad, A}, title = {Gut microbiota as a source of novel antimicrobials.}, journal = {Gut microbes}, volume = {10}, number = {1}, pages = {1-21}, doi = {10.1080/19490976.2018.1455790}, pmid = {29584555}, issn = {1949-0984}, support = {BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Infective Agents/isolation & purification/*metabolism/pharmacology ; Antimicrobial Cationic Peptides/isolation & purification/metabolism/pharmacology ; Bacteria/chemistry/drug effects/*metabolism ; Bacteriocins/isolation & purification/*metabolism/pharmacology ; Gastrointestinal Microbiome/drug effects/*physiology ; Homeostasis ; Humans ; Symbiosis ; }, abstract = {Bacteria, Archaea, Eukarya and viruses coexist in the human gut, and this coexistence is functionally balanced by symbiotic or antagonistic relationships. Antagonism is often characterized by the production of antimicrobials against other organisms occupying the same environmental niche. Indeed, close co-evolution in the gut has led to the development of specialized antimicrobials, which is attracting increased attention as these may serve as novel alternatives to antibiotics and thereby help to address the global problem of antimicrobial resistance. The gastrointestinal (GI) tract is especially suitable for finding novel antimicrobials due to the vast array of microbes that inhabit it, and a considerable number of antimicrobial producers of both wide and narrow spectrum have been described. In this review, we summarize some of the antimicrobial compounds that are produced by bacteria isolated from the gut environment, with a special focus on bacteriocins. We also evaluate the potential therapeutic application of these compounds to maintain homeostasis in the gut and the biocontrol of pathogenic bacteria.}, } @article {pmid30968126, year = {2019}, author = {Berger, A and Boscari, A and Frendo, P and Brouquisse, R}, title = {Nitric oxide signaling, metabolism and toxicity in nitrogen-fixing symbiosis.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erz159}, pmid = {30968126}, issn = {1460-2431}, abstract = {The interactions between legumes and Rhizobia lead to the establishment of a symbiotic relationship characterized by the formation of a new organ, the nodule, which facilitates the fixation of atmospheric nitrogen (N2) by nitrogenase through the creation of a hypoxic environment. Significant amounts of nitric oxide (NO) accumulate at different stages of nodule development, suggesting that NO performs specific signaling and/or metabolic functions during symbiosis. NO, which regulates nodule gene expression, accumulates to high levels in hypoxic nodules. NO accumulation is considered to assist energy metabolism within the hypoxic environment of the nodule via a phytoglobin/NO-mediated respiration process. NO is a potent inhibitor of the activity of nitrogenase and other plant/bacterial enzymes, acting as a developmental signal in the induction of nodule senescence. Hence, key questions concern the relative importance of the signaling/metabolic functions of NO versus its toxic action and how NO levels are regulated to be compatible with nitrogen fixation functions. This review analyses these paradoxical roles of NO at various stages of symbiosis, and highlights the role of plant phytoglobins and bacterial hemoproteins in the control of NO accumulation.}, } @article {pmid30967024, year = {2019}, author = {Kang, L}, title = {Overview: biotic signalling for smart pest management.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1767}, pages = {20180306}, doi = {10.1098/rstb.2018.0306}, pmid = {30967024}, issn = {1471-2970}, abstract = {Biotic signalling refers to species or phylogenetic-clade-specific signals that elicit adaptive and acceptable responses within and among organisms. It is not only the molecular basis of the ecological relationships among different species, such as parasitism, symbiosis and predation, but also serves as ideal targets that can be used to manipulate these ecological relationships. This concept was proposed by a group of scientists from the Chinese Academy of Sciences (CAS) and actively pursued in a five-year research project in 2014 funded by the CAS ($40 million), entitled 'Decoding biotic interactions and mechanism for target management of agricultural pests'. The multi-disciplinary project aimed at a systematic investigation of the intra-species and inter-species and interactions via biotic signalling, with the ultimate goal being the development of novel methods to manage the pest insects and diseases. We hereby propose a topic 'Biotic signalling sheds light on smart pest control' as a theme issue for the Philosophical Transactions of the Royal Society B. It contains a total of 18 reviews and research articles under the topic of signalling manipulation for pest management. Unravelling these complex interactions among plants, microbial pathogens and insects holds promise for developing novel strategies to protect crop plants without compromising agricultural productivity and environmental health. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.}, } @article {pmid30817773, year = {2019}, author = {Weiss, BL and Maltz, MA and Vigneron, A and Wu, Y and Walter, KS and O'Neill, MB and Wang, J and Aksoy, S}, title = {Colonization of the tsetse fly midgut with commensal Kosakonia cowanii Zambiae inhibits trypanosome infection establishment.}, journal = {PLoS pathogens}, volume = {15}, number = {2}, pages = {e1007470}, doi = {10.1371/journal.ppat.1007470}, pmid = {30817773}, issn = {1553-7374}, support = {U01 AI115648/AI/NIAID NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; D43 TW007391/TW/FIC NIH HHS/United States ; R21 AI101456/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Africa South of the Sahara ; Animals ; Anopheles/microbiology ; Enterobacteriaceae ; Female ; Humans ; Male ; Mosquito Vectors/microbiology/parasitology ; Symbiosis ; Trypanosoma brucei brucei/*pathogenicity ; Trypanosoma congolense/*pathogenicity ; Trypanosomiasis, African/metabolism/microbiology/parasitology/*prevention & control ; Tsetse Flies/*microbiology/*parasitology ; }, abstract = {Tsetse flies (Glossina spp.) vector pathogenic trypanosomes (Trypanosoma spp.) in sub-Saharan Africa. These parasites cause human and animal African trypanosomiases, which are debilitating diseases that inflict an enormous socio-economic burden on inhabitants of endemic regions. Current disease control strategies rely primarily on treating infected animals and reducing tsetse population densities. However, relevant programs are costly, labor intensive and difficult to sustain. As such, novel strategies aimed at reducing tsetse vector competence require development. Herein we investigated whether Kosakonia cowanii Zambiae (Kco_Z), which confers Anopheles gambiae with resistance to Plasmodium, is able to colonize tsetse and induce a trypanosome refractory phenotype in the fly. Kco_Z established stable infections in tsetse's gut and exhibited no adverse effect on the fly's survival. Flies with established Kco_Z infections in their gut were significantly more refractory to infection with two distinct trypanosome species (T. congolense, 6% infection; T. brucei, 32% infection) than were age-matched flies that did not house the exogenous bacterium (T. congolense, 36% infected; T. brucei, 70% infected). Additionally, 52% of Kco_Z colonized tsetse survived infection with entomopathogenic Serratia marcescens, compared with only 9% of their wild-type counterparts. These parasite and pathogen refractory phenotypes result from the fact that Kco_Z acidifies tsetse's midgut environment, which inhibits trypanosome and Serratia growth and thus infection establishment. Finally, we determined that Kco_Z infection does not impact the fecundity of male or female tsetse, nor the ability of male flies to compete with their wild-type counterparts for mates. We propose that Kco_Z could be used as one component of an integrated strategy aimed at reducing the ability of tsetse to transmit pathogenic trypanosomes.}, } @article {pmid30789967, year = {2019}, author = {Li, P and Liu, C and Deng, WH and Yao, DM and Pan, LL and Li, YQ and Liu, YQ and Liang, Y and Zhou, XP and Wang, XW}, title = {Plant begomoviruses subvert ubiquitination to suppress plant defenses against insect vectors.}, journal = {PLoS pathogens}, volume = {15}, number = {2}, pages = {e1007607}, doi = {10.1371/journal.ppat.1007607}, pmid = {30789967}, issn = {1553-7374}, mesh = {Animals ; Begomovirus/*metabolism/pathogenicity ; Cyclopentanes/metabolism ; Hemiptera/*metabolism/virology ; Insect Vectors/metabolism ; Oxylipins/metabolism ; Plant Diseases/virology ; Plant Viruses/pathogenicity ; Symbiosis ; Tobacco/virology ; Ubiquitination ; }, abstract = {Most plant viruses are vectored by insects and the interactions of virus-plant-vector have important ecological and evolutionary implications. Insect vectors often perform better on virus-infected plants. This indirect mutualism between plant viruses and insect vectors promotes the spread of virus and has significant agronomical effects. However, few studies have investigated how plant viruses manipulate plant defenses and promote vector performance. Begomoviruses are a prominent group of plant viruses in tropical and sub-tropical agro-ecosystems and are transmitted by whiteflies. Working with the whitefly Bemisia tabaci, begomoviruses and tobacco, we revealed that C2 protein of begomoviruses lacking DNA satellites was responsible for the suppression of plant defenses against whitefly vectors. We found that infection of plants by tomato yellow leaf curl virus (TYLCV), one of the most devastating begomoviruses worldwide, promoted the survival and reproduction of whitefly vectors. TYLCV C2 protein suppressed plant defenses by interacting with plant ubiquitin. This interaction compromised the degradation of JAZ1 protein, thus inhibiting jasmonic acid defense and the expression of MYC2-regulated terpene synthase genes. We further demonstrated that function of C2 protein among begomoviruses not associated with satellites is well conserved and ubiquitination is an evolutionarily conserved target of begomoviruses for the suppression of plant resistance to whitefly vectors. Taken together, these results demonstrate that ubiquitination inhibition by begomovirus C2 protein might be a general mechanism in begomovirus, whitefly and plant interactions.}, } @article {pmid29895336, year = {2018}, author = {Harmer, J and Yurchenko, V and Nenarokova, A and Lukeš, J and Ginger, ML}, title = {Farming, slaving and enslavement: histories of endosymbioses during kinetoplastid evolution.}, journal = {Parasitology}, volume = {145}, number = {10}, pages = {1311-1323}, doi = {10.1017/S0031182018000781}, pmid = {29895336}, issn = {1469-8161}, mesh = {Biodiversity ; *Biological Evolution ; Evolution, Molecular ; Genome, Protozoan ; Kinetoplastida/*genetics ; Leishmania/genetics/physiology ; *Symbiosis ; Trypanosoma/genetics/physiology ; Trypanosomatina/*genetics ; }, abstract = {Parasitic trypanosomatids diverged from free-living kinetoplastid ancestors several hundred million years ago. These parasites are relatively well known, due in part to several unusual cell biological and molecular traits and in part to the significance of a few - pathogenic Leishmania and Trypanosoma species - as aetiological agents of serious neglected tropical diseases. However, the majority of trypanosomatid biodiversity is represented by osmotrophic monoxenous parasites of insects. In two lineages, novymonads and strigomonads, osmotrophic lifestyles are supported by cytoplasmic endosymbionts, providing hosts with macromolecular precursors and vitamins. Here we discuss the two independent origins of endosymbiosis within trypanosomatids and subsequently different evolutionary trajectories that see entrainment vs tolerance of symbiont cell divisions cycles within those of the host. With the potential to inform on the transition to obligate parasitism in the trypanosomatids, interest in the biology and ecology of free-living, phagotrophic kinetoplastids is beginning to enjoy a renaissance. Thus, we take the opportunity to additionally consider the wider relevance of endosymbiosis during kinetoplastid evolution, including the indulged lifestyle and reductive evolution of basal kinetoplastid Perkinsela.}, } @article {pmid29794045, year = {2018}, author = {Harrison, E and Hall, JPJ and Brockhurst, MA}, title = {Migration promotes plasmid stability under spatially heterogeneous positive selection.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1879}, pages = {}, pmid = {29794045}, issn = {1471-2954}, mesh = {Environment ; *Gene Transfer, Horizontal ; Mercury ; Plasmids/*genetics ; Pseudomonas fluorescens/*genetics ; Selection, Genetic ; *Symbiosis ; }, abstract = {Bacteria-plasmid associations can be mutualistic or antagonistic depending on the strength of positive selection for plasmid-encoded genes, with contrasting outcomes for plasmid stability. In mutualistic environments, plasmids are swept to high frequency by positive selection, increasing the likelihood of compensatory evolution to ameliorate the plasmid cost, which promotes long-term stability. In antagonistic environments, plasmids are purged by negative selection, reducing the probability of compensatory evolution and driving their extinction. Here we show, using experimental evolution of Pseudomonas fluorescens and the mercury-resistance plasmid, pQBR103, that migration promotes plasmid stability in spatially heterogeneous selection environments. Specifically, migration from mutualistic environments, by increasing both the frequency of the plasmid and the supply of compensatory mutations, stabilized plasmids in antagonistic environments where, without migration, they approached extinction. These data suggest that spatially heterogeneous positive selection, which is common in natural environments, coupled with migration helps to explain the stability of plasmids and the ecologically important genes that they encode.}, } @article {pmid29701776, year = {2018}, author = {Karimi, E and Slaby, BM and Soares, AR and Blom, J and Hentschel, U and Costa, R}, title = {Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy074}, pmid = {29701776}, issn = {1574-6941}, mesh = {Animals ; Carbon/metabolism ; Genome, Bacterial/genetics ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen/metabolism ; Phylogeny ; Porifera/*microbiology ; Rhodospirillaceae/genetics/*metabolism ; Sulfur/metabolism ; Symbiosis/*physiology ; }, abstract = {Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.}, } @article {pmid29668923, year = {2018}, author = {Lund, MB and Mogensen, MF and Marshall, IPG and Albertsen, M and Viana, F and Schramm, A}, title = {Genomic insights into the Agromyces-like symbiont of earthworms and its distribution among host species.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy068}, pmid = {29668923}, issn = {1574-6941}, mesh = {Actinomycetales/*classification/*genetics/growth & development ; Animals ; Base Sequence ; DNA, Bacterial/genetics ; Genome, Bacterial/*genetics ; Genomics ; Host Microbial Interactions/physiology ; Host Specificity ; Oligochaeta/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis/*physiology ; }, abstract = {The nephridia (excretory organs) of lumbricid earthworms generally harbor symbiotic bacteria. In the compost worms Eisenia fetida and E. andrei, these comprise Verminephrobacter, Ca. Nephrothrix and an Agromyces-like symbiont. While diversity, transmission, and function of the first two symbionts has been unraveled in recent years, little is known about the biology of the uncultured Agromyces-like symbiont or about its distribution within lumbricid earthworms.In this study, we sequenced a cocoon metagenome of E. andrei and assembled a 96.3% complete genome of the Agromyces-like symbiont, which indicates a heterotrophic and potentially microaerophilic lifestyle. A 16S rRNA gene based survey showed that the Agromyces-like symbiont has a narrow host range (present in 10 out of 51 investigated lumbricid earthworm species) and is likely species-specific or at least specific for groups of closely related host species. The Agromyces-like symbionts form a monophyletic group and feature a reduced genome with AT-bias and very low genome-wide similarity to closely related Agromyces spp. (average amino acid identity of 64%); therefore, we suggest establishing a novel genus for the Agromyces-like symbionts of earthworms, for which we propose the name Candidatus Lumbricidophila, with the specific symbiont of Eisenia andrei as novel species Ca. L. eiseniae.}, } @article {pmid29642956, year = {2018}, author = {Silva, FM and Kostygov, AY and Spodareva, VV and Butenko, A and Tossou, R and Lukeš, J and Yurchenko, V and Alves, JMP}, title = {The reduced genome of Candidatus Kinetoplastibacterium sorsogonicusi, the endosymbiont of Kentomonas sorsogonicus (Trypanosomatidae): loss of the haem-synthesis pathway.}, journal = {Parasitology}, volume = {145}, number = {10}, pages = {1287-1293}, doi = {10.1017/S003118201800046X}, pmid = {29642956}, issn = {1469-8161}, mesh = {Betaproteobacteria/drug effects/*genetics/growth & development ; Biosynthetic Pathways ; *Genome, Bacterial ; Heme/*metabolism/pharmacology ; Phylogeny ; Sequence Analysis, DNA ; *Symbiosis ; Trypanosomatina/*microbiology ; }, abstract = {Trypanosomatids of the genera Angomonas and Strigomonas (subfamily Strigomonadinae) have long been known to contain intracellular beta-proteobacteria, which provide them with many important nutrients such as haem, essential amino acids and vitamins. Recently, Kentomonas sorsogonicus, a divergent member of Strigomonadinae, has been described. Herein, we characterize the genome of its endosymbiont, Candidatus Kinetoplastibacterium sorsogonicusi. This genome is completely syntenic with those of other known Ca. Kinetoplastibacterium spp., but more reduced in size (~742 kb, compared with 810-833 kb, respectively). Gene losses are not concentrated in any hot-spots but are instead distributed throughout the genome. The most conspicuous loss is that of the haem-synthesis pathway. For long, removing haemin from the culture medium has been a standard procedure in cultivating trypanosomatids isolated from insects; continued growth was considered as an evidence of endosymbiont presence. However, we demonstrate that, despite bearing the endosymbiont, K. sorsogonicus cannot grow in culture without haem. Thus, the traditional test cannot be taken as a reliable criterion for the absence or presence of endosymbionts in trypanosomatid flagellates. It remains unclear why the ability to synthesize such an essential compound was lost in Ca. K. sorsogonicusi, whereas all other known bacterial endosymbionts of trypanosomatids retain them.}, } @article {pmid29463894, year = {2018}, author = {Nielsen, DA and Petrou, K and Gates, RD}, title = {Coral bleaching from a single cell perspective.}, journal = {The ISME journal}, volume = {12}, number = {6}, pages = {1558-1567}, pmid = {29463894}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*physiology ; *Coral Reefs ; Dinoflagellida/*physiology ; Fluorescent Dyes/chemistry ; Glutathione/metabolism ; Hawaii ; Lipid Peroxidation ; Microscopy, Confocal ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Stress, Physiological ; Symbiosis/*physiology ; Temperature ; }, abstract = {Ocean warming is resulting in increased occurrence of mass coral bleaching; a response in which the intracellular algal endosymbionts (Symbiodinium sp.) are expelled from the coral host due to physiological stress. This detrimental process is often attributed to overproduction of reactive oxygen species (ROS) that leak out of the endosymbionts and causes damage to the host cell, though direct evidence validating this link is limited. Here, for the first time, we used confocal microscopy and fluorescent dyes to investigate if endosymbiont ROS production significantly and predictably affects physiological parameters in its host cell. Heat treatment resulted in a 60% reduction in coral symbiont density, a ~70% increase in median endosymbiont ROS and a small reduction in photosystem efficiency (FV/FM, 11%), indicating absence of severe light stress. Notably, no other physiological parameters were affected in either endosymbionts or host cells, including reduced glutathione and ROS-induced lipid peroxidation. Taken together, the increase in endosymbiont ROS could not be linked to physiological damage in either partner, suggesting that oxidative stress is unlikely to have been the driver for symbiont expulsion in this study.}, } @article {pmid29371249, year = {2018}, author = {Johnson, JM and Thürich, J and Petutschnig, EK and Altschmied, L and Meichsner, D and Sherameti, I and Dindas, J and Mrozinska, A and Paetz, C and Scholz, SS and Furch, ACU and Lipka, V and Hedrich, R and Schneider, B and Svatoš, A and Oelmüller, R}, title = {A Poly(A) Ribonuclease Controls the Cellotriose-Based Interaction between Piriformospora indica and Its Host Arabidopsis.}, journal = {Plant physiology}, volume = {176}, number = {3}, pages = {2496-2514}, pmid = {29371249}, issn = {1532-2548}, mesh = {Arabidopsis/genetics/metabolism/*microbiology ; Arabidopsis Proteins/genetics/metabolism ; Basidiomycota/*physiology ; Calcium/metabolism ; Cellulose/metabolism ; Exoribonucleases/genetics/*metabolism ; Gene Expression Regulation, Plant ; Mutation ; Plants, Genetically Modified ; Protein-Serine-Threonine Kinases/genetics/metabolism ; Seedlings/metabolism/microbiology ; Signal Transduction ; Symbiosis/*physiology ; Trioses/metabolism ; }, abstract = {Piriformospora indica, an endophytic root-colonizing fungus, efficiently promotes plant growth and induces resistance to abiotic stress and biotic diseases. P. indica fungal cell wall extract induces cytoplasmic calcium elevation in host plant roots. Here, we show that cellotriose (CT) is an elicitor-active cell wall moiety released by P. indica into the medium. CT induces a mild defense-like response, including the production of reactive oxygen species, changes in membrane potential, and the expression of genes involved in growth regulation and root development. CT-based cytoplasmic calcium elevation in Arabidopsis (Arabidopsis thaliana) roots does not require the BAK1 coreceptor or the putative Ca2+ channels TPC1, GLR3.3, GLR2.4, and GLR2.5 and operates synergistically with the elicitor chitin. We identified an ethyl methanesulfonate-induced mutant (cytoplasmiccalcium elevation mutant) impaired in the response to CT and various other cellooligomers (n = 2-7), but not to chitooligomers (n = 4-8), in roots. The mutant contains a single nucleotide exchange in the gene encoding a poly(A) ribonuclease (AtPARN; At1g55870) that degrades the poly(A) tails of specific mRNAs. The wild-type PARN cDNA, expressed under the control of a 35S promoter, complements the mutant phenotype. Our identification of cellotriose as a novel chemical mediator casts light on the complex P. indica-plant mutualistic relationship.}, } @article {pmid29284744, year = {2018}, author = {Kryvoruchko, IS and Routray, P and Sinharoy, S and Torres-Jerez, I and Tejada-Jiménez, M and Finney, LA and Nakashima, J and Pislariu, CI and Benedito, VA and González-Guerrero, M and Roberts, DM and Udvardi, MK}, title = {An Iron-Activated Citrate Transporter, MtMATE67, Is Required for Symbiotic Nitrogen Fixation.}, journal = {Plant physiology}, volume = {176}, number = {3}, pages = {2315-2329}, pmid = {29284744}, issn = {1532-2548}, mesh = {Carrier Proteins/genetics/metabolism ; Citrates/metabolism ; Gene Expression Regulation, Plant ; Iron/*metabolism/pharmacokinetics ; Medicago truncatula/microbiology/*physiology ; Mutation ; Nitrogen Fixation/*physiology ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants, Genetically Modified ; Root Nodules, Plant/growth & development/metabolism/microbiology ; Symbiosis/physiology ; }, abstract = {Iron (Fe) is an essential micronutrient for symbiotic nitrogen fixation in legume nodules, where it is required for the activity of bacterial nitrogenase, plant leghemoglobin, respiratory oxidases, and other Fe proteins in both organisms. Fe solubility and transport within and between plant tissues is facilitated by organic chelators, such as nicotianamine and citrate. We have characterized a nodule-specific citrate transporter of the multidrug and toxic compound extrusion family, MtMATE67 of Medicago truncatula The MtMATE67 gene was induced early during nodule development and expressed primarily in the invasion zone of mature nodules. The MtMATE67 protein was localized to the plasma membrane of nodule cells and also the symbiosome membrane surrounding bacteroids in infected cells. In oocytes, MtMATE67 transported citrate out of cells in an Fe-activated manner. Loss of MtMATE67 gene function resulted in accumulation of Fe in the apoplasm of nodule cells and a substantial decrease in symbiotic nitrogen fixation and plant growth. Taken together, the results point to a primary role of MtMATE67 in citrate efflux from nodule cells in response to an Fe signal. This efflux is necessary to ensure Fe(III) solubility and mobility in the apoplasm and uptake into nodule cells. Likewise, MtMATE67-mediated citrate transport into the symbiosome space would increase the solubility and availability of Fe(III) for rhizobial bacteroids.}, } @article {pmid30963950, year = {2019}, author = {Uchiumi, Y and Ohtsuki, H and Sasaki, A}, title = {Evolution of self-limited cell division of symbionts.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1895}, pages = {20182238}, doi = {10.1098/rspb.2018.2238}, pmid = {30963950}, issn = {1471-2954}, abstract = {In mutualism between unicellular hosts and their endosymbionts, symbiont's cell division is often synchronized with its host's, ensuring the permanent relationship between endosymbionts and their hosts. The evolution of synchronized cell division thus has been considered to be an essential step in the evolutionary transition from symbionts to organelles. However, if symbionts would accelerate their cell division without regard for the synchronization with the host, they would proliferate more efficiently. Thus, it is paradoxical that symbionts evolve to limit their own division for synchronized cell division. Here, we theoretically explore the condition for the evolution of self-limited cell division of symbionts, by assuming that symbionts control their division rate and that hosts control symbionts' death rate by intracellular digestion and nutrient supply. Our analysis shows that symbionts can evolve to limit their own cell division. Such evolution occurs if not only symbiont's but also host's benefit through symbiosis is large. Moreover, the coevolution of hosts and symbionts leads to either permanent symbiosis where symbionts proliferate to keep pace with their host, or the arms race between symbionts that behave as lytic parasites and hosts that resist them by rapid digestion.}, } @article {pmid30963860, year = {2019}, author = {Skelton, J and Johnson, AJ and Jusino, MA and Bateman, CC and Li, Y and Hulcr, J}, title = {A selective fungal transport organ (mycangium) maintains coarse phylogenetic congruence between fungus-farming ambrosia beetles and their symbionts.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1894}, pages = {20182127}, doi = {10.1098/rspb.2018.2127}, pmid = {30963860}, issn = {1471-2954}, abstract = {Thousands of species of ambrosia beetles excavate tunnels in wood to farm fungi. They maintain associations with particular lineages of fungi, but the phylogenetic extent and mechanisms of fidelity are unknown. We test the hypothesis that selectivity of their mycangium enforces fidelity at coarse phylogenetic scales, while permitting promiscuity among closely related fungal mutualists. We confirm a single evolutionary origin of the Xylosandrus complex-a group of several xyleborine genera that farm fungi in the genus Ambrosiella. Multi-level co-phylogenetic analysis revealed frequent symbiont switching within major Ambrosiella clades, but not between clades. The loss of the mycangium in Diuncus, a genus of evolutionary cheaters, was commensurate with the loss of fidelity to fungal clades, supporting the hypothesis that the mycangium reinforces fidelity. Finally, in vivo experiments tracked symbiotic compatibility throughout the symbiotic life cycle of Xylosandrus compactus and demonstrated that closely related Ambrosiella symbionts are interchangeable, but the probability of fungal uptake in the mycangium was significantly lower in more phylogenetically distant species of symbionts. Symbiont loads in experimental subjects were similar to wild-caught beetles. We conclude that partner choice in ambrosia beetles is achieved in the mycangium, and co-phylogenetic inferences can be used to predict the likelihood of specific symbiont switches.}, } @article {pmid30962361, year = {2019}, author = {Jäckle, O and Seah, BKB and Tietjen, M and Leisch, N and Liebeke, M and Kleiner, M and Berg, JS and Gruber-Vodicka, HR}, title = {Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1818995116}, pmid = {30962361}, issn = {1091-6490}, abstract = {Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria symbionts in mouthless Paracatenula flatworms comprise up to half of the biomass of the consortium. Each species of Paracatenula harbors a specific Ca Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of Paracatenula from Sant'Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont, Ca R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29-4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs, Ca R. santandreae's versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that Ca R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts-serving as the primary energy storage for its animal host.}, } @article {pmid30961763, year = {2019}, author = {Jin, Y and Kim, HU and Hong, S and Shin, C and Kulkarni, A and Kim, T}, title = {Effect of Copper Foil Crystal Orientation on Graphene Quality Synthesized by Chemical Vapor Deposition.}, journal = {Journal of nanoscience and nanotechnology}, volume = {19}, number = {9}, pages = {5942-5948}, doi = {10.1166/jnn.2019.16599}, pmid = {30961763}, issn = {1533-4880}, abstract = {Line defects such as wrinkles are believed to change the electrical properties of graphene. However, they are often observed in graphene grown via chemical vapor deposition; hence, it is important to study the impact of the substrate condition on graphene quality. In this work, graphene was synthesized on various copper domains with different crystal orientations and surface morphologies. During the synthesis process, three typical crystal orientations were obtained Cu(001), Cu(101), and Cu(111) showing different surface morphologies with various densities of wrinkles. Graphene wrinkles along with copper wrinkles were studied using atomic force microscopy and Kelvin probe force microscopy. The quality of graphene on different crystal orientations and morphologies was evaluated as well. It was found that different crystallographic orientations lead to different degrees of wrinkle and roughness. In addition, these wrinkle defects exhibited characteristic surface potential variations and the density of substrate wrinkles was closely associated with the uniformity of graphene and led to a disordered structure and low crystallinity.}, } @article {pmid30958898, year = {2019}, author = {Zlatogursky, VV and Gerasimova, EA and Drachko, D and Klimov, VI and Shɨshkin, Y and Plotnikov, AO}, title = {Pinjata ruminata gen. et sp. n. - a New Member of Centrohelid Family Yogsothothidae (Haptista: Centroplasthelida) from the Brackish River.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12737}, pmid = {30958898}, issn = {1550-7408}, abstract = {A new genus and species of centrohelid heliozoan Pinjata ruminata from the Tuzlukkol' River (Orenburg Region of Russia) and Gor'koe Lake (Chelyabinsk Region of Russia) is studied with light- and electron microscopy. P. ruminata has two types of plate scales, partially running up the sides of the axopodia. Inner plate scales (3.2-4.9 × 1.5-2.6 μm) are flat, ovate-oblong and have a broad axial thickening and a thin electron-dense border. Outer plate scales (4.2-6.7 ×1.5-3.0 μm) are concave, elongated, of irregular shape, often curved and broadened towards one end. Roundish depressions are forming two rows on both sides of the narrow axial thickening. The cells are attached to the substratum. Molecular phylogenetic analysis based on the SSU rDNA robustly placed P. ruminata in the family Yogsothothidae. This position is confirmed with presence of 5 panacanthocystid increase regions. The morphology of the new genus is in a good accordance with diagnosis of the family. The status of a genus "Heteroraphidiophrys" is discussed. Other potential findings of Pinjata from literature are analyzed. Pinjata represents the third lineage of centrohelids, characterized with the presence of only tangentially-oriented plate scales. The halophilic nature of Yogsothothidae is suggested. This article is protected by copyright. All rights reserved.}, } @article {pmid30957149, year = {2019}, author = {Wu, QS and He, JD and Srivastava, AK and Zou, YN and Kuča, K}, title = {Mycorrhiza enhances drought tolerance of citrus by altering root fatty acid compositions and their saturation levels.}, journal = {Tree physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/treephys/tpz039}, pmid = {30957149}, issn = {1758-4469}, abstract = {Arbuscular mycorrhizas (AMs) have the ability to enhance drought tolerance of citrus, while the underlying mechanisms are not clearly elucidated. Considering the strong association of cell membrane fatty acid (FA) unsaturation with plant drought tolerance, the present study hypothesized that arbuscular mycorrhizal fungi (AMF) modulated the composition and unsaturation of FAs to enhance drought tolerance of host plants. A drought-sensitive citrus rootstock, trifoliate orange (Poncirus trifoliata) seedlings, were inoculated with AMF (Funneliformis mosseae) for 3 months, and were subsequently exposed to drought stress (DS) for 8 weeks. Mycorrhizal seedlings exhibited better plant growth performance, higher leaf water potential, and lower root abscisic acid concentrations under both well-watered (WW) and DS, respectively. AMF inoculation considerably increased root methyl oleate (C18:1), methyl linoleate (C18:2) and methyl linolenate (C18:3 N3) concentrations under both WW and DS and root methyl palmitoleate (C16:1) concentrations under WW, while decreased root methyl stearate (C18:0) levels under both WW and DS. These changes in the composition of FAs of mycorrhized roots resulted in higher unsaturation index of root FAs (UIFA), which later aided in reducing the oxidative damage on account of lower concentration of malondialdehyde and superoxide radicals. The changes of these FAs were a result of AMF-up-regulating root fatty acid desaturase 2 (PtFAD2), fatty acid desaturase 6 (PtFAD6) and Δ9 fatty acid desaturase (PtΔ9) genes under WW and PtFAD2, PtFAD6 and Δ15 fatty acid desaturase (PtΔ15) genes under DS. Our results confirmed that mycorrhization brought significant changes in root FA compositions, in addition to regulation of gene expression responsible for increasing the unsaturation level of FAs, a pre-disposing physiological event for better drought tolerance of citrus.}, } @article {pmid30955777, year = {2019}, author = {McCauley, M and Goulet, TL}, title = {Caribbean gorgonian octocorals cope with nutrient enrichment.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {621-628}, doi = {10.1016/j.marpolbul.2019.02.067}, pmid = {30955777}, issn = {1879-3363}, abstract = {Corals inhabit oligotrophic waters, thriving amidst limited nutrients such as nitrogen and phosphorous. When nutrient levels increase, usually due to human activity, the symbiosis of dinoflagellates (family Symbiodiniaceae) with scleractinian corals can break down. Although gorgonian corals dominate many Caribbean reefs, the impact of enrichment on them and their algae is understudied. We exposed two gorgonian species, Pseudoplexaura porosa and Eunicea tourneforti, to elevated concentrations of either ammonium (10 μM or 50 μM) or phosphate (4 μM). Enrichment with 10 μM ammonium increased chlorophyll content and algal density in both species, whereas the host biochemical composition was unaffected. Exposure to 50 μM ammonium only reduced the quantum yield in P. porosa and mitotic indices in both species. Conversely, algal carbon and nitrogen content within E. tourneforti increased with 4 μM phosphate exposure. These gorgonian species coped with short-term nutrient enrichment, furthering our understanding of the success of Caribbean gorgonians.}, } @article {pmid30545059, year = {2018}, author = {Neupane, A and Feng, C and Feng, J and Kafle, A and Bücking, H and Lee Marzano, SY}, title = {Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus Rhizophagus spp.}, journal = {Viruses}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/v10120707}, pmid = {30545059}, issn = {1999-4915}, mesh = {Fungal Viruses/*genetics/isolation & purification ; *Gene Expression Profiling ; Genome, Viral ; Mycorrhizae/*virology ; Plant Roots/*genetics/microbiology ; Plants/microbiology ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal fungi (AMF), including Rhizophagus spp., can play important roles in nutrient cycling of the rhizosphere. However, the effect of virus infection on AMF's role in nutrient cycling cannot be determined without first knowing the diversity of the mycoviruses in AMF. Therefore, in this study, we sequenced the R. irregularis isolate-09 due to its previously demonstrated high efficiency in increasing the N/P uptake of the plant. We identified one novel mitovirus contig of 3685 bp, further confirmed by reverse transcription-PCR. Also, publicly available Rhizophagus spp. RNA-Seq data were analyzed to recover five partial virus sequences from family Narnaviridae, among which four were from R. diaphanum MUCL-43196 and one was from R. irregularis strain-C2 that was similar to members of the Mitovirus genus. These contigs coded genomes larger than the regular mitoviruses infecting pathogenic fungi and can be translated by either a mitochondrial translation code or a cytoplasmic translation code, which was also reported in previously found mitoviruses infecting mycorrhizae. The five newly identified virus sequences are comprised of functionally conserved RdRp motifs and formed two separate subclades with mitoviruses infecting Gigasporamargarita and Rhizophagusclarus, further supporting virus-host co-evolution theory. This study expands our understanding of virus diversity. Even though AMF is notably hard to investigate due to its biotrophic nature, this study demonstrates the utility of whole root metatranscriptome.}, } @article {pmid30427852, year = {2018}, author = {Brito, TL and Campos, AB and Bastiaan von Meijenfeldt, FA and Daniel, JP and Ribeiro, GB and Silva, GGZ and Wilke, DV and de Moraes, DT and Dutilh, BE and Meirelles, PM and Trindade-Silva, AE}, title = {The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0200437}, pmid = {30427852}, issn = {1932-6203}, mesh = {Animals ; Bivalvia/*microbiology/physiology ; Gammaproteobacteria/*enzymology/genetics/*physiology ; Genomics ; Gills/microbiology ; Glycoside Hydrolases/genetics/*metabolism ; Metagenome ; Microbiota ; Multigene Family ; Phylogeny ; Polysaccharides/*metabolism ; Secondary Metabolism ; *Symbiosis ; Wood/metabolism/parasitology ; }, abstract = {Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae "clade I" strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.}, } @article {pmid30244151, year = {2019}, author = {Schön, I and Kamiya, T and Van den Berghe, T and Van den Broecke, L and Martens, K}, title = {Novel Cardinium strains in non-marine ostracod (Crustacea) hosts from natural populations.}, journal = {Molecular phylogenetics and evolution}, volume = {130}, number = {}, pages = {406-415}, doi = {10.1016/j.ympev.2018.09.008}, pmid = {30244151}, issn = {1095-9513}, mesh = {Animals ; Aquatic Organisms/*microbiology ; Bacteroidetes/genetics/*physiology ; Base Sequence ; Crustacea/genetics/*microbiology ; Diptera/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; }, abstract = {Endosymbiotic bacteria are known from many metazoan taxa, where they manipulate host biology and reproduction. Here, we used classic PCR amplification and direct DNA sequencing with universal primers for four different endosymbionts to test for their presence in more than 300 specimens of three recent non-marine ostracod superfamilies from different geographic areas and aquatic habitats. We verified these results with "high throughput" amplicon sequencing of 16S of nine selected specimens and evolutionary placement algorithms. The phylogenetic position of endosymbionts detected in ostracod hosts was compared to known endosymbionts from other metazoans. While Wolbachia, Spiroplasma and Rickettsia are absent, we find evidence for the general presence of Cardinium bacteria in natural populations of various non-marine ostracod species. Phylogenetic reconstructions based on Cardinium 16S data and estimates of genetic distances both indicate that Cardinium from ostracods are distantly related to Cardinium from Diptera and Nematoda but represent novel strains with a monophyletic origin. Cardinium bacteria from different ostracod hosts have genetic distances of up to 3.8%, providing evidence against recent and frequent horizontal transmissions amongst the three ostracod superfamilies. High throughput sequencing reveals more than 400 different 16S amplicon sequence variants in the investigated ostracods as well as the presence of different Cardinium strains within individual Eucypris virens and Heterocypris hosts. These results call for future, more in-depth investigations. Mapping Cardinium infections on COI trees of non-marine ostracod hosts shows that the occurrence of these endosymbionts is not linked to genetic species identity or phylogenetic host groups and, except for one ostracod morphospecies, prevalence never reaches 100%.}, } @article {pmid29934746, year = {2018}, author = {Fan, X and Song, F}, title = {Responses of nonenzymatic antioxidants to atrazine in arbuscular mycorrhizal roots of Medicago sativa L.}, journal = {Mycorrhiza}, volume = {28}, number = {5-6}, pages = {567-571}, pmid = {29934746}, issn = {1432-1890}, support = {31500431//National Natural Science Foundation of China/ ; 31270535//National Natural Science Foundation of China/ ; 31570635//National Natural Science Foundation of China/ ; UNPYSCT-2016077//Innovative Talents Training Program of Heilongjiang Province for General Universities/ ; 2017RAQXJ065//Scientific and Technological Innovation Talent Project of Harbin/ ; 2017RALXJ008//Scientific and Technological Innovation Talent Project of Harbin/ ; }, mesh = {Antioxidants/*analysis ; Atrazine/*pharmacology ; Flavonoids/analysis ; Medicago sativa/*metabolism/microbiology ; Mycorrhizae/*drug effects/metabolism ; Plant Roots/*drug effects/microbiology ; Stress, Physiological ; *Symbiosis ; }, abstract = {Atrazine induces the production of reactive oxygen species (ROS), which are detoxified by enzymatic and nonenzymatic mechanisms in plants. Arbuscular mycorrhizal fungi improve on this first level of plant resistance to environmental stresses through the antioxidant defense system, but the way in which nonenzymatic antioxidants relate to atrazine in arbuscular mycorrhizal roots is not well-known. In this study, a symbiotic relationship between Funneliformis mosseae and Medicago sativa L. roots was established successfully. Then, a non-targeted metabolite analysis which was hypothesis-free concerning particular metabolites was used to provide a comprehensive metabolic fingerprint and to subsequently identify, quantify, and finally find different nonenzymatic antioxidants in mycorrhizal and non-mycorrhizal roots following atrazine addition. Tocotrienol, (iso)flavonoids, and their derivate concentrations in F. mosseae-M. sativa mycorrhizal roots were significantly higher than in non-mycorrhizal roots. The majority of (iso)flavonoids and their derivates increased significantly via methylation or glycosylation, but dehydroascorbic acid in its oxidized form decreased significantly in mycorrhizal roots. In general, F. mosseae colonization results in significantly greater nonenzymatic antioxidant tocotrienol and (iso)flavonoids derivate concentrations in M. sativa roots, which may be associated with resistance to atrazine.}, } @article {pmid29931404, year = {2018}, author = {Gryndler, M and Šmilauer, P and Püschel, D and Bukovská, P and Hršelová, H and Hujslová, M and Gryndlerová, H and Beskid, O and Konvalinková, T and Jansa, J}, title = {Appropriate nonmycorrhizal controls in arbuscular mycorrhiza research: a microbiome perspective.}, journal = {Mycorrhiza}, volume = {28}, number = {5-6}, pages = {435-450}, pmid = {29931404}, issn = {1432-1890}, mesh = {Andropogon/microbiology ; Bacteria/metabolism ; Biomass ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Mycorrhizae/*physiology ; Phosphorus/analysis ; Plant Roots/*microbiology ; *Soil Microbiology ; Symbiosis ; }, abstract = {Establishment of nonmycorrhizal controls is a "classic and recurrent theme" in mycorrhizal research. For decades, authors reported mycorrhizal plant growth/nutrition as compared to various nonmycorrhizal controls. In such studies, uncertainties remain about which nonmycorrhizal controls are most appropriate and, in particular, what effects the control inoculations have on substrate and root microbiomes. Here, different types of control and mycorrhizal inoculations were compared with respect to plant growth and nutrition, as well as the structure of root and substrate microbiomes, assessed by next-generation sequencing. We compared uninoculated ("absolute") control to inoculation with blank pot culture lacking arbuscular mycorrhizal fungi, filtrate of that blank inoculum, and filtrate of complex pot-produced mycorrhizal inoculum. Those treatments were compared to a standard mycorrhizal treatment, where the previously sterilized substrate was inoculated with complex pot-produced inoculum containing Rhizophagus irregularis SYM5. Besides this, monoxenically produced inoculum of the same fungus was applied either alone or in combination with blank inoculum. The results indicate that the presence of mycorrhizal fungus always resulted in stimulation of Andropogon gerardii plant biomass as well as in elevated phosphorus content of the plants. The microbial (bacterial and fungal) communities developing in the differently inoculated treatments, however, differed substantially from each other and no control could be obtained comparable with the treatment inoculated with complex mycorrhizal inoculum. Soil microorganisms with significant biological competences that could potentially contribute to the effects of the various inoculants on the plants were detected in roots and in plant cultivation substrate in some of the treatments.}, } @article {pmid29766387, year = {2018}, author = {Shutoh, K and Suetsugu, K and Kaneko, S and Kurosawa, T}, title = {Comparative morphological analysis of two parallel mycoheterotrophic transitions reveals divergent and convergent traits in the genus Pyrola (Pyroleae, Ericaceae).}, journal = {Journal of plant research}, volume = {131}, number = {4}, pages = {589-597}, pmid = {29766387}, issn = {1618-0860}, support = {a Grant-in-Aid from Japan Society for the Promotio//Japan Society for the Promotion of Science/ ; }, mesh = {Biological Evolution ; Flowers/anatomy & histology ; Fungi/physiology ; Phylogeny ; Plant Leaves/anatomy & histology ; Pyrola/*anatomy & histology/microbiology/physiology ; Quantitative Trait, Heritable ; *Symbiosis/physiology ; }, abstract = {The genus Pyrola includes species with different degree of mycoheterotrophy; some species possess individuals that rely on all carbon through their associations with fungi (full mycoheterotrophy, FM), whereas some species obtain carbon through both fungi and photosynthesis by itself (partial mycoheterotrophy, PM). To investigate how plant functional traits of photosynthesis and reproduction are related to the degree of mycoheterotrophy in the initial stage of the transition from PM to FM, we determined morphological traits in FM (or nearly FM) and PM species in two independent lineages, P. picta and P. japonica complexes. We used herbarium specimens and examined leaf number, leaf area, flower number, and scape length in FM or nearly FM species (P. aphylla and P. subaphylla) and PM species (P. picta s.l. and P. japonica). We found a leaf area reduction in FM (or nearly FM) species in both lineages, suggesting that this is a convergent trait. The number of flowers was not significantly different between FM (or nearly FM) and PM species in both lineages. On the other hand, differences in the variation between FM (or nearly FM) and PM species were found in some traits between the two lineages. The FM (or nearly FM) species in one lineage only possessed rudimentary leaves, whereas that in the other linage possessed a few small, ordinary leaves in addition to those with only rudimentary leaves. The scape length of the FM (or nearly FM) species was significantly longer than that of PM species in one lineage, whereas it was shorter in the other lineage. The different and common variations are divergent and convergent traits, respectively, that could be associated with the transition to FM in Pylora. In addition, shoots of both PM species occasionally lacked ordinary leaves, possibly indicating possession of these shoots is preadaptation for the transition to FM in Pyrola.}, } @article {pmid28842582, year = {2017}, author = {Tornabene, C and Martindale, RC and Wang, XT and Schaller, MF}, title = {Detecting Photosymbiosis in Fossil Scleractinian Corals.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9465}, pmid = {28842582}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*physiology ; Biological Evolution ; Coral Reefs ; *Fossils ; Nitrogen Isotopes/analysis ; Nutrients/metabolism ; Pacific Ocean ; *Photosynthesis ; *Symbiosis ; }, abstract = {The evolutionary success of reef-building corals is often attributed to photosymbiosis, a mutualistic relationship scleractinian corals developed with zooxanthellae; however, because zooxanthellae are not fossilized, it is difficult (and contentious) to determine whether ancient corals harbored symbionts. In this study, we analyze the δ15N of skeletal organic matrix in a suite of modern and fossil scleractinian corals (zooxanthellate- and azooxanthellate-like) with varying levels of diagenetic alteration. Significantly, we report the first analyses that distinguish shallow-water zooxanthellate and deep-water azooxanthellate fossil corals. Early Miocene (18-20 Ma) corals exhibit the same nitrogen isotopic ratio offset identified in modern corals. These results suggest that the coral organic matrix δ15N proxy can successfully be used to detect photosymbiosis in the fossil record. This proxy will significantly improve our ability to effectively define the evolutionary relationship between photosymbiosis and reef-building through space and time. For example, Late Triassic corals have symbiotic values, which tie photosymbiosis to major coral reef expansion. Furthermore, the early Miocene corals from Indonesia have low δ15N values relative to modern corals, implying that the west Pacific was a nutrient-depleted environment and that oligotrophy may have facilitated the diversification of the reef builders in the Coral Triangle.}, } @article {pmid30953569, year = {2019}, author = {Arimoto, A and Hikosaka-Katayama, T and Hikosaka, A and Tagawa, K and Inoue, T and Ueki, T and Yoshida, MA and Kanda, M and Shoguchi, E and Hisata, K and Satoh, N}, title = {A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, doi = {10.1093/gigascience/giz023}, pmid = {30953569}, issn = {2047-217X}, abstract = {BACKGROUND: Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.

FINDINGS: To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17-kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.

CONCLUSIONS: Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.}, } @article {pmid30952658, year = {2019}, author = {Mohammed, M and Jaiswal, SK and Dakora, FD}, title = {Insights into the phylogeny, nodule functioning and biogeographic distribution of microsymbionts nodulating the orphan Kersting's groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet] in African soils.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00342-19}, pmid = {30952658}, issn = {1098-5336}, abstract = {Kersting's groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet] is a neglected indigenous African legume adapted to growth in N-deficient soils due to its ability to fix atmospheric N2 via symbiosis with rhizobia. Despite its nutritional and medicinal uses, to date, there is little information on the phylogeny and functional traits of its microsymbionts, an aspect much needed for its conservation and improvement. This study explored the morpho-genetic diversity, phylogenetic relationships and N2-fixing efficiency of Kersting's groundnut rhizobial isolates from contrasting environments in Ghana, South Africa and Mozambique. Box-PCR fingerprinting revealed high diversity among rhizobial populations which was influenced by geographic origin. Of the 164 isolates evaluated, 130 Box-PCR types were identified at 70% similarity coefficient, indicating that they were not clones. Soil pH and mineral concentrations were found to influence the distribution of bradyrhizobial populations in African soils. Phylogenetic analysis of 16S rRNA gene and multilocus sequence analysis of protein-coding genes (atpD, glnII, gyrB and rpoB) and symbiotic genes (nifH and nodC) showed that, Kersting's groundnut is primarily nodulated by members of genus Bradyrhizobium, which are closely related to B. vignae 7-2T, B. kavangense 14-3T, B. subterraneum 58-2-1T, B. pachyrhizi PAC48T, B. elkaniiT and novel groups of Bradyrhizobium species. The bradyrhizobial populations identified exhibited high N2 fixation, and induced greater nodulation, leaf chlorophyll concentration and photosynthetic rates on their homologous host when compared to the 5 mM KNO3-fed plants and/or the commercial Bradyrhizobium strain CB756, suggesting that they could be good candidates for inoculant formulations upon field testing.IMPORTANCE Rhizobia play important roles in agroecosystems where they contribute to improving overall soil health through their symbiotic relationship with legumes. This study explored the microsymbionts nodulating Kersting's groundnut, a neglected orphan legume. The results revealed the presence of different bradyrhizobial populations with high N2-fixing efficiencies as the dominant symbionts of this legume across diverse agroecologies in Africa. Our findings represent a useful contribution to the literature in terms of the community of microsymbionts nodulating a neglected cultivated legume, and its potential for elevation as a major food crop. The presence of potentially novel bradyrhizobial symbionts of Kersting's groundnut found in this study offers an opportunity for future studies to properly describe, characterize and delineate these isolates functionally and phylogenetically for use in inoculant production to enhance food/nutritional security.}, } @article {pmid30952451, year = {2019}, author = {Camacho, M and Medina, C and Rodríguez-Navarro, DN and Temprano Vera, F}, title = {Biodiversity of rhizobia present in plant nodules of Biserrula pelecinus across Southwest Spain.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2019.03.005}, pmid = {30952451}, issn = {1618-0984}, abstract = {Biodiversity studies of native Mesorhizobium spp. strains able to nodulate the annual herbaceous legume Biserrula pelecinus L. in soils from Southwest Spain have been carried out. One or two isolates per plant, 30 in total, were randomly selected for further characterization. There was no association between the presence of mesorhizobia nodulating-B. pelecinus and the chemical or textural properties of the soils. The isolates were tested for their symbiotic effectiveness on this forage legume under greenhouse conditions and characterized on the basis of physiological parameters: carbon source utilisation (API 50CH), 16S rRNA sequencing and ERIC-PCR, lipopolysaccharide, protein and plasmid profiles. Our results show that in spite of the great diversity found among the native isolates, most of them belong to the genus Mesorhizobium, the exception being strain B24 which sequence matches 97.52% with Neorhizobium huautlense; this is the first description of a Neorhizobium strain effectively nodulating-biserrula plants. Results of a field trial indicated that some of these isolates could be recommended as inoculants for this legume. B24=DSM 28743=CECT 8815; ENA (HF955513) 16S rRNA sequences of isolates B13, B18, B26, B30 and B1 are deposited at ENA under numbers LS999402 to LS999406, respectively.}, } @article {pmid30951191, year = {2019}, author = {Benavent-González, A and Raggio, J and Villagra, J and Blanquer, JM and Pintado, A and Rozzi, R and Green, TGA and Sancho, LG}, title = {High nitrogen contribution by Gunnera magellanica and nitrogen transfer by mycorrhizas drive an extraordinarily fast primary succession in Sub-Antarctic Chile.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15838}, pmid = {30951191}, issn = {1469-8137}, abstract = {Chronosequences at the forefront of retreating glaciers provide information about colonization rates of bare surfaces. In the northern hemisphere, forest development can take centuries, with rates often limited by low nutrient availability. In contrast, in front of the retreating Pia Glacier (Tierra del Fuego, Chile), a Nothofagus forest is in place after only 34 years of development, while total soil nitrogen (N) increased from near zero to 1.5%, suggesting a strong input of this nutrient. We measured N-fixation rates, carbon fluxes, leaf N and phosphorus contents and leaf δ15 N in the dominant plants, including the herb Gunnera magellanica, which is endosymbiotically associated with a cyanobacterium, in order to investigate the role of N-fixing and mycorrhizal symbionts in N-budget during successional transition. Gunnera magellanica presented some of the highest nitrogenase activities yet reported (potential maximal contribution of 300 kg N ha-1 yr-1). Foliar δ15 N results support the framework of a highly efficient N-uptake and transfer system based on mycorrhizas, with about 80% of N taken up by the mycorrhizas potentially transferred to the host plant. Our results suggest the symbiosis of G. magellanica with cyanobacteria, and trees and shrubs with mycorrhizas, to be the key processes driving this rapid succession. This article is protected by copyright. All rights reserved.}, } @article {pmid30950432, year = {2019}, author = {Tiwari, R and Negandhi, H and Zodpey, S}, title = {Forecasting the future need and gaps in requirements for public health professionals in India up to 2026.}, journal = {WHO South-East Asia journal of public health}, volume = {8}, number = {1}, pages = {56-65}, doi = {10.4103/2224-3151.255351}, pmid = {30950432}, issn = {2304-5272}, abstract = {Current ambitious reforms in India mean that public health professionals (PHPs) will become an increasingly vital component of the health workforce. Despite a rapid growth in schools of public health in India, uptake of places by students without a medical background is low. This paper reports the results of an exercise to estimate the baseline supply of, and need for, PHPs in India in 2017 and to forecast possible supply-need scenarios up to 2026. Supply was estimated using the stock and flow approach and the service-target approach was used to estimate need. The additional need resulting from development of a new public health cadre, as stated in the National Health Policy 2017, was also included. Supply-need gaps were forecast according to three scenarios, which varied according to the future intensity of policy intervention to increase occupancy of training places for PHPs from a non-medical background: "best guess" (no intervention), "optimistic" (feasible intervention), and "aspirational" (significant intervention) scenarios. In the best guess scenario in 2017, i.e. with a low non-medical place occupancy of 60%, there is a supply-need gap of around 28 000 PHPs. In the absence of any intervention to increase place occupancy, this shortfall is forecast to increase to 45 000 PHPs by the year 2026. By contrast, in the aspirational scenario, i.e. with a high place occupancy of 75% for non-medical places, the baseline gap for 2017 of almost 26 000 PHPs reduces by 2026 to around 21 000 PHPs. By 2026, most new PHPs will be produced by public health training programmes offered by institutions other than medical colleges. Without significant interventions, India is likely to have a significant shortfall in PHPs in 2026. Policy-makers will have to carefully examine issues surrounding the current low uptake of non-medical public health seats and review the current framework regulating training of PHPs, in order to respond adequately to future requirements.}, } @article {pmid30950320, year = {2019}, author = {Ingavle, G and Vaidya, A and Kale, V}, title = {Constructing 3D microenvironments using engineered biomaterials for HSC expansion.}, journal = {Tissue engineering. Part B, Reviews}, volume = {}, number = {}, pages = {}, doi = {10.1089/ten.TEB.2018.0286}, pmid = {30950320}, issn = {1937-3376}, abstract = {In a native bone marrow tissue-microenvironment, mesenchymal stem/stromal cells (MSCs) form an important constituent of the stem cell niche, which is composed of extra-cellular matrix (ECM), niche cells, biophysical cues and growth factors. These micro-environmental elements play a major role in guiding stem cell behaviour, such as growth, stemness, maintenance and lineage differentiation. The rapid progress in biomaterials advancement and stem cell biology has opened new directions in stem cell therapy. Ideally, biomaterials intended for tissue regenerative medicine applications should perform the structural and biochemical functions of the native ECM, which provides cells with physical (structural/morphological), chemical and mechanical cues via its three-dimensional architecture, until the cells' own ECM takes over. Advanced techniques related to materials synthesis are significantly important for designing temporary tissue engineering scaffolds, which not only support cell growth but also facilitates three-dimensional tissue formation. This review concisely describes the types of natural and synthetic polymeric biomaterials and the different approaches of designing and developing of porous scaffolds for the expansion of hematopoietic stem cells (HSCs). It also illustrates the relationship between material science and tissue engineering and reviews the most frequently used materials and some exciting recent advancements in scaffold manufacture technologies. Further, this review focuses on an introduction to existing HSC niche concepts and summarizes approaches to mimic them in vitro.}, } @article {pmid30949766, year = {2019}, author = {Rajan, A and Valla, JM and Alappatt, JA and Sharda, M and Shah, A and Ingalhalikar, M and Singh, NC}, title = {Wired for musical rhythm? A diffusion MRI-based study of individual differences in music perception.}, journal = {Brain structure & function}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00429-019-01868-y}, pmid = {30949766}, issn = {1863-2661}, abstract = {Music perceptual abilities are subjective and exhibit high inter-individual variability. Twenty-nine participants with varying degrees of musical training were tested for musical perception ability with the Profile of Music Perception Skills (PROMS) and brain structural measures obtained via diffusion tensor imaging. Controlling for the period of training, TBSS results showed that individuals with better musical perception abilities showed increased deviations from linear anisotropy in the corpus callosum. Specifically, mode of anisotropy in the genu and body of the corpus callosum was negatively correlated with music perception score suggesting the presence of crossing fibers. A multi-compartment model of crossing fibers revealed a significant positive relation for partial volumes of secondary fiber populations with timing aspects of music perception. Our results suggest that inter-hemispheric connectivity differences in the anterior parts of the corpus callosum may reflect innate differences in the processing of the rhythmic aspects of music.}, } @article {pmid30949751, year = {2019}, author = {Hughey, MC and Sokol, ER and Walke, JB and Becker, MH and Belden, LK}, title = {Ecological Correlates of Large-Scale Turnover in the Dominant Members of Pseudacris crucifer Skin Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01372-0}, pmid = {30949751}, issn = {1432-184X}, support = {DEB-1136640//National Science Foundation/ ; D10ZO-028//Morris Animal Foundation/ ; }, abstract = {Animals host a wide diversity of symbiotic microorganisms that contribute important functions to host health, and our knowledge of what drives variation in the composition of these complex communities continues to grow. Microbiome studies at larger spatial scales present opportunities to evaluate the contribution of large-scale factors to variation in the microbiome. We conducted a large-scale field study to assess variation in the bacterial symbiont communities on adult frog skin (Pseudacris crucifer), characterized using 16S rRNA gene amplicon sequencing. We found that skin bacterial communities on frogs were less diverse than, and structurally distinct from, the surrounding habitat. Frog skin was typically dominated by one of two bacterial OTUs: at western sites, a Proteobacteria dominated the community, whereas eastern sites were dominated by an Actinobacteria. Using a metacommunity framework, we then sought to identify factors explaining small- and large-scale variation in community structure-that is, among hosts within a pond, and among ponds spanning the study transect. We focused on the presence of a fungal skin pathogen, Batrachochytrium dendrobatidis (Bd) as one potential driver of variation. We found no direct link between skin bacterial community structure and Bd infection status of individual frog hosts. Differences in pond-level community structure, however, were explained by Bd infection prevalence. Importantly, Bd infection prevalence itself was correlated with numerous other environmental factors; thus, skin bacterial diversity may be influenced by a complex suite of extrinsic factors. Our findings indicate that large-scale factors and processes merit consideration when seeking to understand microbiome diversity.}, } @article {pmid30837458, year = {2019}, author = {Reveillaud, J and Bordenstein, SR and Cruaud, C and Shaiber, A and Esen, ÖC and Weill, M and Makoundou, P and Lolans, K and Watson, AR and Rakotoarivony, I and Bordenstein, SR and Eren, AM}, title = {The Wolbachia mobilome in Culex pipiens includes a putative plasmid.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1051}, doi = {10.1038/s41467-019-08973-w}, pmid = {30837458}, issn = {2041-1723}, support = {R01 AI132581/AI/NIAID NIH HHS/United States ; R21 AI133522/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/genetics ; Culex/*microbiology ; Female ; France ; Genome, Bacterial/*genetics ; Host Microbial Interactions/genetics ; Metagenome/*genetics ; Metagenomics/methods ; Mosquito Vectors/microbiology ; Ovary/microbiology ; Plasmids/*genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; Wolbachia/*genetics/virology ; }, abstract = {Wolbachia is a genus of obligate intracellular bacteria found in nematodes and arthropods worldwide, including insect vectors that transmit dengue, West Nile, and Zika viruses. Wolbachia's unique ability to alter host reproductive behavior through its temperate bacteriophage WO has enabled the development of new vector control strategies. However, our understanding of Wolbachia's mobilome beyond its bacteriophages is incomplete. Here, we reconstruct near-complete Wolbachia genomes from individual ovary metagenomes of four wild Culex pipiens mosquitoes captured in France. In addition to viral genes missing from the Wolbachia reference genome, we identify a putative plasmid (pWCP), consisting of a 9.23-kbp circular element with 14 genes. We validate its presence in additional Culex pipiens mosquitoes using PCR, long-read sequencing, and screening of existing metagenomes. The discovery of this previously unrecognized extrachromosomal element opens additional possibilities for genetic manipulation of Wolbachia.}, } @article {pmid30674665, year = {2019}, author = {Bosch, TCG}, title = {Squid genomes in a bacterial world.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {8}, pages = {2799-2801}, doi = {10.1073/pnas.1822166116}, pmid = {30674665}, issn = {1091-6490}, mesh = {Animals ; Bacteria ; *Cephalopoda ; *Decapodiformes ; Seafood ; Symbiosis ; }, } @article {pmid30944875, year = {2019}, author = {Vannier, N and Mony, C and Bittebiere, AK and Theis, KR and Rosenberg, E and Vandenkoornhuyse, P}, title = {Clonal Plants as Meta-Holobionts.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSystems.00213-18}, pmid = {30944875}, issn = {2379-5077}, abstract = {The holobiont concept defines a given organism and its associated symbionts as a potential level of selection over evolutionary time. In clonal plants, recent experiments demonstrated vertical transmission of part of the microbiota from one ramet (i.e., potentially autonomous individual) to another within the clonal network (i.e., connections by modified stems present in ∼35% of all plants). Because of this heritability, and potentially reciprocal exchange of microbes between generations of ramets, we propose to extend the existing holobiont framework to the concept of meta-holobiont. A meta-holobiont is a network of holobionts that can exchange biomolecules and microbiota across generations, thus impacting the fitness of both biological scales: holobionts and meta-holobionts. Specifically, meta-holobiont dynamics can result in sharing, specialization, and division of labor across plant clonal generations. This paper, which coins the meta-holobiont concept, is expected to stimulate discussion and to be applied beyond the context of networked clonal plants (e.g., to social insects).}, } @article {pmid30944488, year = {2019}, author = {Richards, TA and McCutcheon, JP}, title = {Coral symbiosis is a three-player game.}, journal = {Nature}, volume = {568}, number = {7750}, pages = {41-42}, doi = {10.1038/d41586-019-00949-6}, pmid = {30944488}, issn = {1476-4687}, } @article {pmid30824706, year = {2019}, author = {Lurgi, M and Thomas, T and Wemheuer, B and Webster, NS and Montoya, JM}, title = {Modularity and predicted functions of the global sponge-microbiome network.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {992}, doi = {10.1038/s41467-019-08925-4}, pmid = {30824706}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Biological Evolution ; Ecology ; Host Microbial Interactions/*physiology ; Microbiota/genetics/*physiology ; Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis ; }, abstract = {Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge-microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated 'core' microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life.}, } @article {pmid30482513, year = {2019}, author = {Díaz-Sánchez, S and Hernández-Jarguín, A and Torina, A and de Mera, IGF and Blanda, V and Caracappa, S and Gortazar, C and de la Fuente, J}, title = {Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {2}, pages = {336-343}, doi = {10.1016/j.ttbdis.2018.11.014}, pmid = {30482513}, issn = {1877-9603}, mesh = {Anaplasma/genetics ; Animals ; Borrelia/genetics ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Ixodes/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sicily ; Symbiosis ; }, abstract = {Exploring the microbial diversity of ticks is crucial to understand geographical dispersion and pathogen transmission. Tick microbes participate in many biological processes implicated in the acquisition, maintenance, and transmission of pathogens, and actively promote host phenotypic changes, and adaptation to new environments. The microbial community of Ixodes ventalloi still remains unexplored. In this study, the bacterial microbiota of wild-caught I. ventalloi was characterized using shotgun-metagenomic sequencing in samples from unfed adults collected during December 2013-January 2014 in two locations from Sicily, Italy. The microbiota identified in I. ventalloi was mainly composed of symbiotic, commensal, and environmental bacteria. Interestingly, we identified the genera Anaplasma and Borrelia as members of the microbiota of I. ventalloi. These results advance our information on I. ventalloi microbiota composition, with potential implications in tick-host adaptation, geographic expansion, and vector competence.}, } @article {pmid30941441, year = {2019}, author = {Parihar, M and Meena, VS and Mishra, PK and Rakshit, A and Choudhary, M and Yadav, RP and Rana, K and Bisht, JK}, title = {Arbuscular mycorrhiza: a viable strategy for soil nutrient loss reduction.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-019-01653-9}, pmid = {30941441}, issn = {1432-072X}, abstract = {Arbuscular mycorrhiza fungi's (AMF) role in plant nutrition and stress management is well known, but very few researches and studies have been conducted so far on the fungal ability to reduce different nutrient losses (runoff, leaching and volatilization) from the soil system. This important ecosystem service of AMF had been neglected largely. From the recent findings, it has been confirmed that mycorrhizal symbiosis has potential to check the losses of applied nutrients. The role of soil biota in nutrient cycling is indispensable and determines the nutrient availability to plants. Among these biota, AMF's association with plants is the most prevalent, but the exact mechanisms followed by AMF in nutrient cycling, transformation and reducing nutrient loss ability are still inconclusive. In this review, we will try to unlock this particular aspect of AMF which is important to achieve global food demand in a sustainable way.}, } @article {pmid30940052, year = {2019}, author = {Matthews, AC and Mikonranta, L and Raymond, B}, title = {Shifts along the parasite-mutualist continuum are opposed by fundamental trade-offs.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1900}, pages = {20190236}, doi = {10.1098/rspb.2019.0236}, pmid = {30940052}, issn = {1471-2954}, abstract = {Theory suggests that symbionts can readily evolve more parasitic or mutualistic strategies with respect to hosts. However, many symbionts have stable interactions with hosts that improve nutrient assimilation or confer protection from pathogens. We explored the potential for evolution of increased parasitism or decreased parasitism and mutualism in a natural gut symbiosis between larvae of Plutella xylostella and the microbe Enterobacter cloacae. We focused on interactions with the pathogen, Bacillus thuringiensis: selecting for parasitism in terms of facilitating pathogen infection, or increased mutualism in terms of host protection. Selection for parasitism led to symbionts increasing pathogen-induced mortality but reduced their competitive ability with pathogens and their in vitro growth rates. Symbionts did not evolve to confer protection from pathogens. However, several lineages evolved reduced parasitism, primarily in terms of moderating impacts on host growth, potentially because prudence pays dividends through increased host size. Overall, the evolution of increased parasitism was achievable but was opposed by trade-offs likely to reduce fitness. The evolution of protection may not have occurred because suppressing growth of B. thuringiensis in the gut might provide only weak protection or because evolution towards protective interactions was opposed by the loss of competitive fitness in symbionts.}, } @article {pmid30939810, year = {2019}, author = {Kirienko, AN and Vishnevskaya, NA and Kitaeva, AB and Shtark, OY and Kozyulina, PY and Thompson, R and Dalmais, M and Bendahmane, A and Tikhonovich, IA and Dolgikh, EA}, title = {Structural Variations in LysM Domains of LysM-RLK PsK1 May Result in a Different Effect on Pea⁻Rhizobial Symbiosis Development.}, journal = {International journal of molecular sciences}, volume = {20}, number = {7}, pages = {}, doi = {10.3390/ijms20071624}, pmid = {30939810}, issn = {1422-0067}, support = {16-16-10043//Russian Science Foundation/ ; }, abstract = {Lysin-motif receptor-like kinase PsK1 is involved in symbiosis initiation and the maintenance of infection thread (IT) growth and bacterial release in pea. We verified PsK1 specificity in relation to the Nod factor structure using k1 and rhizobial mutants. Inoculation with nodO and nodE nodO mutants significantly reduced root hair deformations, curling, and the number of ITs in k1-1 and k1-2 mutants. These results indicated that PsK1 function may depend on Nod factor structures. PsK1 with replacement in kinase domain and PsSYM10 co-production in Nicotiana benthamiana leaves did not induce a hypersensitive response (HR) because of the impossibility of signal transduction into the cell. Replacement of P169S in LysM3 domain of PsK1 disturbed the extracellular domain (ECD) interaction with PsSYM10's ECD in Y2H system and reduced HR during the co-production of full-length PsK1 and PsSYM0 in N. benthamiana. Lastly, we explored the role of PsK1 in symbiosis with arbuscular mycorrhizal (AM) fungi; no significant differences between wild-type plants and k1 mutants were found, suggesting a specific role of PsK1 in legume⁻rhizobial symbiosis. However, increased sensitivity to a highly aggressive Fusarium culmorum strain was found in k1 mutants compared with the wild type, which requires the further study of the role of PsK1 in immune response regulation.}, } @article {pmid29779668, year = {2018}, author = {Moore, BS}, title = {Preface.}, journal = {Methods in enzymology}, volume = {604}, number = {}, pages = {xv-xvi}, doi = {10.1016/S0076-6879(18)30193-9}, pmid = {29779668}, issn = {1557-7988}, mesh = {Animals ; *Aquatic Organisms ; Bacteria/enzymology/metabolism ; Enzymes/*metabolism ; Invertebrates/*microbiology ; Symbiosis ; }, } @article {pmid29779656, year = {2018}, author = {Uria, AR and Piel, J and Wakimoto, T}, title = {Biosynthetic Insights of Calyculin- and Misakinolide-Type Compounds in "Candidatus Entotheonella sp.".}, journal = {Methods in enzymology}, volume = {604}, number = {}, pages = {287-330}, doi = {10.1016/bs.mie.2018.02.017}, pmid = {29779656}, issn = {1557-7988}, mesh = {Animals ; Biochemistry/*methods ; Biological Products/*metabolism ; Biosynthetic Pathways ; Computational Biology ; Macrolides/metabolism ; Metagenome ; Metagenomics/*methods ; Multigene Family ; Oxazoles/metabolism ; Peptide Biosynthesis, Nucleic Acid-Independent ; Polyketides/chemistry/*metabolism ; Porifera ; Symbiosis ; }, abstract = {Microbial symbionts are recognized as the important sources of numerous sponge-derived metabolites with potent biological activities. The limitation to cultivate the majority of potential symbionts has hampered attempts to explore and exploit their natural products for further development toward medical applications. Metagenomics-guided approaches have enabled cloning of natural product biosynthesis genes from uncultured microbial symbionts. Subsequent activation of biosynthesis genes in easily culturable bacteria could lead to the sustainable production of rare sponge-derived compounds. In this chapter, we highlight metagenomic strategies to reveal natural product biosynthetic pathways in sponge metagenomes based on the calyculin and misakinolide polyketides. Techniques to identify the compound producer are briefly discussed. We further describe examples of functional studies of the biosynthetic pathways of these two compound types with a special emphasis on the general experimental protocols for the activity assays of key proteins involved in their biosynthesis.}, } @article {pmid29045380, year = {2017}, author = {Bucci, M}, title = {Host-microbe interactions: Aiming at GPCRs.}, journal = {Nature chemical biology}, volume = {13}, number = {11}, pages = {1139}, pmid = {29045380}, issn = {1552-4469}, mesh = {*Bacteria ; Humans ; Ligands ; *Symbiosis ; }, } @article {pmid28892653, year = {2018}, author = {Buskermolen, JK and Janus, MM and Roffel, S and Krom, BP and Gibbs, S}, title = {Saliva-Derived Commensal and Pathogenic Biofilms in a Human Gingiva Model.}, journal = {Journal of dental research}, volume = {97}, number = {2}, pages = {201-208}, doi = {10.1177/0022034517729998}, pmid = {28892653}, issn = {1544-0591}, mesh = {*Biofilms ; Cell Line ; Cells, Cultured ; Cytokines/metabolism ; Elafin/metabolism ; Gingiva/*cytology/*microbiology ; *Host-Pathogen Interactions ; Humans ; In Situ Hybridization, Fluorescence ; In Vitro Techniques ; Phenotype ; Saliva/*microbiology ; Symbiosis ; Tissue Engineering ; }, abstract = {In vitro models that closely mimic human host-microbiome interactions can be a powerful screening tool for antimicrobials and will hold great potential for drug validation and discovery. The aim of this study was to develop an organotypic oral mucosa model that could be exposed to in vitro cultured commensal and pathogenic biofilms in a standardized and scalable manner. The oral mucosa model consisted of a tissue-engineered human gingiva equivalent containing a multilayered differentiated gingiva epithelium (keratinocytes) grown on a collagen hydrogel, containing gingiva fibroblasts, which represented the lamina propria. Keratinocyte and fibroblast telomerase reverse transcriptase-immortalized cell lines were used to overcome the limitations of isolating cells from small biopsies when scalable culture experiments were required. The oral biofilms were grown under defined conditions from human saliva to represent 3 distinct phenotypes: commensal, gingivitis, and cariogenic. The in vitro grown biofilms contained physiologic numbers of bacterial species, averaging >70 operational taxonomic units, including 20 differentiating operational taxonomic units. When the biofilms were applied topically to the gingiva equivalents for 24 h, the gingiva epithelium increased its expression of elafin, a protease inhibitor and antimicrobial protein. This increased elafin expression was observed as a response to all 3 biofilm types, commensal as well as pathogenic (gingivitis and cariogenic). Biofilm exposure also increased secretion of the antimicrobial cytokine CCL20 and inflammatory cytokines IL-6, CXCL8, and CCL2 from gingiva equivalents. This inflammatory response was far greater after commensal biofilm exposure than after pathogenic biofilm exposure. These results show that pathogenic oral biofilms have early immune evasion properties as compared with commensal oral biofilms. The novel host-microbiome model provides an ideal tool for future investigations of gingiva responses to commensal and pathogenic biofilms and for testing novel therapeutics.}, } @article {pmid30939335, year = {2019}, author = {Pereda-Goikoetxea, B and Marín-Fernández, B and Liceaga-Otazu, NE and Elorza-Puyadena, MI}, title = {A qualitative study of hospital birth perceptions: The helix of priority needs.}, journal = {Midwifery}, volume = {74}, number = {}, pages = {91-98}, doi = {10.1016/j.midw.2019.03.018}, pmid = {30939335}, issn = {1532-3099}, abstract = {OBJECTIVE: To understand which needs are considered priorities in the hospital birth experience from the perspectives of postpartum women.

DESIGN: This qualitative prospective study used a phenomenological approach. Data were collected through participant observations and semi-structured interviews recorded at eight weeks and eight months after childbirth. The data were analysed using a thematic approach.

PARTICIPANTS: The study cohort consisted of 43 participants at eight weeks after childbirth and 33 participants eight months after childbirth.

SETTING: Donostia University Hospital, San Sebastián, Spain, in 2016-2017.

FINDINGS: Through the analysis, the following four main themes emerged, each in different categories: (a) Professional care: symbiosis between the woman and the professional: (a.1) professional treatment and its characteristics, (a.2) professional competence, and (a.3) professional information and listening: pillars in the support relationship. (b) Control and hospital safety: (b.1) hospital environment: external control. (c) Presence of the partner: (c.1) support, guidance, and participation. (d) Perception of observed feelings: (d.1) fear of complications or separation from the child, (d.2) fear of internal lack of control, and (d.3) fear of an instrumental delivery and/or caesarean section.

The core of the hospital birth experience is constituted by the need to establish a supportive relationship based on mutual trust, exchange information that offers internal and external control and the security necessary to overcome feelings of fear, and obtain support and guidance from an involved partner.}, } @article {pmid30939203, year = {2019}, author = {Hernandez-Agreda, A and Leggat, W and Ainsworth, TD}, title = {A place for taxonomic profiling in the study of the coral prokaryotic microbiome.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz063}, pmid = {30939203}, issn = {1574-6968}, abstract = {The enormous variability in richness, abundance, and diversity of unknown bacterial organisms inhabiting the coral microbiome have challenged our understanding of their functional contribution to coral health. Identifying the attributes of the healthy meta-organism is paramount for contemporary approaches aiming to manipulate dysbiotic stages of the coral microbiome. This review evaluates the current knowledge on the structure and mechanisms driving bacterial communities in the coral microbiome and discusses two topics requiring further research to define the healthy coral microbiome. 1) We examine the necessity to establish microbial baselines to understand the spatial and temporal dynamics of the healthy coral microbiome and summarize conceptual and logistic challenges to consider in the design of these baselines. 2) We propose potential mechanical, physical and chemical mechanisms driving bacterial distribution within coral compartments and suggest experiments to test them. Finally, we highlight aspects of the use of 16S amplicon sequencing requiring standardization and discuss its contribution to other multi-omics approaches.}, } @article {pmid30937635, year = {2019}, author = {Baruah, MM and Sharma, N}, title = {In silico identification of key genes and signaling pathways targeted by a panel of signature microRNAs in prostate cancer.}, journal = {Medical oncology (Northwood, London, England)}, volume = {36}, number = {5}, pages = {43}, doi = {10.1007/s12032-019-1268-y}, pmid = {30937635}, issn = {1559-131X}, abstract = {Accumulating evidence have suggested that some microRNAs are aberrantly expressed in prostate cancer. In our previous work, we had identified a panel of four differentially expressed microRNAs in prostate cancer. In the present study, we have investigated common molecular targets of this panel of miRNAs (DEMs) and key hub genes that can serve as potential candidate biomarkers in the pathogenesis and progression of prostate cancer. A joint bioinformatics approach was employed to identify differentially expressed genes (DEGs) in prostate cancer. Gene enrichment analysis followed by the protein-protein interaction (PPI) network construction and selection of hub genes was further performed using String and Cytoscape, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the identified hub genes was conducted using the Database for Annotation, Visualization and Integrated Discovery (DAVID) tool. In total, 496 genes were identified to be common targets of DEMs in prostate cancer and 13 key hub genes were identified from three modules of the PPI network of the DEGs. Further top five genes viz Rhoa, PI3KCA, CDC42, MAPK3, TP53 were used for Enrichment analysis which revealed their association with vital cellular and functional pathways in prostate cancer indicating their potential as candidate biomarkers in prostate cancer.}, } @article {pmid30936859, year = {2019}, author = {Mewalal, R and Yin, H and Hu, R and Jawdy, S and Vion, P and Tuskan, GA and Le Tacon, F and Labbé, JL and Yang, X}, title = {Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {515}, doi = {10.3389/fmicb.2019.00515}, pmid = {30936859}, issn = {1664-302X}, abstract = {Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, (1) within the genomic regions lacking annotated genes in the Populus genome and (2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments. Root colonization by either fungus was more effective in P. trichocarpa than in P. deltoides, thus the relatively few differentially-expressed miRNAs predicted in P. deltoides might reflect the extent of the symbiosis. Finally, we predicted several genes targets for the plant miRNAs identified here, including potential fungal gene targets. Our findings shed light on additional molecular tiers with a role in Populus-fungal mutualistic associations and provides a set of potential molecular targets for future enhancement.}, } @article {pmid30936484, year = {2019}, author = {Tianero, MD and Balaich, JN and Donia, MS}, title = {Localized production of defence chemicals by intracellular symbionts of Haliclona sponges.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0415-8}, pmid = {30936484}, issn = {2058-5276}, abstract = {Marine sponges often house small-molecule-producing symbionts extracellularly in their mesohyl, providing the host with a means of chemical defence against predation and microbial infection. Here, we report an intriguing case of chemically mediated symbiosis between the renieramycin-containing sponge Haliclona sp. and its herein discovered renieramycin-producing symbiont Candidatus Endohaliclona renieramycinifaciens. Remarkably, Ca. E. renieramycinifaciens has undergone extreme genome reduction where it has lost almost all necessary elements for free living while maintaining a complex, multi-copy plasmid-encoded biosynthetic gene cluster for renieramycin biosynthesis. In return, the sponge houses Ca. E. renieramycinifaciens in previously uncharacterized cellular reservoirs (chemobacteriocytes), where it can acquire nutrients from the host and avoid bacterial competition. This relationship is highly specific to a single clade of Haliclona sponges. Our study reveals intracellular symbionts as an understudied source for defence chemicals in the oldest-living metazoans and paves the way towards discovering similar systems in other marine sponges.}, } @article {pmid30936458, year = {2019}, author = {Ippolito, L and Morandi, A and Taddei, ML and Parri, M and Comito, G and Iscaro, A and Raspollini, MR and Magherini, F and Rapizzi, E and Masquelier, J and Muccioli, GG and Sonveaux, P and Chiarugi, P and Giannoni, E}, title = {Cancer-associated fibroblasts promote prostate cancer malignancy via metabolic rewiring and mitochondrial transfer.}, journal = {Oncogene}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41388-019-0805-7}, pmid = {30936458}, issn = {1476-5594}, support = {fellowship to Andrea Morandi//Fondazione Umberto Veronesi (Umberto Veronesi Foundation)/ ; 0203607//Istituto Toscano Tumori (ITT)/ ; 19515//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; }, abstract = {Cancer-associated fibroblasts (CAFs) are the major cellular stromal component of many solid tumors. In prostate cancer (PCa), CAFs establish a metabolic symbiosis with PCa cells, contributing to cancer aggressiveness through lactate shuttle. In this study, we report that lactate uptake alters the NAD+/NADH ratio in the cancer cells, which culminates with SIRT1-dependent PGC-1α activation and subsequent enhancement of mitochondrial mass and activity. The high exploitation of mitochondria results in tricarboxylic acid cycle deregulation, accumulation of oncometabolites and in the altered expression of mitochondrial complexes, responsible for superoxide generation. Additionally, cancer cells hijack CAF-derived functional mitochondria through the formation of cellular bridges, a phenomenon that we observed in both in vitro and in vivo PCa models. Our work reveals a crucial function of tumor mitochondria as the energy sensors and transducers of CAF-dependent metabolic reprogramming and underscores the reliance of PCa cells on CAF catabolic activity and mitochondria trading.}, } @article {pmid30935957, year = {2019}, author = {Shibasaki, S}, title = {The evolutionary game of interspecific mutualism in the multi-species model.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtbi.2019.03.026}, pmid = {30935957}, issn = {1095-8541}, abstract = {Mutualistic interspecific interactions, including Müllerian mimicry and division of labor, are common in nature. In contrast to antagonistic interactions, where faster evolution is favored, mutualism can favor slower evolution under certain conditions. This is called the Red King effect. Since Bergstrom and Lachmann (2003) proposed the Red King effect, it has been investigated only in two-species models. However, biological examples suggest that mutualism can include three or more species. Here, I modeled the evolutionary dynamics of mutualism in communities where involving two or more species, and in which all species mutually interact. Regardless of the number of species in the community, it is possible to derive conditions for stable equilibria. Although nonlinear relationships exist between the evolutionary rates and the evolutionary fate of each species in the multi-species communities, the model suggests that it is possible to predict whether faster evolution is favored or disfavored for the relatively rapidly evolving species; however, it is difficult to predict the evolutionary fate of species that evolve relatively slowly because their evolutionary dynamics are affected by the evolutionary fate of species evolving rapidly.}, } @article {pmid30934751, year = {2019}, author = {Ali, A and Ghani, MI and Ding, H and Fan, Y and Cheng, Z and Iqbal, M}, title = {Co-Amended Synergistic Interactions between Arbuscular Mycorrhizal Fungi and the Organic Substrate-Induced Cucumber Yield and Fruit Quality Associated with the Regulation of the AM-Fungal Community Structure under Anthropogenic Cultivated Soil.}, journal = {International journal of molecular sciences}, volume = {20}, number = {7}, pages = {}, doi = {10.3390/ijms20071539}, pmid = {30934751}, issn = {1422-0067}, support = {2016KTCL02-01//Shaanxi Provincial Sci-Tech Innovation Plan/ ; 2016NY-048//Shaanxi Provincial Agricultural Sci-Tech Innovation and Development Plan/ ; }, abstract = {Monotonous cucumber double-cropping systems under plastic greenhouse vegetable cultivation (PGVC) previously intensified by long-term anthropogenic activities and manipulative treatments leads to a crop productivity reduction and soil biota disturbances. In this study, the role of the indigenous arbuscular mycorrhizal strain (AM: Glomus versiforme L.) and organic substrate (GS: Garlic stalk) application were assessed for plant microbe interaction and crop productivity feedback in a greenhouse (2016⁻2018) under a cultivated Anthrosol characterized as a replanted degraded soil. We found that repetitively adding AM inocula with organic substrates (GS) improved the cucumber growth and physiology. The useful trait of AM symbiosis with C-amended organic substrates preferentially manifested as increased root colonization, hyphal density proliferation, AM sporulation, root activity, and suppressed Fusarium incidence. The post AM development further prevailed the synergistic interaction, and the co-inoculation effect resulted in an increase in fruit nutrition uptake, seasonal cucumber yield and fruit quality attributes. Illumina MiSeq analysis of the 18S rRNA gene amplicons revealed that the dominant AM genera that are particularly enriched with the Glomus taxon may be important ecological drivers associated with plant productivity and fruit quality characteristics. These results suggest that the AM-organic substrate association might be a pragmatic option for use as an economic and efficient biological resource and as a newly-sustainable plant microbe mediator to enhance the regional ecosystem services and plant productivity of the anthropogenic PGVC of this region.}, } @article {pmid30934700, year = {2019}, author = {Shan, H and Yang, J and Wei, G}, title = {Industrial Symbiosis Systems: Promoting Carbon Emission Reduction Activities.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/ijerph16071093}, pmid = {30934700}, issn = {1660-4601}, support = {71503135//National Natural Science Foundation of China/ ; }, abstract = {The carbon emission problem in China needs to be solved urgently. Industrial symbiosis, as an effective means to improve resource efficiency, can better alleviate the carbon emission problem. Under such a circumstance, this paper regards an industrial symbiosis system as a collection of producers, consumers and decomposers, and analyzes the strategic selections and behavioral characteristics of their carbon emission reduction activities through a tripartite evolutionary game model, and then the effects of related parameters on the evolutionary stable strategies of stakeholders are discussed. The results demonstrate that: (1) the regular return and the rate of return determine the ability of stakeholders to undertake carbon reduction activities; (2) the initial willingness of stakeholders to participate will affect the evolutionary speed of the strategies; (3) a high opportunity cost reduces the inertia of stakeholders to carry out carbon emission reductions; (4) producers, consumers and decomposers can avoid "free rides" by signing agreements or adopting punitive measures.}, } @article {pmid30930920, year = {2019}, author = {Serova, TA and Tsyganova, AV and Tikhonovich, IA and Tsyganov, VE}, title = {Gibberellins Inhibit Nodule Senescence and Stimulate Nodule Meristem Bifurcation in Pea (Pisum sativum L.).}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {285}, doi = {10.3389/fpls.2019.00285}, pmid = {30930920}, issn = {1664-462X}, abstract = {The development of nitrogen-fixing nodules formed during Rhizobium-legume symbiosis is strongly controlled by phytohormones. In this study, we investigated the effect of gibberellins (GAs) on senescence of pea (Pisum sativum) symbiotic nodules. Pea wild-type line SGE, as well as corresponding mutant lines SGEFix--1 (sym40), SGEFix--2 (sym33), SGEFix--3 (sym26), and SGEFix--7 (sym27), blocked at different stages of nodule development, were used in the study. An increase in expression of the GA2ox1 gene, encoding an enzyme involved in GA deactivation (GA 2-oxidase), and a decrease in the transcript abundance of the GA20ox1 gene, encoding one of the enzymes involved in GA biosynthesis (GA 20-oxidase), were observed in analyzed genotypes during nodule aging. A reduction in the amount of bioactive GA3 was demonstrated by immunolocalization in the early senescent mutant and wild-type lines during aging of symbiotic nodules. Down-regulated expression of senescence-associated genes encoding cysteine proteases 1 and 15a, thiol protease, bZIP transcription factor, 1-aminocyclopropane-1-carboxylate (ACC) synthase, ACC oxidase, and aldehyde oxidase was observed in the nodules of wild-type plants treated with exogenous GA3 relative to the untreated plants. GA3-treated plants also showed increases in nodule size and the nitrogen fixation zone, and decreases in the number of nodules and the senescence zone. Immunogold localization revealed higher levels of GA3 in the peribacteroid spaces in symbiosomes than in the matrix of infection threads. Furthermore, a decrease in GA3 label in mature and senescent symbiosomes in comparison with juvenile symbiosomes was observed. These results suggest a negative effect of GAs on the senescence of the pea symbiotic nodule and possible involvement of GAs in functioning of the mature nodule. Simultaneously, GA3 treatment led to nodule meristem bifurcation, indicating a possible role of GAs in nodule meristem functioning.}, } @article {pmid30930915, year = {2019}, author = {Ho-Plágaro, T and Molinero-Rosales, N and Fariña Flores, D and Villena Díaz, M and García-Garrido, JM}, title = {Identification and Expression Analysis of GRAS Transcription Factor Genes Involved in the Control of Arbuscular Mycorrhizal Development in Tomato.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {268}, doi = {10.3389/fpls.2019.00268}, pmid = {30930915}, issn = {1664-462X}, abstract = {The formation and functioning of arbuscular mycorrhizal (AM) symbiosis are complex and tightly regulated processes. Transcriptional regulation mechanisms have been reported to mediate gene expression changes closely associated with arbuscule formation, where nutrients move between the plant and fungus. Numerous genes encoding transcription factors (TFs), with those belonging to the GRAS family being of particular importance, are induced upon mycorrhization. In this study, a screening for candidate transcription factor genes differentially regulated in AM tomato roots showed that more than 30% of known GRAS tomato genes are upregulated upon mycorrhization. Some AM-upregulated GRAS genes were identified as encoding for transcription factors which are putative orthologs of previously identified regulators of mycorrhization in other plant species. The symbiotic role played by other newly identified AM-upregulated GRAS genes remains unknown. Preliminary results on the involvement of tomato SlGRAS18, SlGRAS38, and SlGRAS43 from the SCL3, SCL32, and SCR clades, respectively, in mycorrhization are presented. All three showed high transcript levels in the late stages of mycorrhization, and the analysis of promoter activity demonstrated that SlGRAS18 and SlGRAS43 are significantly induced in cells containing arbuscules. When SlGRAS18 and SlGRAS38 genes were silenced using RNA interference in hairy root composite tomato plants, a delay in mycorrhizal infection was observed, while an increase in mycorrhizal colonization was observed in SlGRAS43 RNAi roots. The possible mode of action of these TFs during mycorrhization is discussed, with a particular emphasis on the potential involvement of the SHR/SCR/SCL3 module of GRAS TFs in the regulation of gibberellin signaling during mycorrhization, which is analogous to other plant developmental processes.}, } @article {pmid30930885, year = {2019}, author = {Safronova, V and Belimov, A and Sazanova, A and Chirak, E and Kuznetsova, I and Andronov, E and Pinaev, A and Tsyganova, A and Seliverstova, E and Kitaeva, A and Tsyganov, V and Tikhonovich, I}, title = {Two Broad Host Range Rhizobial Strains Isolated From Relict Legumes Have Various Complementary Effects on Symbiotic Parameters of Co-inoculated Plants.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {514}, doi = {10.3389/fmicb.2019.00514}, pmid = {30930885}, issn = {1664-302X}, abstract = {Two bacterial strains Ach-343 and Opo-235 were isolated, respectively from nodules of Miocene-Pliocene relict legumes Astragalus chorinensis Bunge and Oxytropis popoviana Peschkova originated from Buryatia (Baikal Lake region, Russia). For identification of these strains the sequencing of 16S rRNA (rrs) gene was used. Strain Opo-235 belonged to the species Mesorhizobium japonicum, while the strain Ach-343 was identified as M. kowhaii (100 and 99.9% rrs similarity with the type strains MAFF 303099T and ICMP 19512T, respectively). Symbiotic genes of these strains as well as some genes that promote plant growth (acdS, gibberellin- and auxin-synthesis related genes) were searched throughout the whole genome sequences. The sets of plant growth-promoting genes found were almost identical in both strains, whereas the sets of symbiotic genes were different and complemented each other with several nod, nif, and fix genes. Effects of mono- and co-inoculation of Astragalus sericeocanus, Oxytropis caespitosa, Glycyrrhiza uralensis, Medicago sativa, and Trifolium pratense plants with the strains M. kowhaii Ach-343 and M. japonicum Opo-235 expressing fluorescent proteins mCherry (red) and EGFP (green) were studied in the gnotobiotic plant nodulation assay. It was shown that both strains had a wide range of host specificity, including species of different legume genera from two tribes (Galegeae and Trifolieae). The effects of co-microsymbionts on plants depended on the plant species and varied from decrease, no effect, to increase in the number of nodules, nitrogen-fixing activity and plant biomass. One of the reasons for this phenomenon may be the discovered complementarity in co-microsymbionts of symbiotic genes responsible for the specific modification of Nod-factors and nitrogenase activity. Localization and co-localization of the strains in nodules was confirmed by the confocal microscopy. Analysis of histological and ultrastructural organization of A. chorinensis and O. popoviana root nodules was performed. It can be concluded that the strains M. kowhaii Ach-343 and M. japonicum Opo-235 demonstrate lack of high symbiotic specificity that is characteristic for primitive legume-rhizobia systems. Further study of the root nodule bacteria having complementary sets of symbiotic genes will contribute to clarify the evolutionary paths of legume-rhizobia relationships and the mechanisms of effective integration between partners.}, } @article {pmid30152217, year = {2018}, author = {Liu, J and Liu, Y and Lv, H and Liu, Q and Li, M}, title = {[Research progress in human symbiotic bacteria and their antibacterial molecules].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {34}, number = {8}, pages = {1316-1325}, doi = {10.13345/j.cjb.170520}, pmid = {30152217}, issn = {1000-3061}, mesh = {Anti-Bacterial Agents/*chemistry ; Bacteria/*chemistry ; Genomics ; Humans ; *Symbiosis ; Synthetic Biology ; }, abstract = {With the emergence and globally spread of drug-resistant bacteria, the discovery and development of new antibacterial drugs is imminent. The symbiotic bacteria distributed in different parts of the body can produce a variety of antibacterial molecules to inhibit the colonization and infection of pathogenic bacteria. Human symbiotic bacteria provide a potential treasure house of resource for the research and development of new drugs with broad new molecular structures and action mechanism. With the further development of bioinformatics tools, synthetic biology and omics technology such as genomics, the mining of human symbiotic bacteria antibacterial molecules will be more in-depth and provide an effective way to solve the problem of drug resistance. Here, we review the antimicrobial molecules produced by human symbiotic bacteria and introduce several methods to explore the resources of natural antibacterial drugs. With the development of modern biotechnology, the antimicrobial molecules of human symbiotic bacteria will be more comprehensively and systematically explored and applied.}, } @article {pmid29987713, year = {2018}, author = {Botté, CY and Yamaryo-Botté, Y}, title = {Complex Endosymbioses II: The Nonphotosynthetic Plastid of Apicomplexa Parasites (The Apicoplast) and Its Integrated Metabolism.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {37-54}, doi = {10.1007/978-1-4939-8654-5_3}, pmid = {29987713}, issn = {1940-6029}, mesh = {Antiparasitic Agents/pharmacology ; Apicoplasts/drug effects/*physiology ; Drug Development ; Energy Metabolism ; Genome ; Malaria ; Metabolic Networks and Pathways ; Photosynthesis ; Plastids/*genetics/*metabolism ; Protein Transport ; *Symbiosis ; }, abstract = {Chloroplasts are essential organelles that are responsible for photosynthesis in a wide range of organisms that have colonized all biotopes on Earth such as plants and unicellular algae. Interestingly, a secondary endosymbiotic event of a red algal ancestor gave rise to a group of organisms that have adopted an obligate parasitic lifestyle named Apicomplexa parasites. Apicomplexa parasites are some of the most widespread and poorly controlled pathogens in the world. These infectious agents are responsible for major human diseases such as toxoplasmosis, caused by Toxoplasma gondii, and malaria caused by Plasmodium spp. Most of these parasites harbor this relict plastid named the apicoplast, which is essential for parasite survival. The apicoplast has lost photosynthetic capacities but are metabolically similar to plant and algal chloroplasts. The apicoplast is considered a novel and important drug target against Apicomplexa parasites. This chapter focuses on the apicoplast of apicomplexa parasites, its maintenance, and its metabolic pathways.}, } @article {pmid29987712, year = {2018}, author = {Füssy, Z and Oborník, M}, title = {Complex Endosymbioses I: From Primary to Complex Plastids, Multiple Independent Events.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {17-35}, doi = {10.1007/978-1-4939-8654-5_2}, pmid = {29987712}, issn = {1940-6029}, mesh = {Biological Evolution ; Eukaryota/classification/genetics/metabolism ; Photosynthesis ; Plastids/*genetics/*metabolism ; *Symbiosis ; }, abstract = {A substantial portion of eukaryote diversity consists of algae with complex plastids, i.e., plastids originating from eukaryote-to-eukaryote endosymbioses. These plastids are characteristic by a deviating number of envelope membranes (higher than two), and sometimes a remnant nucleus of the endosymbiont alga, termed the nucleomorph, is present. Complex plastid-bearing algae are therefore much like living matryoshka dolls, eukaryotes within eukaryotes. In comparison, primary plastids of Archaeplastida (plants, green algae, red algae, and glaucophytes) arose upon a single endosymbiosis event with a cyanobacterium and are surrounded by two membranes. Complex plastids were acquired several times by unrelated groups nested within eukaryotic heterotrophs, suggesting complex plastids are somewhat easier to obtain than primary plastids. This is consistent with the existence of higher-order and serial endosymbioses, i.e., engulfment of complex plastid-bearing algae by (tertiary) eukaryotic hosts and functional plastid replacements, respectively. Plastid endosymbiosis is typical by a massive transfer of genetic material from the endosymbiont to the host nucleus and metabolic rearrangements related to the trophic switch to phototrophy; this is necessary to establish metabolic integration of the plastid and control over its division. Although photosynthesis is the main advantage of plastid acquisition, algae that lost photosynthesis often maintain complex plastids, suggesting their roles beyond photosynthesis. This chapter summarizes basic knowledge on acquisition and functions of complex plastid.}, } @article {pmid29987711, year = {2018}, author = {Maréchal, E}, title = {Primary Endosymbiosis: Emergence of the Primary Chloroplast and the Chromatophore, Two Independent Events.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {3-16}, doi = {10.1007/978-1-4939-8654-5_1}, pmid = {29987711}, issn = {1940-6029}, mesh = {Alphaproteobacteria/genetics ; Cell Membrane/metabolism ; Chlamydia/genetics/metabolism ; Chloroplasts/*pathology ; Chromatophores/*physiology ; Cyanobacteria/metabolism ; Eukaryota/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glaucophyta/genetics/metabolism ; Inheritance Patterns ; Mitochondria/genetics/metabolism ; Rhizaria ; *Symbiosis ; }, abstract = {The emergence of semiautonomous organelles, such as the mitochondrion, the chloroplast, and more recently, the chromatophore, are critical steps in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and finally the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter describes our current understanding of primary endosymbiosis, with a specific focus on primary chloroplasts considered to have emerged more than one billion years ago, and on the chromatophore, having emerged about one hundred million years ago.}, } @article {pmid29650391, year = {2018}, author = {Dietel, AK and Kaltenpoth, M and Kost, C}, title = {Convergent Evolution in Intracellular Elements: Plasmids as Model Endosymbionts.}, journal = {Trends in microbiology}, volume = {26}, number = {9}, pages = {755-768}, doi = {10.1016/j.tim.2018.03.004}, pmid = {29650391}, issn = {1878-4380}, mesh = {*Bacteria/genetics/metabolism ; Chromosome Segregation ; Cytoplasm ; DNA Transposable Elements ; Eukaryota ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host Microbial Interactions/genetics/physiology ; Mutation ; *Plasmids/genetics/metabolism ; *Symbiosis/genetics/physiology ; }, abstract = {Endosymbionts are organisms that live inside the cells of other species. This lifestyle is ubiquitous across the tree of life and is featured by unicellular eukaryotes, prokaryotes, and by extrachromosomal genetic elements such as plasmids. Given that all of these elements dwell in the cytoplasm of their host cell, they should be subject to similar selection pressures. Here we show that strikingly similar features have evolved in both bacterial endosymbionts and plasmids. Since host and endosymbiont are often metabolically tightly intertwined, they are difficult to disentangle experimentally. We propose that using plasmids as tractable model systems can help to solve this problem, thus allowing fundamental questions to be experimentally addressed about the ecology and evolution of endosymbiotic interactions.}, } @article {pmid30928040, year = {2019}, author = {Yoshino, K and Yamamoto, K and Hara, K and Sonoda, M and Yamamoto, Y and Sakamoto, K}, title = {The conservation of polyol transporter proteins and their involvement in lichenized Ascomycota.}, journal = {Fungal biology}, volume = {123}, number = {4}, pages = {318-329}, doi = {10.1016/j.funbio.2019.01.006}, pmid = {30928040}, issn = {1878-6146}, abstract = {In lichen symbiosis, polyol transfer from green algae is important for acquiring the fungal carbon source. However, the existence of polyol transporter genes and their correlation with lichenization remain unclear. Here, we report candidate polyol transporter genes selected from the genome of the lichen-forming fungus (LFF) Ramalina conduplicans. A phylogenetic analysis using characterized polyol and monosaccharide transporter proteins and hypothetical polyol transporter proteins of R. conduplicans and various ascomycetous fungi suggested that the characterized yeast' polyol transporters form multiple clades with the polyol transporter-like proteins selected from the diverse ascomycetous taxa. Thus, polyol transporter genes are widely conserved among Ascomycota, regardless of lichen-forming status. In addition, the phylogenetic clusters suggested that LFFs belonging to Lecanoromycetes have duplicated proteins in each cluster. Consequently, the number of sequences similar to characterized yeast' polyol transporters were evaluated using the genomes of 472 species or strains of Ascomycota. Among these, LFFs belonging to Lecanoromycetes had greater numbers of deduced polyol transporter proteins. Thus, various polyol transporters are conserved in Ascomycota and polyol transporter genes appear to have expanded during the evolution of Lecanoromycetes.}, } @article {pmid30925791, year = {2019}, author = {Somerville, J and Zhou, L and Raymond, B}, title = {Aseptic Rearing and Infection with Gut Bacteria Improve the Fitness of Transgenic Diamondback Moth, Plutella xylostella.}, journal = {Insects}, volume = {10}, number = {4}, pages = {}, doi = {10.3390/insects10040089}, pmid = {30925791}, issn = {2075-4450}, support = {BB/L00819X/2//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Mass insect rearing can have a range of applications, for example in biological control of pests. The competitive fitness of released insects is extremely important in a number of applications. Here, we investigated how to improve the fitness of a transgenic diamondback moth, which has shown variation in mating ability when reared in different insectaries. Specifically we tested whether infection with a gut bacteria, Enterobacter cloacae, and aseptic rearing of larvae could improve insect growth and male performance. All larvae were readily infected with E. cloacae. Under aseptic rearing, pupal weights were reduced and there was a marginal reduction in larval survival. However, aseptic rearing substantially improved the fitness of transgenic males. In addition, under aseptic rearing, inoculation with E. cloacae increased pupal weights and male fitness, increasing the proportion of transgenic progeny from 20% to 30% relative to uninfected insects. Aseptic conditions may improve the fitness of transgenic males by excluding microbial contaminants, while symbiont inoculation could further improve fitness by providing additional protection against infection, or by normalizing insect physiology. The simple innovation of incorporating antibiotic into diet, and inoculating insects with symbiotic bacteria that are resistant to that antibiotic, could provide a readily transferable tool for other insect rearing systems.}, } @article {pmid30925664, year = {2019}, author = {da Costa, RR and Hu, H and Li, H and Poulsen, M}, title = {Symbiotic Plant Biomass Decomposition in Fungus-Growing Termites.}, journal = {Insects}, volume = {10}, number = {4}, pages = {}, doi = {10.3390/insects10040087}, pmid = {30925664}, issn = {2075-4450}, support = {VKR10101//Villum Fonden/ ; DE-FC02-07ER64494//Department of Energy Great Lakes Bioenergy Research Center Office of Science Grant/ ; }, abstract = {Termites are among the most successful animal groups, accomplishing nutrient acquisition through long-term associations and enzyme provisioning from microbial symbionts. Fungus farming has evolved only once in a single termite sub-family: Macrotermitinae. This sub-family has become a dominant decomposer in the Old World; through enzymatic contributions from insects, fungi, and bacteria, managed in an intricate decomposition pathway, the termites obtain near-complete utilisation of essentially any plant substrate. Here we review recent insights into our understanding of the process of plant biomass decomposition in fungus-growing termites. To this end, we outline research avenues that we believe can help shed light on how evolution has shaped the optimisation of plant-biomass decomposition in this complex multipartite symbiosis.}, } @article {pmid30923350, year = {2019}, author = {Raina, JB and Fernandez, V and Lambert, B and Stocker, R and Seymour, JR}, title = {The role of microbial motility and chemotaxis in symbiosis.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41579-019-0182-9}, pmid = {30923350}, issn = {1740-1534}, abstract = {Many symbiotic relationships rely on the acquisition of microbial partners from the environment. However, the mechanisms by which microbial symbionts find and colonize their hosts are often unknown. We propose that the acquisition of environmental symbionts often necessitates active migration and colonization by the symbionts through motility and chemotaxis. The pivotal role of these behaviours in the onset and maintenance of symbiotic interactions is well established in a small number of model systems but remains largely overlooked for the many symbioses that involve the recruitment of microbial partners from the environment. In this Review, we highlight when, where and how chemotaxis and motility can enable symbiont recruitment and propose that these symbiont behaviours are important across a wide range of hosts and environments.}, } @article {pmid30922601, year = {2019}, author = {Buysse, M and Plantard, O and McCoy, KD and Duron, O and Menard, C}, title = {Tissue localization of Coxiella-like endosymbionts in three European tick species through fluorescence in situ hybridization.}, journal = {Ticks and tick-borne diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ttbdis.2019.03.014}, pmid = {30922601}, issn = {1877-9603}, abstract = {Ticks are commonly infected by Coxiella-like endosymbionts (Coxiella-LE) which are thought to supply missing B vitamin nutrients required for blood digestion.While this nutritional symbiosis is essential for the survival and reproduction of infected tick species, our knowledge of where Coxiella-LE is localized in tick tissues is partial at best since previous studies have focused on a limited number of Asian or American tick species. To fill this gap, we investigated the tissue localization of Coxiella-LE in three European tick species, Ornithodoros maritimus, Dermacentor marginatus and Ixodes hexagonus, using a diagnostic fluorescence in situ hybridization (FISH) assay, combined with PCR-based detection. Specific fluorescent foci were observed in several tick tissues. We visualized a pronounced tissue tropism of Coxiella-LE for tick ovaries and Malpighian tubules, a pattern suggestive of a high degree of lifestyle specialization toward mutualism: infection of the ovaries is indicative of transovarial transmission, whereas infection of the Malpighian tubules suggests a nutritional function. We postulate that Malpighian tubules are key organs for the nutritional symbiosis, notably the synthesis of B vitamins by Coxiella-LE, whereas the infection of the ovaries ensures vertical transmission of the symbionts to future generations. We also detected occasional infections in other organs, such as salivary glands and the midgut. Finally, we discuss the potential significance of the different tissue tropism for tick biology.}, } @article {pmid30835731, year = {2019}, author = {Di Lelio, I and Illiano, A and Astarita, F and Gianfranceschi, L and Horner, D and Varricchio, P and Amoresano, A and Pucci, P and Pennacchio, F and Caccia, S}, title = {Evolution of an insect immune barrier through horizontal gene transfer mediated by a parasitic wasp.}, journal = {PLoS genetics}, volume = {15}, number = {3}, pages = {e1007998}, doi = {10.1371/journal.pgen.1007998}, pmid = {30835731}, issn = {1553-7404}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Hemolymph/immunology/virology ; Larva/genetics/*immunology/virology ; Phylogeny ; Proteomics ; Symbiosis/genetics/immunology ; Wasps/genetics/*immunology/virology ; }, abstract = {Genome sequencing data have recently demonstrated that eukaryote evolution has been remarkably influenced by the acquisition of a large number of genes by horizontal gene transfer (HGT) across different kingdoms. However, in depth-studies on the physiological traits conferred by these accidental DNA acquisitions are largely lacking. Here we elucidate the functional role of Sl gasmin, a gene of a symbiotic virus of a parasitic wasp that has been transferred to an ancestor of the moth species Spodoptera littoralis and domesticated. This gene is highly expressed in circulating immune cells (haemocytes) of larval stages, where its transcription is rapidly boosted by injection of microorganisms into the body cavity. RNAi silencing of Sl gasmin generates a phenotype characterized by a precocious suppression of phagocytic activity by haemocytes, which is rescued when these immune cells are incubated in plasma samples of control larvae, containing high levels of the encoded protein. Proteomic analysis demonstrates that the protein Sl gasmin is released by haemocytes into the haemolymph, where it opsonizes the invading bacteria to promote their phagocytosis, both in vitro and in vivo. Our results show that important physiological traits do not necessarily originate from evolution of pre-existing genes, but can be acquired by HGT events, through unique pathways of symbiotic evolution. These findings indicate that insects can paradoxically acquire selective advantages with the help of their natural enemies.}, } @article {pmid30818326, year = {2019}, author = {von Geldern, TW and Morton, HE and Clark, RF and Brown, BS and Johnston, KL and Ford, L and Specht, S and Carr, RA and Stolarik, DF and Ma, J and Rieser, MJ and Struever, D and Frohberger, SJ and Koschel, M and Ehrens, A and Turner, JD and Hübner, MP and Hoerauf, A and Taylor, MJ and Ward, SA and Marsh, K and Kempf, DJ}, title = {Discovery of ABBV-4083, a novel analog of Tylosin A that has potent anti-Wolbachia and anti-filarial activity.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {2}, pages = {e0007159}, doi = {10.1371/journal.pntd.0007159}, pmid = {30818326}, issn = {1935-2735}, mesh = {Animals ; Anti-Bacterial Agents/pharmacokinetics/*pharmacology ; *Drug Discovery ; Elephantiasis, Filarial/drug therapy ; Female ; Filaricides/pharmacokinetics/*pharmacology ; Filarioidea/drug effects/microbiology ; Gerbillinae ; Mice ; Mice, Inbred BALB C ; Onchocerciasis/drug therapy ; Symbiosis/drug effects ; Tylosin/*analogs & derivatives/*pharmacology ; Wolbachia/*drug effects ; }, abstract = {There is a significant need for improved treatments for onchocerciasis and lymphatic filariasis, diseases caused by filarial worm infection. In particular, an agent able to selectively kill adult worms (macrofilaricide) would be expected to substantially augment the benefits of mass drug administration (MDA) with current microfilaricides, and to provide a solution to treatment of onchocerciasis / loiasis co-infection, where MDA is restricted. We have identified a novel macrofilaricidal agent, Tylosin A (TylA), which acts by targeting the worm-symbiont Wolbachia bacterium. Chemical modification of TylA leads to improvements in anti-Wolbachia activity and oral pharmacokinetic properties; an optimized analog (ABBV-4083) has been selected for clinical evaluation.}, } @article {pmid30741934, year = {2019}, author = {Osterman, J and Wintermantel, D and Locke, B and Jonsson, O and Semberg, E and Onorati, P and Forsgren, E and Rosenkranz, P and Rahbek-Pedersen, T and Bommarco, R and Smith, HG and Rundlöf, M and de Miranda, JR}, title = {Clothianidin seed-treatment has no detectable negative impact on honeybee colonies and their pathogens.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {692}, doi = {10.1038/s41467-019-08523-4}, pmid = {30741934}, issn = {2041-1723}, mesh = {Animals ; Bacteria/drug effects/pathogenicity ; Bees/*drug effects/growth & development/immunology ; Dicistroviridae/drug effects ; Environmental Monitoring ; Gammaproteobacteria/drug effects ; Gene Expression/drug effects ; Guanidines/*pharmacology ; Honey/analysis ; Neonicotinoids/*pharmacology ; Plant Extracts/*pharmacology ; Plant Nectar/chemistry ; Plant Oils/pharmacology ; Pollen/chemistry ; Seeds/*chemistry ; Sweden ; Symbiosis ; Thiazoles/*pharmacology ; Viruses/drug effects/pathogenicity ; }, abstract = {Interactions between multiple stressors have been implicated in elevated honeybee colony losses. Here, we extend our landscape-scale study on the effects of placement at clothianidin seed-treated oilseed rape fields on honeybees with an additional year and new data on honeybee colony development, swarming, mortality, pathogens and immune gene expression. Clothianidin residues in pollen, nectar and honeybees were consistently higher at clothianidin-treated fields, with large differences between fields and years. We found large variations in colony development and microbial composition and no observable negative impact of placement at clothianidin-treated fields. Clothianidin treatment was associated with an increase in brood, adult bees and Gilliamella apicola (beneficial gut symbiont) and a decrease in Aphid lethal paralysis virus and Black queen cell virus - particularly in the second year. The results suggest that at colony level, honeybees are relatively robust to the effects of clothianidin in real-world agricultural landscapes, with moderate, natural disease pressure.}, } @article {pmid29693244, year = {2018}, author = {Hembry, DH and Raimundo, RLG and Newman, EA and Atkinson, L and Guo, C and Guimarães, PR and Gillespie, RG}, title = {Does biological intimacy shape ecological network structure? A test using a brood pollination mutualism on continental and oceanic islands.}, journal = {The Journal of animal ecology}, volume = {87}, number = {4}, pages = {1160-1171}, doi = {10.1111/1365-2656.12841}, pmid = {29693244}, issn = {1365-2656}, mesh = {Animals ; Biological Evolution ; Insect Proteins/analysis ; Islands ; Japan ; Larva/growth & development/physiology ; Moths/growth & development/*physiology ; Phyllanthus/growth & development/*physiology ; *Phylogeny ; *Pollination ; Polynesia ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Biological intimacy-the degree of physical proximity or integration of partner taxa during their life cycles-is thought to promote the evolution of reciprocal specialization and modularity in the networks formed by co-occurring mutualistic species, but this hypothesis has rarely been tested. Here, we test this "biological intimacy hypothesis" by comparing the network architecture of brood pollination mutualisms, in which specialized insects are simultaneously parasites (as larvae) and pollinators (as adults) of their host plants to that of other mutualisms which vary in their biological intimacy (including ant-myrmecophyte, ant-extrafloral nectary, plant-pollinator and plant-seed disperser assemblages). We use a novel dataset sampled from leafflower trees (Phyllanthaceae: Phyllanthus s. l. [Glochidion]) and their pollinating leafflower moths (Lepidoptera: Epicephala) on three oceanic islands (French Polynesia) and compare it to equivalent published data from congeners on continental islands (Japan). We infer taxonomic diversity of leafflower moths using multilocus molecular phylogenetic analysis and examine several network structural properties: modularity (compartmentalization), reciprocality (symmetry) of specialization and algebraic connectivity. We find that most leafflower-moth networks are reciprocally specialized and modular, as hypothesized. However, we also find that two oceanic island networks differ in their modularity and reciprocal specialization from the others, as a result of a supergeneralist moth taxon which interacts with nine of 10 available hosts. Our results generally support the biological intimacy hypothesis, finding that leafflower-moth networks (usually) share a reciprocally specialized and modular structure with other intimate mutualisms such as ant-myrmecophyte symbioses, but unlike nonintimate mutualisms such as seed dispersal and nonintimate pollination. Additionally, we show that generalists-common in nonintimate mutualisms-can also evolve in intimate mutualisms, and that their effect is similar in both types of assemblages: once generalists emerge they reshape the network organization by connecting otherwise isolated modules.}, } @article {pmid29603211, year = {2018}, author = {Simmons, BI and Sutherland, WJ and Dicks, LV and Albrecht, J and Farwig, N and García, D and Jordano, P and González-Varo, JP}, title = {Moving from frugivory to seed dispersal: Incorporating the functional outcomes of interactions in plant-frugivore networks.}, journal = {The Journal of animal ecology}, volume = {87}, number = {4}, pages = {995-1007}, doi = {10.1111/1365-2656.12831}, pmid = {29603211}, issn = {1365-2656}, mesh = {Animals ; Birds/*physiology ; *Food Chain ; Fruit/physiology ; *Herbivory ; Magnoliopsida/*physiology ; *Seed Dispersal ; Symbiosis ; }, abstract = {There is growing interest in understanding the functional outcomes of species interactions in ecological networks. For many mutualistic networks, including pollination and seed dispersal networks, interactions are generally sampled by recording animal foraging visits to plants. However, these visits may not reflect actual pollination or seed dispersal events, despite these typically being the ecological processes of interest. Frugivorous animals can act as seed dispersers, by swallowing entire fruits and dispersing their seeds, or as pulp peckers or seed predators, by pecking fruits to consume pieces of pulp or seeds. These processes have opposing consequences for plant reproductive success. Therefore, equating visitation with seed dispersal could lead to biased inferences about the ecology, evolution and conservation of seed dispersal mutualisms. Here, we use natural history information on the functional outcomes of pairwise bird-plant interactions to examine changes in the structure of seven European plant-frugivore visitation networks after non-mutualistic interactions (pulp pecking and seed predation) have been removed. Following existing knowledge of the contrasting structures of mutualistic and antagonistic networks, we hypothesized a number of changes following interaction removal, such as increased nestedness and lower specialization. Non-mutualistic interactions with pulp peckers and seed predators occurred in all seven networks, accounting for 21%-48% of all interactions and 6%-24% of total interaction frequency. When non-mutualistic interactions were removed, there were significant increases in network-level metrics such as connectance and nestedness, while robustness decreased. These changes were generally small, homogenous and driven by decreases in network size. Conversely, changes in species-level metrics were more variable and sometimes large, with significant decreases in plant degree, interaction frequency, specialization and resilience to animal extinctions and significant increases in frugivore species strength. Visitation data can overestimate the actual frequency of seed dispersal services in plant-frugivore networks. We show here that incorporating natural history information on the functions of species interactions can bring us closer to understanding the processes and functions operating in ecological communities. Our categorical approach lays the foundation for future work quantifying functional interaction outcomes along a mutualism-antagonism continuum, as documented in other frugivore faunas.}, } @article {pmid29504629, year = {2018}, author = {Câmara, T and Leal, IR and Blüthgen, N and Oliveira, FMP and Queiroz, RT and Arnan, X}, title = {Effects of chronic anthropogenic disturbance and rainfall on the specialization of ant-plant mutualistic networks in the Caatinga, a Brazilian dry forest.}, journal = {The Journal of animal ecology}, volume = {87}, number = {4}, pages = {1022-1033}, doi = {10.1111/1365-2656.12820}, pmid = {29504629}, issn = {1365-2656}, mesh = {Animal Husbandry ; Animals ; Ants/*physiology ; Brazil ; Climate Change ; Forestry ; *Forests ; *Human Activities ; Humans ; *Plant Physiological Phenomena ; *Rain ; *Symbiosis ; }, abstract = {Anthropogenic disturbance and climate change might negatively affect the ecosystem services provided by mutualistic networks. However, the effects of such forces remain poorly characterized. They may be especially important in dry forests, which (1) experience chronic anthropogenic disturbances (CADs) as human populations exploit forest resources, and (2) are predicted to face a 22% decline in rainfall under climate change. In this study, we investigated the separate and combined effects of CADs and rainfall levels on the specialization of mutualistic networks in the Caatinga, a seasonally dry tropical forest typical of north-eastern Brazil. More specifically, we examined interactions between plants bearing extrafloral nectaries (EFNs) and ants. We analysed whether differences in network specialization could arise from environmentally mediated variation in the species composition, namely via the replacement of specialist by generalist species. We characterized these ant-plant networks in 15 plots (20 × 20 m) that varied in CAD intensity and mean annual rainfall. We quantified CAD intensity by calculating three indices related to the main sources of disturbance in the Caatinga: livestock grazing (LG), wood extraction (WE) and miscellaneous resource use (MU). We determined the degree of ant-plant network specialization using four metrics: generality, vulnerability, interaction evenness and H2 '. Our results indicate that CADs differentially influenced network specialization: we observed positive, negative, and neutral responses along LG, MU and WE gradients, respectively. The pattern was most pronounced with LG. Rainfall also shaped network specialization, markedly increasing it. While LG and rainfall were associated with changes in network species composition, this trend was not related to the degree of species specialization. This result suggests that shifts in network specialization might be related to changes in species behaviour, not species composition. Our study highlights the vulnerability of such dry forest ant-plant networks to climate change. Moreover, dry forests experience highly heterogeneous anthropogenic disturbances, creating a geographic mosaic of selective forces that may shape the co-evolution of interactions between ants and EFN-bearing plants.}, } @article {pmid30919981, year = {2019}, author = {Field, KJ and Bidartondo, MI and Rimington, WR and Hoysted, GA and Beerling, DJ and Cameron, DD and Duckett, JG and Leake, JR and Pressel, S}, title = {Functional complementarity of ancient plant-fungal mutualisms: contrasting nitrogen, phosphorus and carbon exchanges between Mucoromycotina and Glomeromycotina fungal symbionts of liverworts.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15819}, pmid = {30919981}, issn = {1469-8137}, abstract = {Liverworts, which are amongst the earliest-divergent plant lineages and important ecosystem pioneers, often form nutritional mutualisms with arbuscular mycorrhiza-forming Glomeromycotina and fine root endophyte Mucoromycotina fungi, both of which co-evolved with early land plants. Some liverworts, in common with many later-divergent plants, harbour both fungal groups, suggesting these fungi may complementarily improve plant access to different soil nutrients. We tested this hypothesis by growing liverworts in single and dual fungal partnerships under a modern atmosphere and under 1500 ppm [CO2 ], as experienced by early land plants. Access to soil nutrients via fungal partners was investigated with 15 N-labelled algal necromass and 33 P orthophosphate. Photosynthate allocation to fungi was traced using 14 CO2 . Only Mucoromycotina fungal partners provided liverworts with substantial access to algal 15 N, irrespective of atmospheric CO2 concentration. Both symbionts increased 33 P uptake, but Glomeromycotina were often more effective. Dual partnerships showed complementarity of nutrient pool use and greatest photosynthate allocation to symbiotic fungi. We show there are important functional differences between the plant-fungal symbioses tested, providing new insights into the functional biology of Glomeromycotina and Mucoromycotina fungal groups that form symbioses with plants. This may explain the persistence of both fungal lineages in symbioses across the evolution of land plants. This article is protected by copyright. All rights reserved.}, } @article {pmid30919462, year = {2019}, author = {Matsuo, K and Haku, A and Bi, B and Takahashi, H and Kamada, N and Yaguchi, T and Saijo, S and Yoneyama, M and Goto, Y}, title = {Fecal microbiota transplantation prevents Candida albicans from colonizing the gastrointestinal tract.}, journal = {Microbiology and immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1348-0421.12680}, pmid = {30919462}, issn = {1348-0421}, abstract = {Gut microbes symbiotically colonize the gastrointestinal (GI) tract, interacting with each other and their host to maintain GI tract homeostasis. Recent reports have shown that gut microbes help protect the gut from colonization by pathogenic microbes. Here, we report that commensal microbes prevent colonization of the pathogenic fungus, Candida albicans, in the GI tract. Wild-type specific pathogen-free (SPF) mice are resistant to C. albicans colonization in the GI tract. However, administering certain antibiotics to SPF mice enables C. albicans colonization. Quantitative kinetics of commensal bacteria are inversely correlated with the number of C. albicans in the gut. Here, we provide further evidence that fecal microbiota transplantation effectively prevents Candida colonization in the GI tract. These data demonstrate the importance of commensal bacteria as a barrier of the GI tract surface, and highlight the potential clinical applications of commensal bacteria for preventing pathogenic fungal infections. This article is protected by copyright. All rights reserved.}, } @article {pmid30918316, year = {2019}, author = {Nissinen, R and Helander, M and Kumar, M and Saikkonen, K}, title = {Heritable Epichloë symbiosis shapes fungal but not bacterial communities of plant leaves.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5253}, doi = {10.1038/s41598-019-41603-5}, pmid = {30918316}, issn = {2045-2322}, abstract = {Keystone microbial species have driven eco-evolutionary processes since the origin of life. However, due to our inability to detect the majority of microbiota, members of diverse microbial communities of fungi, bacteria and viruses have largely been ignored as keystone species in past literature. Here we tested whether heritable Epichloë species of pooidae grasses modulate microbiota of their shared host plant.}, } @article {pmid30917916, year = {2019}, author = {Hajialilo, E and Rezaeian, M and Niyyati, M and Pourmand, MR and Mohebali, M and Norouzi, M and Pashabeyg, KR and Rezaie, S and Khodavaisy, S}, title = {Molecular characterization of bacterial, viral and fungal endosymbionts of Acanthamoeba isolates in keratitis patients of Iran.}, journal = {Experimental parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.exppara.2019.03.013}, pmid = {30917916}, issn = {1090-2449}, abstract = {Free-living amoebae belong to the genus Acanthamoeba; can feed on microbial population by phagocytosis, and with the capability to act as a reservoir and a vehicle of microorganisms to susceptible host. Therefore, the role of endosymbiosis in the pathogenesis of Acanthamoeba is complex and not fully understood. The aim of the present study was to identify bacterial, fungal, and human adenovirus (HADV) endosymbionts as well as evaluating the endosymbionts role of such organisms in the pathogenesis of Acanthamoeba in keratitis patients living in Iran. Fifteen Acanthamoeba (T4 genotype) isolates were recovered from corneal scrapes and contact lenses of patients with keratitis. Cloning and purification was performed for all isolate. Gram staining was performed to identify bacterial endosymbionts. DNA extraction, PCR, and nested PCR was set up to identify endosymbiont of amoeba. Evaluation of pathogenicity was conducted by osmo-tolerance and thermo-tolerance assays and cell culture, and then CPE (cytopathic effect) was survey. Statistical analysis was used between Acanthamoeba associated endosymbionts and Acanthamoeba without endosymbiont at 24, 48, 72, and 96 h. A p value < 0.05 was considered as significant, statistically. A total of 9 (60%) Acanthamoeba (T4 genotypes) isolates were successfully cloned for detecting microorganism endosymbionts. The only isolate negative for the presence of endosymbiont was ICS9. ICS7 (Pseudomonas aeruginosa, Aspergillus sp., and human adenovirus endosymbionts) and ICS2 (Escherichia coli endosymbiont) isolates were considered as Acanthamoeba associated endosymbionts. ICS7 and ICS2 isolates were highly pathogen whereas ICS9 isolate showed low pathogenicity in pathogenicity evaluated. Positive CPE for ICS7 and ICS2 isolates and negative CPE for ICS9 isolate were observed in cell culture. The average number of cells, trophozoites, and cysts among ICS7, ICS2, and ICS9 isolates at 24, 48, 72, and 96 h was significant. This is the first survey on microbial endosymbionts of Acanthamoeba in keratitis patients of Iran, and also the first report of Aspergillus sp, Achromobacter sp., Microbacterium sp., Brevibacillus sp, Brevundimonas sp and Mastadenovirus sp in Acanthamoeba as endosymbionts. Our study demonstrated that microbial endosymbionts can affect the pathogenicity of Acanthamoeba; however, further research is required to clarify the exact pattern of symbiosis, in order to modify treatment protocol.}, } @article {pmid30917551, year = {2019}, author = {Qi, Y and Chen, X and Hu, Z and Song, C and Cui, Y}, title = {Bibliometric Analysis of Algal-Bacterial Symbiosis in Wastewater Treatment.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ijerph16061077}, pmid = {30917551}, issn = {1660-4601}, support = {2016YFB0601003//National key research and development program-China/ ; 16JCYBJC20700//Natural Science Foundation of Tianjin/ ; }, abstract = {In recent years, the algae-bacteria symbiotic system has played a significant role in the sustainable development of wastewater treatment. With the continuous expansion of research outputs, publications related to wastewater treatment via algal-bacterial consortia appear to be on the rise. Based on SCI-EXPANDED database, this study investigated the research activities and tendencies of algae-bacteria symbiotic wastewater treatment technology by bibliometric method from 1998 to 2017. The results indicated that environmental sciences and ecology was the most productive subject categories, followed by engineering. Bioresource Technology was the most prominent journal in this field with considerable academic influence. China (146), USA (139) and Spain (76) had the largest amount of publications. Among them, USA was in a leading position in international cooperation, with the highest h-index (67) in 79 countries/territories. The cooperation between China and USA was the closest. The cooperative publishing rate of the Chinese Academy of Sciences was 83.33%, but most of them were in cooperation with domestic institutions, while international cooperation was relatively limited. Methane production, biofuel production, and extracellular polymeric substance were future focal frontiers of research, and this field had gradually become a multi-perspective and inter-disciplinary approach combining biological, environmental and energy technologies.}, } @article {pmid30917525, year = {2019}, author = {Salgado-Morales, R and Martínez-Ocampo, F and Obregón-Barboza, V and Vilchis-Martínez, K and Jiménez-Pérez, A and Dantán-González, E}, title = {Assessing the Pathogenicity of Two Bacteria Isolated from the Entomopathogenic Nematode Heterorhabditis indica against Galleria mellonella and Some Pest Insects.}, journal = {Insects}, volume = {10}, number = {3}, pages = {}, doi = {10.3390/insects10030083}, pmid = {30917525}, issn = {2075-4450}, support = {PDCPN 0247780//Consejo Nacional de Ciencia y Tecnología/ ; 296934//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {The entomopathogenic nematodes Heterorhabditis are parasites of insects and are associated with mutualist symbiosis enterobacteria of the genus Photorhabdus; these bacteria are lethal to their host insects. Heterorhabditis indica MOR03 was isolated from sugarcane soil in Morelos state, Mexico. The molecular identification of the nematode was confirmed using sequences of the ITS1-5.8S-ITS2 region and the D2/D3 expansion segment of the 28S rRNA gene. In addition, two bacteria HIM3 and NA04 strains were isolated from the entomopathogenic nematode. The genomes of both bacteria were sequenced and assembled de novo. Phylogenetic analysis was confirmed by concatenated gene sequence datasets as Photorhabdus luminescens HIM3 (16S rRNA, 23S rRNA, dnaN, gyrA, and gyrB genes) and Pseudomonas aeruginosa NA04 (16S rRNA, 23S rRNA and gyrB genes). H. indica MOR03 infects Galleria mellonella, Tenebrio molitor, Heliothis subflexa, and Diatraea magnifactella larvae with LC50 values of 1.4, 23.5, 13.7, and 21.7 IJs/cm², respectively, at 48 h. These bacteria are pathogenic to various insects and have high injectable insecticide activity at 24 h.}, } @article {pmid30026291, year = {2018}, author = {Magne, K and Couzigou, JM and Schiessl, K and Liu, S and George, J and Zhukov, V and Sahl, L and Boyer, F and Iantcheva, A and Mysore, KS and Wen, J and Citerne, S and Oldroyd, GED and Ratet, P}, title = {MtNODULE ROOT1 and MtNODULE ROOT2 Are Essential for Indeterminate Nodule Identity.}, journal = {Plant physiology}, volume = {178}, number = {1}, pages = {295-316}, pmid = {30026291}, issn = {1532-2548}, mesh = {Amino Acid Sequence ; *Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Medicago truncatula/*genetics/growth & development/metabolism ; Meristem/genetics/growth & development/metabolism ; Mutation ; Nitrogen Fixation/genetics ; Phylogeny ; Plant Proteins/classification/*genetics/metabolism ; Plant Roots/genetics/growth & development/metabolism ; Plants, Genetically Modified ; Root Nodules, Plant/*genetics/growth & development/metabolism ; Sequence Homology, Amino Acid ; Symbiosis/genetics ; }, abstract = {Symbiotic interactions between legume plants and rhizobia result in the formation of nitrogen-fixing nodules, but the molecular actors and the mechanisms allowing for the maintenance of nodule identity are poorly understood. Medicago truncatula NODULE ROOT1 (MtNOOT1), Pisum sativum COCHLEATA1 (PsCOCH1), and Lotus japonicus NOOT-BOP-COCH-LIKE1 (LjNBCL1) are orthologs of Arabidopsis (Arabidopsis thaliana) AtBLADE-ON-PETIOLE1/2 and are members of the NBCL gene family, which has conserved roles in plant development and is essential for indeterminate and determinate nodule identity in legumes. The loss of function of MtNOOT1, PsCOCH1, and LjNBCL1 triggers a partial loss of nodule identity characterized by the development of ectopic roots arising from nodule vascular meristems. Here, we report the identification and characterization of a second gene involved in regulating indeterminate nodule identity in M. truncatula, MtNOOT2MtNOOT2 is the paralog of MtNOOT1 and belongs to a second legume-specific NBCL subclade, the NBCL2 clade. MtNOOT2 expression was induced during early nodule formation, and it was expressed primarily in the nodule central meristem. Mtnoot2 mutants did not present any particular symbiotic phenotype; however, the loss of function of both MtNOOT1 and MtNOOT2 resulted in the complete loss of nodule identity and was accompanied by drastic changes in the expression of symbiotic, defense, and root apical meristem marker genes. Mtnoot1 noot2 double mutants developed only nonfixing root-like structures that were no longer able to host symbiotic rhizobia. This study provides original insights into the molecular basis underlying nodule identity in legumes forming indeterminate nodules.}, } @article {pmid29676724, year = {2018}, author = {Monsanto-Hearne, V and Johnson, KN}, title = {Wolbachia-mediated protection of Drosophila melanogaster against systemic infection with its natural viral pathogen Drosophila C virus does not involve changes in levels of highly abundant miRNAs.}, journal = {The Journal of general virology}, volume = {99}, number = {6}, pages = {827-831}, doi = {10.1099/jgv.0.001064}, pmid = {29676724}, issn = {1465-2099}, mesh = {Animals ; Dicistroviridae/*pathogenicity ; Drosophila melanogaster/*genetics/microbiology/virology ; Host-Pathogen Interactions/*genetics ; MicroRNAs/*genetics ; Real-Time Polymerase Chain Reaction ; Symbiosis ; Virus Diseases/microbiology ; Wolbachia/*physiology ; }, abstract = {The presence of Wolbachia confers virus protection to insects. The molecular mechanism underlying Wolbachia-mediated protection in this tripartite host-endosymbiont-virus interaction is not yet fully understood. In the bipartite association between Drosophila melanogaster and Drosophila C virus (DCV), changes in the expression of microRNAs (miRNAs) influence the outcome of viral pathogenesis. Here we examined whether changes in miRNA expression are similarly involved in the Drosophila-Wolbachia-DCV association. The levels of highly abundant miRNAs in D. melanogaster, Wolbachia-mono-infected D. melanogaster, and DCV- and Wolbachia-bi-infected D. melanogaster were quantified using RT-qPCR and compared. The results show that the abundance of the 17 tested D. melanogaster miRNAs is not affected by Wolbachia endosymbiosis or by bi-infection of Wolbachia and DCV. These results suggest that the in vivo protection conferred by Wolbachia to its native host against D. melanogaster's natural pathogen DCV is not likely to be dependent on or associated with changes in the levels of highly expressed miRNAs.}, } @article {pmid30917160, year = {2019}, author = {Del Cerro, P and Megías, M and López-Baena, FJ and Gil-Serrano, A and Pérez-Montaño, F and Ollero, FJ}, title = {Osmotic stress activates nif and fix genes and induces the Rhizobium tropici CIAT 899 Nod factor production via NodD2 by up-regulation of the nodA2 operon and the nodA3 gene.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213298}, doi = {10.1371/journal.pone.0213298}, pmid = {30917160}, issn = {1932-6203}, abstract = {The symbiosis between rhizobia and legumes is characterized by a complex molecular dialogue in which the bacterial NodD protein plays a major role due to its capacity to activate the expression of the nodulation genes in the presence of appropiate flavonoids. These genes are involved in the synthesis of molecules, the nodulation factors (NF), responsible for launching the nodulation process. Rhizobium tropici CIAT 899, a rhizobial strain that nodulates Phaseolus vulgaris, is characterized by its tolerance to multiple environmental stresses such as high temperatures, acidity or elevated osmolarity. This strain produces nodulation factors under saline stress and the same set of CIAT 899 nodulation genes activated by inducing flavonoids are also up-regulated in a process controlled by the NodD2 protein. In this paper, we have studied the effect of osmotic stress (high mannitol concentrations) on the R. tropici CIAT 899 transcriptomic response. In the same manner as with saline stress, the osmotic stress mediated NF production and export was controlled directly by NodD2. In contrast to previous reports, the nodA2FE operon and the nodA3 and nodD1 genes were up-regulated with mannitol, which correlated with an increase in the production of biologically active NF. Interestingly, in these conditions, this regulatory protein controlled not only the expression of nodulation genes but also the expression of other genes involved in protein folding and synthesis, motility, synthesis of polysaccharides and, surprinsingly, nitrogen fixation. Moreover, the non-metabolizable sugar dulcitol was also able to induce the NF production and the activation of nod genes in CIAT 899.}, } @article {pmid30916398, year = {2019}, author = {Quiroga, G and Erice, G and Ding, L and Chaumont, F and Aroca, R and Ruiz-Lozano, JM}, title = {The arbuscular mycorrhizal symbiosis regulates aquaporins activity and improves root cell water permeability in maize plants subjected to water stress.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13551}, pmid = {30916398}, issn = {1365-3040}, abstract = {Studies have suggested that increased root hydraulic conductivity in mycorrhizal roots could be the result of increased cell-to-cell water flux via aquaporins. This study aimed to elucidate if the key effect of the regulation of maize aquaporins by the arbuscular mycorrhizal (AM) symbiosis is the enhancement of root cell water transport capacity. Thus water permeability coefficient (Pf) and cell hydraulic conductivity (Lpc) were measured in root protoplast and intact cortex cells of AM and non-AM plants subjected or not to water stress. Results showed that cells from droughted-AM roots maintained Pf and Lpc values of non-stressed plants, while in non-AM roots these values declined drastically as consequence of water deficit. Interestingly, the phosphorylation status of PIP2 aquaporins increased in AM plants subjected to water deficit, and Pf values higher than 12 μm s-1 were found only in protoplasts from AM roots, revealing the higher water permeability of AM root cells. In parallel, the AM symbiosis increased stomatal conductance, net photosynthesis and related parameters, showing a higher photosynthetic capacity in these plants. This study demonstrate a better performance of AM root cells in water transport under water deficit, which is connected to the shoot physiological performance in terms of photosynthetic capacity.}, } @article {pmid30915091, year = {2019}, author = {Goh, DM and Cosme, M and Kisiala, AB and Mulholland, S and Said, ZMF and Spíchal, L and Emery, RJN and Declerck, S and Guinel, FC}, title = {A Stimulatory Role for Cytokinin in the Arbuscular Mycorrhizal Symbiosis of Pea.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {262}, doi = {10.3389/fpls.2019.00262}, pmid = {30915091}, issn = {1664-462X}, abstract = {The arbuscular mycorrhizal (AM) symbiosis between terrestrial plants and AM fungi is regulated by plant hormones. For most of these, a role has been clearly assigned in this mutualistic interaction; however, there are still contradictory reports for cytokinin (CK). Here, pea plants, the wild type (WT) cv. Sparkle and its mutant E151 (Pssym15), were inoculated with the AM fungus Rhizophagus irregularis. E151 has previously been characterized as possessing high CK levels in non-mycorrhizal (myc-) roots and exhibiting high number of fungal structures in mycorrhizal (myc+) roots. Myc- and myc+ plants were treated 7, 9, and 11 days after inoculation (DAI) with synthetic compounds known to alter CK status. WT plants were treated with a synthetic CK [6-benzylaminopurine (BAP)] or the CK degradation inhibitor INCYDE, whereas E151 plants were treated with the CK receptor antagonist PI-55. At 13 DAI, plant CK content was analyzed by mass spectrometry. The effects of the synthetic compounds on AM colonization were assessed at 28 (WT) or 35 (E151) DAI via a modified magnified intersections method. The only noticeable difference seen between myc- and myc+ plants in terms of CK content was in the levels of nucleotides (NTs). Whereas WT plants responded to fungi by lowering their NT levels, E151 plants did not. Since NTs are thought to be converted into active CK forms, this result suggests that active CKs were synthesized more effectively in WT than in E151. In general, myc+ and myc- WT plants responded similarly to INCYDE by lowering significantly their NT levels and increasing slightly their active CK levels; these responses were less obvious in BAP-treated WT plants. In contrast, the response of E151 plants to PI-55 depended on the plant mycorrhizal status. Whereas treated myc- plants exhibited high NT and low active CK levels, treated myc+ plants displayed low levels of both NTs and active CKs. Moreover, treated WT plants were more colonized than treated E151 plants. We concluded that CKs have a stimulatory role in AM colonization because increased active CK levels were paralleled with increased AM colonization while decreased CK levels corresponded to reduced AM colonization.}, } @article {pmid30914318, year = {2019}, author = {Xiao, R and Wang, X and Xie, E and Ji, T and Li, X and Muhammad, A and Yin, X and Hou, Y and Shi, Z}, title = {An IMD-like pathway mediates the intestinal immunity to modulate the homeostasis of gut microbiota in Rhynchophorus ferrugineus Olivier (Coleoptera: Dryophthoridae).}, journal = {Developmental and comparative immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.dci.2019.03.013}, pmid = {30914318}, issn = {1879-0089}, abstract = {Most animals have established the mutualistic interactions with their intestinal microbes which provide multiple benefits to their host physiology. However, the mechanisms behind hosts determine the load and composition of gut microbiota are still poorly understood outside dipteran insects. Here, the gene, encoding the NF-κB-like transcription factor Relish, being designated as RfRelish, was identified and analyzed in red palm weevil (RPW), Rhynchophorus ferrugineus Olivier. We revealed that the abundance of RfRelish transcripts in the fat body, hemolymph and gut are significantly higher than that in non-immunity-related tissues, and its expression level can be markedly induced by bacterial challenges. When RfRelish was silenced, the ability of individuals to clear the pathogenic bacteria in body cavity and gut was significantly compromised, suggesting that both the systemic and gut local immunity were impaired dramatically by RfRelish knockdown. Additionally, the silenced insects exhibited increased gut bacterial load, and the relative abundance of some gut bacteria was changed as compared to controls. Collectively, our findings demonstrate that the IMD-like pathway restricts the proliferation of gut bacteria and shapes the commensal community structure in the intestine of R. ferrugineus by mediating the secretion of antimicrobial peptides. We provide a striking example on how an insect pest maintains the homeostasis of gut microbiota via a conserved immune pathway without compromising the advantages of the mutualistic relationships.}, } @article {pmid29688526, year = {2018}, author = {Arkhipova, IR}, title = {Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution.}, journal = {Molecular biology and evolution}, volume = {35}, number = {6}, pages = {1332-1337}, doi = {10.1093/molbev/msy083}, pmid = {29688526}, issn = {1537-1719}, support = {R01 GM111917/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA Transposable Elements ; *Genetic Drift ; *Genome ; Humans ; Metagenomics ; Symbiosis ; }, abstract = {Among the multitude of papers published yearly in scientific journals, precious few publications may be worth looking back in half a century to appreciate the significance of the discoveries that would later become common knowledge and get a chance to shape a field or several adjacent fields. Here, Kimura's fundamental concept of neutral mutation-random drift, which was published 50 years ago, is re-examined in light of its pervasive influence on comparative genomics and, more specifically, on the contribution of transposable elements to eukaryotic genome evolution.}, } @article {pmid29580322, year = {2018}, author = {Zhang, P and Liu, W and Cao, M and Massart, S and Wang, X}, title = {Two novel totiviruses in the white-backed planthopper, Sogatella furcifera.}, journal = {The Journal of general virology}, volume = {99}, number = {5}, pages = {710-716}, doi = {10.1099/jgv.0.001052}, pmid = {29580322}, issn = {1465-2099}, mesh = {Animals ; Genome, Viral ; Hemiptera/*virology ; Hemolymph/virology ; High-Throughput Nucleotide Sequencing ; Insect Viruses/*classification/genetics/isolation & purification ; Phylogeny ; Symbiosis ; Totivirus/*classification/genetics/isolation & purification ; Virus Diseases/transmission ; }, abstract = {There is little information about commensal viruses in the white-backed planthopper, Sogatella furcifera, although it is an important agricultural insect. Here, two novel double-stranded RNA viruses related to the viruses in the family Totiviridae were identified using next-generation sequencing and tentatively named Sogatella furcifera totivirus 1 and 2 (SfTV1 and SfTV2). Their complete genomes consist of 6310 and 6303 nt, respectively, showing typical genomic features with viruses in the family Totiviridae. Identity, phylogenetic and conserved sequence analyses showed that SfTV1, SfTV2 and three other insect viruses may form a proposed novel genus of the family Totiviridae. Vertical transmission of the two viruses was highly efficient, and they were detected in all insect tissues and developmental stages, with the highest titres in the adult and in the haemolymph and reproductive organs. To our knowledge, this is the first report of viruses in the family Totiviridae found in a hemipteran insect.}, } @article {pmid30913327, year = {2019}, author = {Fan, J and Qin, H and Zhang, Y and Jiang, S}, title = {Degradation of 4-chlorophenol by BM Fe/Cu-O2 system: The symbiosis of ·O2- and ·OH radicals.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {}, number = {}, pages = {}, doi = {10.1002/wer.1107}, pmid = {30913327}, issn = {1061-4303}, abstract = {In this study, Fe/Cu bimetal composite was prepared by high energy ball milling (BM) method for the removal of refractory organics. The BM Fe/Cu bimetal was characterized by SEM-EDS, XRD, and XPS. Evenly distributed Fe and Cu was observed in the EDS-mapping. In contrasting experiments, the removal rate of 4-chlorophenol (4-CP) by BM Fe/Cu materials was about 10-fold faster than that by chemical substitution deposition (CSD) Fe/Cu material. Complete 4-CP removal and 66.7% of total organic carbon (TOC) mineralization in the BM Fe/Cu-O2 system were achieved. Dissolved oxygen plays a crucial role for 4-CP degradation through the in situ generation of reactive oxygen species (ROSs) like H2 O2 , ·OH and ·O2- via oxygen activation reactions. The predominant reactive radicals were identified to be ·O2- and ·OH through ESR technique and inhibition experiments. The coexistence of oxidation and reduction of 4-CP in the BM Fe/Cu-O2 system was proposed. This article is protected by copyright. All rights reserved.}, } @article {pmid30912397, year = {2019}, author = {Chen, BD and Yu, M and Hao, ZP and Xie, W and Zhang, X}, title = {Research progress in arbuscular mycorrhizal technology.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {3}, pages = {1035-1046}, doi = {10.13287/j.1001-9332.201903.037}, pmid = {30912397}, issn = {1001-9332}, abstract = {Arbuscular mycorrhizal (AM) symbiosis facilitates plant mineral nutrient acquisition and plays key roles in plant adaptation to environmental stresses. The application of AM fungi is a component of sustainable agriculture and ecological restoration. We introduced the current status of AM fungi collections, production of commercial inocula and AM fungi related patents, summarized the research advances in inoculum production, inoculation techniques, and factors influencing the success of inoculation practice in the field, based on case studies of mycorrhizal technology in agriculture, horticulture, and ecological restoration. Finally, we proposed some basic scientific questions and technical bottleneck that deserve futher studies, to promote the development and application of mycorrhizal technologies.}, } @article {pmid30911691, year = {2019}, author = {Agarkar, AA and Agrawal, H}, title = {LRSPPP: lightweight R-LWE-based secure and privacy-preserving scheme for prosumer side network in smart grid.}, journal = {Heliyon}, volume = {5}, number = {3}, pages = {e01321}, doi = {10.1016/j.heliyon.2019.e01321}, pmid = {30911691}, issn = {2405-8440}, abstract = {In recent years, researchers have made tremendous progress to address an important question of how to provide security and privacy in Internet of Things systems. Privacy protection refers to safeguarding leakage of private information of the customers. In the context of Smart Grid, majority of the studies are based on addressing consumer side privacy. A recent research work has revealed that consumer side network has evolved into prosumer side network. Prosumer refers to consumer and producer, which means a dual role of a customer in the smart grid network. In this paper, we attempt to address the security and privacy issues at the prosumer side of smart grid network. Our work is different from the previous works in two ways. The paper proposes a lightweight encryption based privacy preservation scheme; Lightweight R-LWE-based Secure and Privacy-Preserving Scheme for Prosumer side network (LRSPPP). In LRSPPP, a new messaging scheme is defined which effectively minimizes the number of messages thus making it lightweight. Furthermore, the proposed privacy preservation scheme is using Learning With Errors over Rings (R-LWE) lattice cryptography. There is no previous evidence of use of R-LWE based encryption for prosumer's privacy protection in smart grid. The security and performance analysis shows that the LRSPPP is superior compared to three other existing schemes.}, } @article {pmid30911658, year = {2018}, author = {Oliver Goetze, T and Al-Batran, SE and Pabst, U and Reymond, M and Tempfer, C and Bechstein, WO and Bankstahl, U and Gockel, I and Königsrainer, A and Kraus, T and Mönig, SP and Rau, B and Schwarzbach, M and Piso, P}, title = {Pressurized intraperitoneal aerosol chemotherapy (PIPAC) in combination with standard of care chemotherapy in primarily untreated chemo naïve upper gi-adenocarcinomas with peritoneal seeding - a phase II/III trial of the AIO/CAOGI/ACO.}, journal = {Pleura and peritoneum}, volume = {3}, number = {2}, pages = {20180113}, doi = {10.1515/pp-2018-0113}, pmid = {30911658}, issn = {2364-768X}, abstract = {Background: Peritoneal metastasis is a common and dismal evolution of several gastrointestinal (GI) tumors, including gastric, colorectal, hepatobiliary, pancreatic, and other cancers. The therapy of peritoneal metastasis is largely palliative; with the aim of prolonging life and preserving its quality. In the meantime, a significant pharmacological advantage of intraperitoneal chemotherapy was documented in the preclinical model, and numerous clinical studies have delivered promising clinical results.

Methods: This is a prospective, open, randomized multicenter phase III clinical study with two arms that aims to evaluate the effects of pressurized intraperitoneal aerosol chemotherapy (PIPAC) combined with systemic chemotherapy vs. intravenous systemic chemotherapy alone on patients with metastatic upper GI tumors with a peritoneal seeding. Upper GI-adenocarcinomas originated from biliary tract, pancreas and stomach, or esophago- gastric junction are eligible. Patients in the study are treated with standard of care systemic palliative chemotherapy (mFOLFOX6) vs. PIPAC with intravenous (i.v.) chemotherapy (mFOLFOX6). Patients in first line with first diagnosed peritoneal seeding are eligible. Primary outcome is progression free survival (PFS).

Conclusions: PIPAC-procedure is explicit a palliative method but it delivers cytotoxic therapy like in hyperthermic intraperitoneal chemotherapy (HIPEC)-procedure directly to the tumor in a minimally invasive technique, without the need for consideration of the peritoneal-plasma barrier. The technique of PIPAC is minimally invasive and very gentle and the complete procedure takes only round about 45 min and, therefore, optimal in a clearly palliative situation where cure is not the goal. It is also ideal for using this approach in a first line situation, where deepest response should be achieved. The symbiosis of systemic therapy and potentially effective surgery has to be well-planned without deterioration of the patient due to aggressive way of surgery like in cytoreductive surgery (CRS)+HIPEC.

Trial registration: EudraCT: 2018-001035-40.}, } @article {pmid30910773, year = {2019}, author = {Chiu, CH and Paszkowski, U}, title = {Mechanisms and Impact of Symbiotic Phosphate Acquisition.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/cshperspect.a034603}, pmid = {30910773}, issn = {1943-0264}, abstract = {Phosphorous is important for life but often limiting for plants. The symbiotic pathway of phosphate uptake via arbuscular mycorrhizal fungi (AMF) is evolutionarily ancient and today occurs in natural and agricultural ecosystems alike. Plants capable of this symbiosis can obtain up to all of the phosphate from symbiotic fungi, and this offers potential means to develop crops less dependent on unsustainable P fertilizers. Here, we review the mechanisms and insights gleaned from the fine-tuned signal exchanges that orchestrate the intimate mutualistic symbiosis between plants and AMF. As the currency of trade, nutrients have signaling functions beyond being the nutritional goal of mutualism. We propose that such signaling roles and metabolic reprogramming may represent commitments for a mutualistic symbiosis that act across the stages of symbiosis development.}, } @article {pmid30658297, year = {2019}, author = {Company, R and Antúnez, O and Cosson, RP and Serafim, A and Shillito, B and Cajaraville, M and Bebianno, MJ and Torreblanca, A}, title = {Protein expression profiles in Bathymodiolus azoricus exposed to cadmium.}, journal = {Ecotoxicology and environmental safety}, volume = {171}, number = {}, pages = {621-630}, doi = {10.1016/j.ecoenv.2019.01.031}, pmid = {30658297}, issn = {1090-2414}, mesh = {Animals ; Bacteria/drug effects/metabolism ; Cadmium/*toxicity ; Electrophoresis, Gel, Two-Dimensional ; Gene Expression Regulation ; Gills/drug effects/metabolism/microbiology ; Hydrothermal Vents ; Mytilidae/*drug effects/metabolism/microbiology ; Oxidative Stress/drug effects ; *Proteome/metabolism ; Symbiosis ; }, abstract = {Proteomic changes in the "gill-bacteria complex" of the hydrothermal vent mussel B. azoricus exposed to cadmium in pressurized chambers ((Incubateurs Pressurises pour l'Observation en Culture d'Animaux Marins Profonds - IPOCAMP) were analyzed and compared with the non-exposed control group. 2-D Fluorescence Difference Gel Electrophoresis (2D-DIGE) showed that less than 1.5% of the proteome of mussels and symbiotic bacteria were affected by a short-term (24 h) Cd exposure. Twelve proteins of the more abundant differentially expressed proteins of which six were up-regulated and six were down-regulated were excised, digested and identified by mass spectrometry. The identified proteins included structural proteins (actin/actin like proteins), metabolic proteins (calreticulin/calnexin, peptidyl-prolyl cis-trans isomerase, aminotransferase class-III, electron transfer flavoprotein, proteasome, alpha-subunit and carbonic anhydrase) and stress response proteins (chaperone protein htpG, selenium-binding protein and glutathione transferases). All differently expressed proteins are tightly connected to Cd exposure and are affected by oxidative stress. It was also demonstrated that B. azoricus was well adapted to Cd contamination therefore B. azoricus from hydrothermal vent areas may be considered a good bioindicator.}, } @article {pmid30443676, year = {2019}, author = {Hettiarachchige, IK and Elkins, AC and Reddy, P and Mann, RC and Guthridge, KM and Sawbridge, TI and Forster, JW and Spangenberg, GC}, title = {Genetic modification of asexual Epichloë endophytes with the perA gene for peramine biosynthesis.}, journal = {Molecular genetics and genomics : MGG}, volume = {294}, number = {2}, pages = {315-328}, doi = {10.1007/s00438-018-1510-x}, pmid = {30443676}, issn = {1617-4623}, mesh = {Alkaloids/genetics ; Animals ; Disease Resistance/genetics ; Endophytes/*genetics ; Epichloe/*genetics/growth & development ; Gene Editing ; Heterocyclic Compounds, 2-Ring/*metabolism ; Pest Control, Biological ; Phylogeny ; Plant Diseases/genetics/microbiology ; Poaceae/*genetics/microbiology ; Polyamines/*metabolism ; Reproduction, Asexual/genetics ; Symbiosis/genetics ; Weevils/genetics/pathogenicity ; }, abstract = {Development of grass-endophyte associations with minimal or no detrimental effects in combination with beneficial characteristics is important for pastoral agriculture. The feasibility of enhancing production of an endophyte-derived beneficial alkaloid through introduction of an additional gene copy was assessed in a proof-of-concept study. Sexual and asexual Epichloë species that form symbiotic associations with cool-season grasses of the Poaceae sub-family Pooideae produce bioactive alkaloids that confer resistance to herbivory by a number of organisms. Of these, peramine is thought to be crucial for protection of perennial ryegrass (Lolium perenne L.) from the Argentinian stem weevil, an economically important exotic pest in New Zealand, contributing significantly to pasture persistence. A single gene (perA) has been identified as solely responsible for peramine biosynthesis and is distributed widely across Epichloë taxa. In the present study, a functional copy of the perA gene was introduced into three recipient endophyte genomes by Agrobacterium tumefaciens-mediated transformation. The target strains included some that do not produce peramine, and others containing different perA gene copies. Mitotically stable transformants generated from all three endophyte strains were able to produce peramine in culture and in planta at variable levels. In summary, this study provides an insight into the potential for artificial combinations of alkaloid biosynthesis in a single endophyte strain through transgenesis, as well as the possibility of using novel genome editing techniques to edit the perA gene of non-peramine producing strains.}, } @article {pmid30905896, year = {2019}, author = {Uchi, N and Fukudome, M and Nozaki, N and Suzuki, M and Osuki, KI and Shigenobu, S and Uchiumi, T}, title = {Antimicrobial Activities of Cysteine-rich Peptides Specific to Bacteriocytes of the Pea Aphid Acyrthosiphon pisum.}, journal = {Microbes and environments}, volume = {}, number = {}, pages = {}, doi = {10.1264/jsme2.ME18148}, pmid = {30905896}, issn = {1347-4405}, abstract = {Aphids have a mutualistic relationship with the bacterial endosymbiont Buchnera aphidicola. We previously reported seven cysteine-rich peptides in the pea aphid Acyrthosiphon pisum and named them Bacteriocyte-specific Cysteine-Rich (BCR) peptides; these peptides are exclusively expressed in bacteriocytes, special aphid cells that harbor symbionts. Similar symbiotic organ-specific cysteine-rich peptides identified in the root nodules of leguminous plants are named Nodule-specific Cysteine-Rich (NCR) peptides. NCR peptides target rhizobia in the nodules and are essential for symbiotic nitrogen fixation. A BacA (membrane protein) mutant of Sinorhizobium is sensitive to NCR peptides and is unable to establish symbiosis. Based on the structural and expressional similarities between BCR peptides and NCR peptides, we hypothesized that aphid BCR peptides exhibit antimicrobial activity, similar to some NCR peptides. We herein synthesized BCR peptides and investigated their antimicrobial activities and effects on the bacterial membrane of Escherichia coli. The peptides BCR1, BCR3, BCR5, and BCR8 exhibited antimicrobial activities with increased membrane permeability. An sbmA mutant of E. coli, a homolog of bacA of S. meliloti, was more sensitive to BCR peptides than the wild type. Our results suggest that BCR peptides have properties that may be required to control the endosymbiont, similar to NCR peptides in legumes.}, } @article {pmid30905198, year = {2019}, author = {Bartolomaeus, H and Markó, L and Wilck, N and Luft, FC and Forslund, SK and Muller, DN}, title = {Precarious Symbiosis Between Host and Microbiome in Cardiovascular Health.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {}, number = {}, pages = {HYPERTENSIONAHA11911786}, doi = {10.1161/HYPERTENSIONAHA.119.11786}, pmid = {30905198}, issn = {1524-4563}, } @article {pmid30903405, year = {2019}, author = {Kord, H and Fakheri, B and Ghabooli, M and Solouki, M and Emamjomeh, A and Khatabi, B and Sepehri, M and Salekdeh, GH and Ghaffari, MR}, title = {Salinity-associated microRNAs and their potential roles in mediating salt tolerance in rice colonized by the endophytic root fungus Piriformospora indica.}, journal = {Functional & integrative genomics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10142-019-00671-6}, pmid = {30903405}, issn = {1438-7948}, support = {-//Agricultural Biotechnology Research Institute of Iran/ ; }, abstract = {Piriformospora indica (P. indica), an endophytic root fungus, supports the growth and enhanced tolerance of plants to biotic and abiotic stresses. Several recent studies showed the significant role of small RNA (sRNA) molecules including microRNAs (miRNAs) in plant adaption to environmental stress, but little is known concerning the symbiosis-mediated salt stress tolerance regulated at miRNAs level. The overarching goal of this research is to elucidate the impact of miRNAs in regulating the P. indica-mediated salt tolerance in rice. Applying sRNA-seq analysis led to identify a set of 547 differentially abundant miRNAs in response to P. indica inoculation and salt stress. These included 206 rice-specific and 341 previously known miRNAs from other plant species. In silico analysis of miRNAs predictions of the differentially abundant miRNAs led to identifying of 193 putatively target genes, most of which were encoded either genes or transcription factors involved in nutrient uptake, sodium ion transporters, growth regulators, and auxin- responsive proteins. The rice-specific miRNAs targeted the transcription factors involved in the import of potassium ions into the root cells, the export of sodium ions, and plant growth and development. Interestingly, P. indica affected the differential abundance of miRNAs regulated genes and transcription factors linked to salt stress tolerance. Our data helps to understand the molecular basis of salt stress tolerance mediated by symbionts in plant and the potential impact of miRNAs for genetic improvement of rice varieties for tolerance to salt stress.}, } @article {pmid30544819, year = {2018}, author = {Strodtman, KN and Frank, S and Stevenson, S and Thelen, JJ and Emerich, DW}, title = {Proteomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123947}, pmid = {30544819}, issn = {1422-0067}, support = {2004-35604-14708//United States Department of Agriculure Cooperative State Research Education and Extension Service National Research Initiative/ ; 2004-35604-14708//United States Department of Agriculture Cooperative State Research Education and Extension Service National Research Initiative/ ; }, mesh = {Bacterial Proteins/metabolism ; Bacteroides/enzymology/isolation & purification/*metabolism ; Bradyrhizobium/*metabolism ; Hydroxybutyrates/metabolism ; Leghemoglobin/metabolism ; Periplasm/metabolism ; Polyesters/metabolism ; Proteomics/*methods ; Root Nodules, Plant/*microbiology ; Soybeans/*growth & development/*microbiology ; *Symbiosis ; }, abstract = {The form and physiology of Bradyrhizobium diazoefficiens after the decline of symbiotic nitrogen fixation has been characterized. Proteomic analyses showed that post-symbiotic B. diazoefficiens underwent metabolic remodeling as well-defined groups of proteins declined, increased or remained unchanged from 56 to 119 days after planting, suggesting a transition to a hemibiotrophic-like lifestyle. Enzymatic analysis showed distinct patterns in both the cytoplasm and the periplasm. Similar to the bacteroid, the post-symbiotic bacteria rely on a non-citric acid cycle supply of succinate and, although viable, they did not demonstrate the ability to grow within the senescent nodule.}, } @article {pmid30007415, year = {2018}, author = {Martin, WF and Allen, JF}, title = {An Algal Greening of Land.}, journal = {Cell}, volume = {174}, number = {2}, pages = {256-258}, doi = {10.1016/j.cell.2018.06.034}, pmid = {30007415}, issn = {1097-4172}, mesh = {Biological Evolution ; Chara/*genetics ; Eukaryota/*genetics ; Plants/genetics ; Symbiosis/genetics ; }, abstract = {Photosynthetic eukaryotes arose ∼1.5 billion years ago by endosymbiosis with a cyanobacterium. Algae then evolved for a billion years before one lineage finally colonized land. Why the wait? The Chara braunii genome details a decisive step linking plant origins with Earth's history.}, } @article {pmid30900053, year = {2019}, author = {Ricks, KD and Koide, RT}, title = {Biotic filtering of endophytic fungal communities in Bromus tectorum.}, journal = {Oecologia}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00442-019-04388-y}, pmid = {30900053}, issn = {1432-1939}, support = {2011-67009-20072//National Institute of Food and Agriculture/ ; }, abstract = {The assembly of horizontally transmitted endophytic fungi within plant tissues may be affected by "biotic filtering". In other words, only particular endophytic fungal taxa from the available inoculum pool may be able to colonize a given plant species. We tested that hypothesis in Bromus tectorum, an important invasive species in the arid, western United States. We collected seed from Bromus tectorum and sources of inoculum for endophytic fungi including soil and various kinds of plant litter at a field site in central Utah. We characterized, using Illumina sequencing, the endophytic fungal communities in the various inoculum sources, inoculated Bromus tectorum seedlings under gnotobiotic conditions with the various sources, and then characterized the communities of endophytic fungi that assembled in their roots and leaves. Different inoculum sources containing significantly different endophytic fungal communities produced complex communities of endophytic fungi in leaves and roots of Bromus tectorum. In leaves, the communities assembling from the various inoculum sources were not significantly different from each other and, in roots, they were only slightly different from each other, mainly due to variation in a single fungal OTU, Coprinopsis brunneofibrillosa. Consequently, there was significantly more variation in the structure of the communities of endophytic fungi among the inoculum sources than in the resultant endophytic fungal communities in the leaves and roots of Bromus tectorum. These results are consistent with biotic filtering playing a significant role in endophytic fungal community assembly.}, } @article {pmid30898860, year = {2019}, author = {Zhang, D and Frenette, PS}, title = {Crosstalk between neutrophils and the microbiota.}, journal = {Blood}, volume = {}, number = {}, pages = {}, doi = {10.1182/blood-2018-11-844555}, pmid = {30898860}, issn = {1528-0020}, abstract = {TThe microbiota has emerged as an important regulator of the host immunity by the induction, functional modulation or suppression of local and systemic immune responses. In return, the host immune system restricts translocation and fine-tunes the composition and distribution of the microbiota to maintain a beneficial symbiosis. This paradigm applies to neutrophils, a critical component of the innate immunity, allowing their production and function to be influenced by microbial components and metabolites derived from the microbiota, and engaging them in the process of microbiota containment and regulation. The crosstalk between neutrophils and the microbiota adjusts the magnitude of neutrophil-mediated inflammation upon challenge while preventing neutrophil responses against commensals under steady state. Here, we review the major molecular and cellular mediators of the interactions between neutrophils and the microbiota, and discuss their interplay and contribution in chronic inflammatory diseases and cancer.}, } @article {pmid30626679, year = {2019}, author = {Dunigan, DD and Al-Sammak, M and Al-Ameeli, Z and Agarkova, IV and DeLong, JP and Van Etten, JL}, title = {Chloroviruses Lure Hosts through Long-Distance Chemical Signaling.}, journal = {Journal of virology}, volume = {93}, number = {7}, pages = {}, doi = {10.1128/JVI.01688-18}, pmid = {30626679}, issn = {1098-5514}, abstract = {Chloroviruses exist in aquatic systems around the planet and they infect certain eukaryotic green algae that are mutualistic endosymbionts in a variety of protists and metazoans. Natural chlorovirus populations are seasonally dynamic, but the precise temporal changes in these populations and the mechanisms that underlie them have heretofore been unclear. We recently reported the novel concept that predator/prey-mediated virus activation regulates chlorovirus population dynamics, and in the current study, we demonstrate virus-packaged chemotactic modulation of prey behavior.IMPORTANCE Viruses have not previously been reported to act as chemotactic/chemoattractive agents. Rather, viruses as extracellular entities are generally viewed as non-metabolically active spore-like agents that await further infection events upon collision with appropriate host cells. That a virus might actively contribute to its fate via chemotaxis and change the behavior of an organism independent of infection is unprecedented.}, } @article {pmid30261347, year = {2019}, author = {Nalini, S and Inbakandan, D and Venkatnarayanan, S and Mohammed Riyaz, SU and Dheenan, PS and Vinithkumar, NV and Sriyutha Murthy, P and Parthasarathi, R and Kirubagaran, R}, title = {PYRROLO isolated from marine sponge associated bacterium Halobacillus kuroshimensis SNSAB01 - Antifouling study based on molecular docking, diatom adhesion and mussel byssal thread inhibition.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {173}, number = {}, pages = {9-17}, doi = {10.1016/j.colsurfb.2018.09.044}, pmid = {30261347}, issn = {1873-4367}, mesh = {Acetylglucosamine/analogs & derivatives/metabolism ; Animals ; Anti-Infective Agents/chemistry/isolation & purification/*pharmacology ; Binding Sites ; Bivalvia/*drug effects/growth & development ; Complex Mixtures/chemistry ; Diatoms/*drug effects/growth & development ; Extracellular Matrix/chemistry ; Halobacillus/*chemistry/classification ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Phylogeny ; Porifera/microbiology ; Pyrazines/chemistry/isolation & purification/*pharmacology ; Pyrroles/chemistry/isolation & purification/*pharmacology ; Symbiosis/physiology ; }, abstract = {In the present study, an attempt has been made to explore the antifouling potential of bioactive compound isolated from sponge associated bacterium Halobacillus kuroshimensis SNSAB01. The crude extract of SNSAB01 strongly inhibited the growth of fouling bacterial strains with least minimal inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The bioactive compound was characterized through FT-IR, HPLC, GCMS and NMR predicted as 'pyrrolo". From the mass spectral library, structure was elucidated as pyrrolo [1, 2-a] pyrazine-1, 4-dione, hexahydro. The in silico studies provided encouraging docking scores with two interactions by GLN 200 and GLU 304. The extract inhibited 89% diatom adhesion at 350 μg/ml concentration against Amphora sp. An EC50 value of 150 μg/ml for 50% inhibition of byssal thread of Perna viridis and LC50 was found to be 500 μg/ml. The LC50/EC50 ratio of 3.0 indicated nontoxic to nature. The result suggested that pyrrolo[1,2-a]pyrazine-1,4-dione can be used for antifouling coating.}, } @article {pmid29664560, year = {2018}, author = {McCormick, S}, title = {An arbuscular mycorrhizal fungus adjusts its secretome depending on developmental stage and host plant.}, journal = {The Plant journal : for cell and molecular biology}, volume = {94}, number = {3}, pages = {409-410}, doi = {10.1111/tpj.13917}, pmid = {29664560}, issn = {1365-313X}, mesh = {*Glomeromycota ; *Mycorrhizae ; Plants ; Symbiosis ; }, } @article {pmid30895295, year = {2019}, author = {Jonnalagadda, M and Ashhad Faizan, M and Ozarkar, S and Ashma, R and Kulkarni, S and Norton, HL and Parra, E}, title = {A genome-wide association study of skin and iris pigmentation among individuals of South Asian ancestry.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz057}, pmid = {30895295}, issn = {1759-6653}, abstract = {South Asia has a complex history of migrations, and is characterized by substantial pigmentary and genetic diversity. For this reason, it is an ideal region to study the genetic architecture of normal pigmentation variation. Here, we present a meta-analysis of two GWAS of skin pigmentation using skin reflectance (M-index) as a quantitative phenotype. The meta-analysis includes a sample of individuals of South Asian descent living in Canada (N = 348), and a sample of individuals from two caste and four tribal groups from West Maharashtra, India (N = 480). We also present the first GWAS of iris color in South Asian populations. This GWAS was based on quantitative measures of iris color obtained from high resolution iris pictures. We identified genome-wide significant associations of variants within the well-known gene SLC24A5, including the non-synonymous rs1426654 polymorphism, with both skin pigmentation and iris color, highlighting the pleiotropic effects of this gene on pigmentation. Variants in the HERC2 gene (e.g. rs12913832) were also associated with iris color and iris heterochromia. Our study emphasizes the usefulness of quantitative methods to study iris color variation. We also identified novel genome-wide significant associations with skin pigmentation and iris color, but we could not replicate these associations due to the lack of independent samples. It will be critical to expand the number of studies in South Asian populations in order to better understand the genetic variation driving the diversity of skin pigmentation and iris color observed in this region.}, } @article {pmid30894837, year = {2019}, author = {Tolley, SJA and Nonacs, P and Sapountzis, P}, title = {Wolbachia Horizontal Transmission Events in Ants: What Do We Know and What Can We Learn?.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {296}, doi = {10.3389/fmicb.2019.00296}, pmid = {30894837}, issn = {1664-302X}, abstract = {While strict vertical transmission insures the durability of intracellular symbioses, phylogenetic incongruences between hosts and endosymbionts suggest horizontal transmission must also occur. These horizontal acquisitions can have important implications for the biology of the host. Wolbachia is one of the most ecologically successful prokaryotes in arthropods, infecting an estimated 50-70% of all insect species. Much of this success is likely due to the fact that, in arthropods, Wolbachia is notorious for manipulating host reproduction to favor transmission through the female germline. However, its natural potential for horizontal transmission remains poorly understood. Here we evaluate the fundamental prerequisites for successful horizontal transfer, including necessary environmental conditions, genetic potential of bacterial strains, and means of mediating transfers. Furthermore, we revisit the relatedness of Wolbachia strains infecting the Panamanian leaf-cutting ant, Acromyrmex echinatior, and its inquiline social parasite, Acromyrmex insinuator, and compare our results to a study published more than 15 years ago by Van Borm et al. (2003). The results of this pilot study prompt us to reevaluate previous notions that obligate social parasitism reliably facilitates horizontal transfer and suggest that not all Wolbachia strains associated with ants have the same genetic potential for horizontal transmission.}, } @article {pmid30629162, year = {2019}, author = {Ševcíková, T and Yurchenko, T and Fawley, KP and Amaral, R and Strnad, H and Santos, LMA and Fawley, MW and Eliáš, M}, title = {Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts.}, journal = {Genome biology and evolution}, volume = {11}, number = {2}, pages = {362-379}, doi = {10.1093/gbe/evz004}, pmid = {30629162}, issn = {1759-6653}, support = {P20 GM103429/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Biological Evolution ; *Genome, Plastid ; *Operon ; Rickettsiaceae/*genetics ; Stramenopiles/*genetics/microbiology ; Symbiosis ; }, abstract = {Eustigmatophytes, a class of stramenopile algae (ochrophytes), include not only the extensively studied biotechnologically important genus Nannochloropsis but also a rapidly expanding diversity of lineages with much less well characterized biology. Recent discoveries have led to exciting additions to our knowledge about eustigmatophytes. Some proved to harbor bacterial endosymbionts representing a novel genus, Candidatus Phycorickettsia, and an operon of unclear function (ebo) obtained by horizontal gene transfer from the endosymbiont lineage was found in the plastid genomes of still other eustigmatophytes. To shed more light on the latter event, as well as to generally improve our understanding of the eustigmatophyte evolutionary history, we sequenced plastid genomes of seven phylogenetically diverse representatives (including new isolates representing undescribed taxa). A phylogenomic analysis of plastid genome-encoded proteins resolved the phylogenetic relationships among the main eustigmatophyte lineages and provided a framework for the interpretation of plastid gene gains and losses in the group. The ebo operon gain was inferred to have probably occurred within the order Eustigmatales, after the divergence of the two basalmost lineages (a newly discovered hitherto undescribed strain and the Pseudellipsoidion group). When looking for nuclear genes potentially compensating for plastid gene losses, we noticed a gene for a plastid-targeted acyl carrier protein that was apparently acquired by horizontal gene transfer from Phycorickettsia. The presence of this gene in all eustigmatophytes studied, including representatives of both principal clades (Eustigmatales and Goniochloridales), is a genetic footprint indicating that the eustigmatophyte-Phycorickettsia partnership started no later than in the last eustigmatophyte common ancestor.}, } @article {pmid30561673, year = {2019}, author = {Amos, BA and Hayes, RA and Leemon, DM and Furlong, MJ}, title = {Small Hive Beetle (Coleoptera: Nitidulidae) and the Yeast, Kodamaea ohmeri: A Facultative Relationship Under Laboratory Conditions.}, journal = {Journal of economic entomology}, volume = {112}, number = {2}, pages = {515-524}, doi = {10.1093/jee/toy378}, pmid = {30561673}, issn = {1938-291X}, abstract = {The small hive beetle, Aethina tumida Murray, is a pest of honeybees, Apis mellifera L. (Hymenoptera: Apidae). We investigated the significance of its association with the yeast, Kodamaea ohmeri (Etchells & Bell) (Ascomycota: Saccharomycotina), in laboratory experiments. The mean (± SEM) viability of A. tumida eggs was 84 (± 3)%; the viability was not affected if eggs were separated from clutches or if mucilage containing K. ohmeri was removed from the egg surface. Life tables of conventional (= K. ohmeri contaminated) A. tumida and K. ohmeri-free A. tumida revealed no differences in stage-specific mortality between the treatments; in both cases, the highest mortality occurred in the first larval instar. There was no significant difference in the initial egg production of conventionally reared and K. ohmeri-free A. tumida under laboratory conditions. The volatile profiles of pollen dough (Bee Build) fed on by conventional and K. ohmeri-free A. tumida larvae were qualitatively and quantitatively different; the volatiles produced by pollen dough fed on by conventional A. tumida were more attractive to adult beetles. There was a clear difference between growth of K. ohmeri on pollen dough substrate in the presence and absence of A. tumida. Results suggest that this association is facultative for A. tumida under laboratory conditions but has benefit for the yeast associate, K. ohmeri. A clearer understanding of the nature of this fungus-insect association is essential for the development of management strategies for this pest, especially in the development of fermentate-based attractants in trapping systems.}, } @article {pmid30497380, year = {2018}, author = {Zamora-Lagos, MA and Eckstein, S and Langer, A and Gazanis, A and Pfeiffer, F and Habermann, B and Heermann, R}, title = {Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {854}, pmid = {30497380}, issn = {1471-2164}, support = {HE5247/5-2//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Biofilms/drug effects ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/drug effects/*genetics ; *Genome, Bacterial ; *Genomics ; Hemolysis/drug effects ; Mutation/genetics ; Open Reading Frames/genetics ; Phenotype ; Photorhabdus/drug effects/*genetics/growth & development/isolation & purification ; Prophages/physiology ; Rifampin/*pharmacology ; Sequence Analysis, DNA ; Symbiosis/drug effects/genetics ; }, abstract = {BACKGROUND: Photorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strain P. luminescens subsp. laumondii TT01, which was originally isolated in Trinidad and Tobago, has been described earlier. Subsequently, a rifampicin resistant P. luminescens strain has been generated with superior possibilities for experimental characterization. This strain, which is widely used in research, was described as a spontaneous rifampicin resistant mutant of TT01 and is known as TT01-RifR.

RESULTS: Unexpectedly, upon phenotypic comparison between the rifampicin resistant strain and its presumed parent TT01, major differences were found with respect to bioluminescence, pigmentation, biofilm formation, haemolysis as well as growth. Therefore, we renamed the strain TT01-RifR to DJC. To unravel the genomic basis of the observed differences, we generated a complete genome sequence for strain DJC using the PacBio long read technology. As strain DJC was supposed to be a spontaneous mutant, only few sequence differences were expected. In order to distinguish these from potential sequencing errors in the published TT01 genome, we re-sequenced a derivative of strain TT01 in parallel, also using the PacBio technology. The two TT01 genomes differed at only 30 positions. In contrast, the genome of strain DJC varied extensively from TT01, showing 13,000 point mutations, 330 frameshifts, and 220 strain-specific regions with a total length of more than 300 kb in each of the compared genomes.

CONCLUSIONS: According to the major phenotypic and genotypic differences, the rifampicin resistant P. luminescens strain, now named strain DJC, has to be considered as an independent isolate rather than a derivative of strain TT01. Strains TT01 and DJC both belong to P. luminescens subsp. laumondii.}, } @article {pmid30160099, year = {2018}, author = {Dose, B and Niehs, SP and Scherlach, K and Flórez, LV and Kaltenpoth, M and Hertweck, C}, title = {Unexpected Bacterial Origin of the Antibiotic Icosalide: Two-Tailed Depsipeptide Assembly in Multifarious Burkholderia Symbionts.}, journal = {ACS chemical biology}, volume = {13}, number = {9}, pages = {2414-2420}, doi = {10.1021/acschembio.8b00600}, pmid = {30160099}, issn = {1554-8937}, mesh = {Animals ; Anti-Bacterial Agents/*metabolism ; Burkholderia/enzymology/genetics/*physiology ; Coleoptera/*microbiology ; Genes, Bacterial ; Peptide Synthases/genetics/metabolism ; Peptides, Cyclic/genetics/*metabolism ; *Symbiosis ; }, abstract = {Icosalide is an unusual two-tailed lipocyclopeptide antibiotic that was originally isolated from a fungal culture. Yet, its biosynthesis and ecological function have remained enigmatic. By genome mining and metabolic profiling of a bacterial endosymbiont (Burkholderia gladioli) of the pest beetle Lagria villosa, we unveiled a bacterial origin of icosalide. Functional analysis of the biosynthetic gene locus revealed an unprecedented nonribosomal peptide synthetase (NRPS) that incorporates two β-hydroxy acids by means of two starter condensation domains in different modules. This unusual assembly line, which may inspire new synthetic biology approaches, is widespread among many symbiotic Burkholderia species from diverse habitats. Biological assays showed that icosalide is active against entomopathogenic bacteria, thus adding to the chemical armory protecting beetle offspring. By creating a null mutant, we found that icosalide is a swarming inhibitor, which may play a role in symbiotic interactions and bears the potential for therapeutic applications.}, } @article {pmid30009332, year = {2019}, author = {Bag, S and Ghosh, TS and Banerjee, S and Mehta, O and Verma, J and Dayal, M and Desigamani, A and Kumar, P and Saha, B and Kedia, S and Ahuja, V and Ramamurthy, T and Das, B}, title = {Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {546-557}, doi = {10.1007/s00248-018-1228-7}, pmid = {30009332}, issn = {1432-184X}, support = {BT/MB/THSTI/HMC-SFC/2011//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/isolation & purification ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Genotype ; Humans ; Interspersed Repetitive Sequences/genetics ; Metagenome/genetics ; Microbial Sensitivity Tests ; *Phenotype ; *Symbiosis ; Transformation, Genetic/genetics ; Vibrio cholerae/genetics ; Whole Genome Sequencing ; }, abstract = {Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.}, } @article {pmid30003276, year = {2019}, author = {Miranda, V and Rothen, C and Yela, N and Aranda-Rickert, A and Barros, J and Calcagno, J and Fracchia, S}, title = {Subterranean Desert Rodents (Genus Ctenomys) Create Soil Patches Enriched in Root Endophytic Fungal Propagules.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {451-459}, doi = {10.1007/s00248-018-1227-8}, pmid = {30003276}, issn = {1432-184X}, support = {PICT 0546//Consejo Nacional de Innovación, Ciencia y Tecnología/ ; }, mesh = {Animals ; Argentina ; *Desert Climate ; Ecosystem ; Endophytes/*growth & development ; Environment ; Fungi/*growth & development ; Mycorrhizae/growth & development ; Plant Roots/*microbiology ; Rodentia/*physiology ; Soil/*chemistry ; Soil Microbiology ; Symbiosis ; }, abstract = {Subterranean rodents are considered major soil engineers, as they can locally modify soil properties by their burrowing activities. In this study, the effect of a subterranean rodent of the genus Ctenomys on soil properties and root endophytic fungal propagules in a shrub desert of northwest Argentina was examined. Our main goal was to include among root endophytic fungi not only arbuscular mycorrhiza but also the dark septate endophytes. We compared the abundance of fungal propagules as well as several microbiological and physicochemical parameters between soils from burrows and those from the surrounding landscape. Our results show that food haulage, the deposition of excretions, and soil mixing by rodents' burrowing promote soil patchiness by (1) the enrichment in both types of root endophytic fungal propagules; (2) the increase in organic matter and nutrients; and (3) changes in soil edaphic properties including moisture, field capacity, and texture. These patches may play a critical role as a source of soil heterogeneity in desert ecosystems, where burrows constructed in interpatches of bare soil can act, once abandoned, as "islands of fertility," promoting the establishment of plants in an otherwise hostile environment.}, } @article {pmid30893001, year = {2019}, author = {Jonathan, RL and Hernández-López, A and Estrada-Navarrete, G and Sanchez, F and Díaz-Camino, C}, title = {The non-canonical heat shock protein PvNod22 is essential for infection thread progression during rhizobial endosymbiosis in common bean.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-02-19-0041-R}, pmid = {30893001}, issn = {0894-0282}, abstract = {In the establishment of plant-rhizobial symbiosis, the plant hosts express nodulin proteins during root nodule organogenesis. A limited number of nodulins have been characterized, and these perform essential functions in root nodule development and metabolism. Most nodulins are expressed in the nodule and at lower levels in other plant tissues. Previously, we isolated Nodulin 22 (PvNod22) from a common bean (Phaseolus vulgaris L.) cDNA library derived from Rhizobium-infected roots. PvNod22 is a non-canonical, endoplasmic reticulum (ER)-localized, small heat shock protein (sHsp) that confers protection against oxidative stress when over-expressed in Escherichia coli. Virus-induced gene silencing of PvNod22 resulted in necrotic lesions in the aerial organs of P. vulgaris plants cultivated under optimal conditions, activation of the ER-unfolded protein response (UPR) and, finally, in plant death. Here, we examined the expression of PvNod22 in common bean plants during the establishment of rhizobial endosymbiosis and its relationship with two cellular processes associated with plant immunity, the UPR and autophagy. In the RNA interference lines, numerous infection threads stopped their progression before reaching the cortex cell layer of the root, and nodules contained fewer nitrogen-fixing bacteroids. Collectively, our results suggest that PvNod22 has a non-redundant function during legume-rhizobia symbiosis associated with infection thread elongation likely by sustaining protein homeostasis in the ER.}, } @article {pmid30891218, year = {2019}, author = {Bayliss, SLJ and Scott, ZR and Coffroth, MA and terHorst, CP}, title = {Genetic variation in Breviolum antillogorgium, a coral reef symbiont, in response to temperature and nutrients.}, journal = {Ecology and evolution}, volume = {9}, number = {5}, pages = {2803-2813}, doi = {10.1002/ece3.4959}, pmid = {30891218}, issn = {2045-7758}, abstract = {Symbionts within the family Symbiodiniaceae are important on coral reefs because they provide significant amounts of carbon to many different reef species. The breakdown of this mutualism that occurs as a result of increasingly warmer ocean temperatures is a major threat to coral reef ecosystems globally. Recombination during sexual reproduction and high rates of somatic mutation can lead to increased genetic variation within symbiont species, which may provide the fuel for natural selection and adaptation. However, few studies have asked whether such variation in functional traits exists within these symbionts. We used several genotypes of two closely related species, Breviolum antillogorgium and B. minutum, to examine variation of traits related to symbiosis in response to increases in temperature or nitrogen availability in laboratory cultures. We found significant genetic variation within and among symbiont species in chlorophyll content, photosynthetic efficiency, and growth rate. Two genotypes showed decreases in traits in response to increased temperatures predicted by climate change, but one genotype responded positively. Similarly, some genotypes within a species responded positively to high-nitrogen environments, such as those expected within hosts or eutrophication associated with global change, while other genotypes in the same species responded negatively, suggesting context-dependency in the strength of mutualism. Such variation in traits implies that there is potential for natural selection on symbionts in response to temperature and nutrients, which could confer an adaptive advantage to the holobiont.}, } @article {pmid30825940, year = {2019}, author = {Afzal, I and Shinwari, ZK and Sikandar, S and Shahzad, S}, title = {Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants.}, journal = {Microbiological research}, volume = {221}, number = {}, pages = {36-49}, doi = {10.1016/j.micres.2019.02.001}, pmid = {30825940}, issn = {1618-0623}, mesh = {Bacteria/genetics/growth & development/*metabolism ; Endophytes/genetics/growth & development/*metabolism ; Host Specificity ; Plant Development/*physiology ; Plant Roots/*microbiology ; Plants/*microbiology ; Rhizosphere ; Symbiosis/physiology ; }, abstract = {Endophytic bacteria are the plant beneficial bacteria that thrive inside plants and can improve plant growth under normal and challenging conditions. They can benefit host plants directly by improving plant nutrient uptake and by modulating growth and stress related phytohormones. Indirectly, endophytic bacteria can improve plant health by targeting pests and pathogens with antibiotics, hydrolytic enzymes, nutrient limitation, and by priming plant defenses. To confer these benefits, the bacteria have to colonize the plant endosphere after colonizing the rhizosphere. The colonization is achieved using a battery of traits involving motility, attachment, plant-polymer degradation, and evasion of plant defenses. The diversity of endophytic colonizers depends on several bacteria, plant and environment specific factors. Some endophytic bacteria can have a broad host range and can be used as bioinoculants in developing a safe and sustainable agriculture system. This review elaborates the factors affecting diversity of bacterial endophytes, their host specificity and mechanisms of plant growth promotion. The review also accentuates various methods used to study endophytic communities, wild plants as a source of novel endophytic bacteria, and innovative approaches that may improve plant-endophyte association. Moreover, bacterial genes expressed in planta and challenges to study them are also discussed.}, } @article {pmid30825937, year = {2019}, author = {Muresu, R and Porceddu, A and Sulas, L and Squartini, A}, title = {Nodule-associated microbiome diversity in wild populations of Sulla coronaria reveals clues on the relative importance of culturable rhizobial symbionts and co-infecting endophytes.}, journal = {Microbiological research}, volume = {221}, number = {}, pages = {10-14}, doi = {10.1016/j.micres.2019.01.004}, pmid = {30825937}, issn = {1618-0623}, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Endophytes/classification/genetics/*isolation & purification ; Fabaceae/*microbiology ; Microbiota ; Pantoea/genetics/isolation & purification ; Pseudomonas/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Rhizobium/classification/genetics/*isolation & purification ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The culturable bacteria from root nodules of Sulla coronaria growing in spontaneous conditions in Sardinia were characterized. This plant's peculiarity is to represent a legume still found in both wild and cropped statuses. We tested whether culturable bacteria would differ from those commonly isolated from its field-cropped varieties, to date exclusively represented by Rhizobium sullae. 63 isolates from 60 surface-sterilized nodules were analyzed by ARDRA and 16S rDNA sequencing. The official nitrogen-fixing symbiont Rhizobium sullae was found only in 25 nodules out of 60. The remaining nodules did not yield culturable rhizobia but a number of different endophytic genera including Pseudomonas sp. (17 nodules), Microbacterium sp. (15 nodules), Pantoea agglomerans (5 nodules). The situation appears therefore a hybrid between what is commonly observed in other Mediterranean legumes occurring only in wild status (featuring non-culturable rhizobia and arrays of culturable endophytes within nodules), as opposed to cropped legumes (endowed with fully culturable rhizobia and minimal endophytic occurrence). These findings, within a species bridging the ecology between native and cropped conditions, suggest insights on the relative importance of endophytic co-occupancy vs. true N-fixing symbiont culturability within nodules. The latter trait thus appears to accompany the domestication path of plants with a main trade-off of renouncing to interactions with a diversity of endophytic co-invaders; the relationships with those being critical in the non-cropped status. In fact, endophytes are known to promote plant growth in harsh conditions, which can be particularly stressful in the Mediterranean due to drought, highly calcareous soils, and pathogens outbreaks.}, } @article {pmid30651549, year = {2019}, author = {Wu, F and Lopatkin, AJ and Needs, DA and Lee, CT and Mukherjee, S and You, L}, title = {A unifying framework for interpreting and predicting mutualistic systems.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {242}, doi = {10.1038/s41467-018-08188-5}, pmid = {30651549}, issn = {2041-1723}, support = {R01GM098642/NH/NIH HHS/United States ; R01GM110494/NH/NIH HHS/United States ; }, mesh = {Calibration ; Feasibility Studies ; Food Chain ; *Models, Biological ; Probability ; *Support Vector Machine ; *Symbiosis ; }, abstract = {Coarse-grained rules are widely used in chemistry, physics and engineering. In biology, however, such rules are less common and under-appreciated. This gap can be attributed to the difficulty in establishing general rules to encompass the immense diversity and complexity of biological systems. Furthermore, even when a rule is established, it is often challenging to map it to mechanistic details and to quantify these details. Here we report a framework that addresses these challenges for mutualistic systems. We first deduce a general rule that predicts the various outcomes of mutualistic systems, including coexistence and productivity. We further develop a standardized machine-learning-based calibration procedure to use the rule without the need to fully elucidate or characterize their mechanistic underpinnings. Our approach consistently provides explanatory and predictive power with various simulated and experimental mutualistic systems. Our strategy can pave the way for establishing and implementing other simple rules for biological systems.}, } @article {pmid30588205, year = {2018}, author = {Cropp, RA and Norbury, J}, title = {Obligate Mutualism in an Extended Consumer-Resource Framework.}, journal = {The Yale journal of biology and medicine}, volume = {91}, number = {4}, pages = {375-389}, pmid = {30588205}, issn = {1551-4056}, mesh = {Linear Models ; Models, Biological ; *Symbiosis ; }, abstract = {The development of a theory to underpin the obligate mutualist interactions that appear to be ubiquitous in nature has not proceeded at the same pace as the development of theory to support competition and predation. A constraint may be that obligate mutualism appears unable to be presented in the simple linear models that have so successfully served as heuristics for the other interactions. A number of simple nonlinear models have been used to propose explanations of obligate mutualism, but these solutions are often predicated on careful choices of functional forms. We present a theory of obligate mutualism in an explicit mass-conserving framework using simple models that are robust to choices of functional forms.}, } @article {pmid30419937, year = {2018}, author = {Derakhshani, H and Plaizier, JC and De Buck, J and Barkema, HW and Khafipour, E}, title = {Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {203}, pmid = {30419937}, issn = {2049-2618}, mesh = {Animals ; Cattle ; Colostrum/*microbiology ; DNA, Intergenic/genetics ; Female ; Genetic Predisposition to Disease ; Histocompatibility Antigens Class II/*genetics ; Lactation/*genetics ; Mastitis, Bovine/*genetics/microbiology ; Microbiota ; Milk/*microbiology ; Polymorphism, Single Nucleotide/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {BACKGROUND: The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility complex (BoLA) gene has been associated with susceptibility to several infectious diseases, most importantly mastitis. However, mechanisms underlying this association are yet poorly understood. In the present study, we sought to explore the association of BoLA gene polymorphism with the dynamics of mammary microbiota during the first week of lactation.

RESULTS: Colostrum and milk samples were collected from multiparous Holstein dairy cows at the day of calving and days 1 and 6 after calving. Microbiota profiling was performed using high-throughput sequencing of the V1-V2 regions of the bacterial 16S rRNA genes and ITS2 region of the fungal ribosomal DNA. Polymorphism of BoLA genes was determined using PCR-RFLP of exon 2 of the BoLA-DRB3. In general, transition from colostrum to milk resulted in increased species richness and diversity of both bacterial and fungal communities. The most dominant members of intramammary microbiota included Staphylococcus, Ruminococcaceae, and Clostridiales within the bacterial community and Alternaria, Aspergillus, Candida, and Cryptococcus within the fungal community. Comparing the composition of intramammary microbiota between identified BoLA-DRB3.2 variants (n = 2) revealed distinct clustering pattern on day 0, whereas th