@article {pmid30775775, year = {2019}, author = {Liang, J and Klingl, A and Lin, YY and Boul, E and Thomas-Oates, J and Marín, M}, title = {A sub-compatible rhizobium strain reveals infection duality in Lotus.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erz057}, pmid = {30775775}, issn = {1460-2431}, abstract = {Lotus species develop infection threads to guide rhizobia into nodule cells. However, there is evidence that some species have a genetic repertoire to allow other modes of infection. Conducting confocal and electron microscopy, quantification of marker gene expression, and phenotypic analysis of transgenic roots infected with mutant rhizobia we elucidated the infection mechanism used by Rhizobium leguminosarum Norway to colonise Lotus burttii. R. leguminosarum Norway induces a distinct host transcriptional response compared to Mesorhizobium loti. It infects L.burttii utilising an epidermal and trans-cellular infection thread-independent mechanism at high frequency. The entry into plant cells occurs directly from the apoplast and is primarily mediated by "peg"-like structures, the formation of which is dependent on the production of Nod factor by the rhizobia. These results demonstrate that Lotus species can exhibit duality in their infection mechanisms depending on the rhizobial strain that they encounter. This is especially relevant in the context of interactions in the rhizosphere where legumes do not encounter single strains, but complex rhizobial communities. Additionally, our findings support a perception mechanism at the nodule cell entry interface reinforcing the idea that there are successive checkpoints during rhizobial infection.}, } @article {pmid30772337, year = {2019}, author = {Mishra, N and Damle, G and Dhas, Y and Banerjee, J}, title = {Association of vitamin D deficiency with insulin resistance in middle-aged type 2 diabetics.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cca.2019.02.014}, pmid = {30772337}, issn = {1873-3492}, abstract = {BACKGROUND: Vitamin D deficiency contributes to the pathophysiology of insulin resistance (IR) and type 2 diabetes mellitus (T2DM). We investigated the association of 25-hydroxyvitamin D [25(OH)D] with IR and β-cell function in middle-aged participants.

METHODS: We enrolled 90 controls and 90 T2DM patients of both genders aged 30-50 y. Serum 25(OH)D, fasting plasma insulin (FPI), fasting plasma glucose (FPG), HbA1c, and lipid profile were measured by standard methods. Insulin resistance and sensitivity were assessed by triglyceride glucose (TyG) index, homeostatic model assessment (HOMA-IR), and quantitative insulin sensitivity check index (QUICKI), and β-cell function by HOMA-B.

RESULTS: 25(OH)D deficiency was reported as 40% in control and 70% in T2DM patients. 25(OH)D concentration was positively associated with age, blood pressure, T2DM duration, FPG, HbA1c, TyG index, and HOMA-IR and negatively associated with HOMA-B and QUICKI among all the participants (p ≤.001). Participants with severe 25(OH)D deficiency (<10 ng/ml) were 38.927 times higher odds of being T2DM, while, those with moderate deficiency (10-19n g/ml) and insufficiency (20-29 ng/ml) were 15 times and 13 times higher odds of being T2DM, respectively.

CONCLUSION: Sufficient 25(OH)D concentration may lower the risk of development of IR and T2DM in middle-aged control and diabetic participants.}, } @article {pmid30772172, year = {2019}, author = {Yu, H and Bao, H and Zhang, Z and Cao, Y}, title = {Immune Signaling Pathway during Terminal Bacteroid Differentiation in Nodules.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2019.01.010}, pmid = {30772172}, issn = {1878-4372}, abstract = {Plant innate immunity plays an important role in regulating symbiotic associations with rhizobia, including during rhizobial infection, rhizobial colonization, and bacteroid differentiation in leguminous plants. Here we propose that an immune signaling pathway similar to plant pattern-triggered immunity (PTI) is required for the regulation of bacteroid differentiation in Medicago truncatula nodules.}, } @article {pmid30765781, year = {2019}, author = {Yoshida, T and Furihata, HY and To, TK and Kakutani, T and Kawabe, A}, title = {Genome defense against integrated organellar DNA fragments from plastids into plant nuclear genomes through DNA methylation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2060}, doi = {10.1038/s41598-019-38607-6}, pmid = {30765781}, issn = {2045-2322}, support = {201508708//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 18K14758//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; S1511023//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; }, abstract = {Nuclear genomes are always faced with the modification of themselves by insertions and integrations of foreign DNAs and intrinsic parasites such as transposable elements. There is also substantial number of integrations from symbiotic organellar genomes to their host nuclear genomes. Such integration might have acted as a beneficial mutation during the evolution of symbiosis, while most of them have more or less deleterious effects on the stability of current genomes. Here we report the pattern of DNA substitution and methylation on organellar DNA fragments integrated from plastid into plant nuclear genomes. The genome analyses of 17 plants show homology-dependent DNA substitution bias. A certain number of these sequences are DNA methylated in the nuclear genome. The intensity of DNA methylation also decays according to the increase of relative evolutionary times after being integrated into nuclear genomes. The methylome data of epigenetic mutants shows that the DNA methylation of organellar DNA fragments in nuclear genomes are mainly dependent on the methylation maintenance machinery, while other mechanisms may also affect on the DNA methylation level. The DNA methylation on organellar DNA fragments may contribute to maintaining the genome stability and evolutionary dynamics of symbiotic organellar and their host's genomes.}, } @article {pmid30765481, year = {2019}, author = {Zhou, D and Li, Y and Wang, X and Xie, F and Chen, D and Ma, B and Li, Y}, title = {Mesorhizobium huakuii HtpG interaction with nsLTP AsE246 is required for symbiotic nitrogen fixation.}, journal = {Plant physiology}, volume = {}, number = {}, pages = {}, doi = {10.1104/pp.18.00336}, pmid = {30765481}, issn = {1532-2548}, abstract = {Plant non-specific lipid transfer proteins (nsLTPs) are involved in a number of biological processes including root nodule symbiosis. However, the role of nsLTPs in legume-rhizobium symbiosis remains poorly understood, and no rhizobia proteins that interact with nsLTPs have been reported to date. In this study, we used a bacteria two-hybrid system and identified the HtpG protein from Mesorhizobium huakuii that interacts with the nsLTP AsE246. The interaction between HtpG and AsE246 was confirmed by far-western blotting and bimolecular fluorescence complementation. Our results indicated that the HSP90 domain of HtpG mediates the HtpG-AsE246 interaction. Immunofluorescence assay showed that HtpG was co-localized with AsE246 in infected nodule cells and symbiosome membranes. Expression of the htpG gene was relatively higher in young nodules and was highly expressed in the infection zones. Further investigaton showed that htpG expression affects lipid abundance and profiles in root nodules and plays an essential role in nodule development and nitrogen fixation. Our findings provide further insights into the functional mechanisms behind the transport of symbiosome lipids via nsLTPs in root nodules.}, } @article {pmid30422992, year = {2018}, author = {Grobler, Y and Yun, CY and Kahler, DJ and Bergman, CM and Lee, H and Oliver, B and Lehmann, R}, title = {Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation.}, journal = {PLoS pathogens}, volume = {14}, number = {11}, pages = {e1007445}, pmid = {30422992}, issn = {1553-7374}, support = {/Howard Hughes Medical Institute/Howard Hughes Medical Institute/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; P40 OD018537/OD/NIH HHS/United States ; }, mesh = {Animals ; Culicidae ; Drosophila/genetics/microbiology ; Drosophila melanogaster/*genetics/microbiology ; Genome ; Host Microbial Interactions/*genetics ; Host-Pathogen Interactions/genetics ; Humans ; In Situ Hybridization, Fluorescence/methods ; Mosquito Vectors ; RNA Interference ; Symbiosis ; Viruses/genetics ; Whole Genome Sequencing/methods ; Wolbachia/*genetics ; }, abstract = {Wolbachia is an intracellular bacterium that infects a remarkable range of insect hosts. Insects such as mosquitos act as vectors for many devastating human viruses such as Dengue, West Nile, and Zika. Remarkably, Wolbachia infection provides insect hosts with resistance to many arboviruses thereby rendering the insects ineffective as vectors. To utilize Wolbachia effectively as a tool against vector-borne viruses a better understanding of the host-Wolbachia relationship is needed. To investigate Wolbachia-insect interactions we used the Wolbachia/Drosophila model that provides a genetically tractable system for studying host-pathogen interactions. We coupled genome-wide RNAi screening with a novel high-throughput fluorescence in situ hybridization (FISH) assay to detect changes in Wolbachia levels in a Wolbachia-infected Drosophila cell line JW18. 1117 genes altered Wolbachia levels when knocked down by RNAi of which 329 genes increased and 788 genes decreased the level of Wolbachia. Validation of hits included in depth secondary screening using in vitro RNAi, Drosophila mutants, and Wolbachia-detection by DNA qPCR. A diverse set of host gene networks was identified to regulate Wolbachia levels and unexpectedly revealed that perturbations of host translation components such as the ribosome and translation initiation factors results in increased Wolbachia levels both in vitro using RNAi and in vivo using mutants and a chemical-based translation inhibition assay. This work provides evidence for Wolbachia-host translation interaction and strengthens our general understanding of the Wolbachia-host intracellular relationship.}, } @article {pmid30332402, year = {2018}, author = {Pang, R and Chen, M and Yue, L and Xing, K and Li, T and Kang, K and Liang, Z and Yuan, L and Zhang, W}, title = {A distinct strain of Arsenophonus symbiont decreases insecticide resistance in its insect host.}, journal = {PLoS genetics}, volume = {14}, number = {10}, pages = {e1007725}, pmid = {30332402}, issn = {1553-7404}, mesh = {Animals ; Asia ; Bacteria/genetics ; DNA, Bacterial/genetics ; Enterobacteriaceae/*genetics ; Hemiptera ; Insecta/genetics ; Insecticide Resistance/*genetics/physiology ; Insecticides ; Polymorphism, Single Nucleotide/genetics ; Symbiosis/genetics ; }, abstract = {Symbiotic bacteria are important drivers of phenotypic diversity in insects. One of the widespread symbionts to have emerged belongs to the genus Arsenophonus, however, its biological functions in most host insects remain entirely unknown. Here we report two distinct Arsenophonus strains in the brown planthopper (BPH), Nilaparvata lugens, a major pest insect in Asian countries that causes significant economic damage through rice crop destruction. Genomic resequencing data suggested that one Arsenophonus strain (S-type) negatively affected the insecticide resistance of the host. Indeed, replacement of the resident Arsenophonus with the S-type Arsenophonus significantly decreased host insecticide resistance. Transcriptome and metabolome analysis revealed down-regulation of xenobiotic metabolism and increased amino acid accumulation in the S-type Arsenophonus infected host. This study demonstrates how a symbiont-mediated phenotypic change can occur. The results of this study will aid in developing strategies that work through imposing an ecological disadvantage on insect pests, which will be of great value for pest control in agricultural industry.}, } @article {pmid29267881, year = {2018}, author = {Britstein, M and Saurav, K and Teta, R and Sala, GD and Bar-Shalom, R and Stoppelli, N and Zoccarato, L and Costantino, V and Steindler, L}, title = {Identification and chemical characterization of N-acyl-homoserine lactone quorum sensing signals across sponge species and time.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {2}, pages = {}, doi = {10.1093/femsec/fix182}, pmid = {29267881}, issn = {1574-6941}, mesh = {Acyl-Butyrolactones/*metabolism ; Animals ; Humans ; Indian Ocean ; Porifera/*microbiology ; Quorum Sensing/*physiology ; Signal Transduction ; Symbiosis ; }, abstract = {Marine sponges form symbiotic relationships with complex microbial communities, yet little is known about the mechanisms by which these microbes regulate their behavior through gene expression. Many bacterial communities regulate gene expression using chemical signaling termed quorum sensing. While a few previous studies have shown presence of N-acyl-homoserine lactone (AHL)-based quorum sensing in marine sponges, the chemical identity of AHL signals has been published for only two sponge species. In this study, we screened for AHLs in extracts from 15 sponge species (109 specimens in total) from the Mediterranean and Red Sea, using a wide-range AHL biosensor. This is the first time that AHL presence was examined over time in sponges. We detected the presence of AHL in 46% of the sponge species and found that AHL signals differ for certain sponge species in time and across sponge individuals. Furthermore, for the Mediterranean sponge species Sarcotragus fasciculatus, we identified 14 different AHLs. The constant presence of specific AHL molecules in all specimens, together with varying signaling molecules between the different specimens, makes Sa. fasciculatus a good model to further investigate the function of quorum sensing in sponge-associated bacteria. This study extends the knowledge of AHL-based quorum sensing in marine sponges.}, } @article {pmid30763666, year = {2019}, author = {Cao-Pham, AH and Hiong, KC and Boo, MV and Choo, CYL and Pang, CZ and Wong, WP and Neo, ML and Chew, SF and Ip, YK}, title = {Molecular characterization, cellular localization, and light-enhanced expression of Beta-Na+/H+ Exchanger-like in the whitish inner mantle of the giant clam, Tridacna squamosa, denote its role in light-enhanced shell formation.}, journal = {Gene}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gene.2019.02.009}, pmid = {30763666}, issn = {1879-0038}, abstract = {The fluted giant clam, Tridacna squamosa, lives in symbiosis with photosynthetic zooxanthellae, and can engage in light-enhanced growth and shell formation. Light-enhanced shell formation necessitates the elimination of excess H+ from the extrapallial fluid adjacent to the shell. This study aimed to clone Na+/H+Exchanger (NHE) from the whitish inner mantle adjacent to the extrapallial fluid of T. squamosa, to determine its cellular and subcellular localization, and to evaluate the effect of light exposure on its mRNA expression level and protein abundance therein. The complete coding cDNA sequence of NHE obtained was identified as a homolog of beta NHE (βNHE-like). It consisted of 2925 bp, encoding for a polypeptide of 974 amino acids and 107.1 kDa, and was expressed predominantly in the inner mantle. There, βNHE-like was localized in the apical membrane of the seawater-facing epithelium by immunofluorescence microscopy. After exposure to light for 12 h, the seawater-facing epithelium of the inner mantle displayed consistently stronger immunostaining than that of the control exposed to 12 h of darkness. Western blotting confirmed that light exposure significantly enhanced the protein abundance of βNHE-like in the inner mantle. These results denote that some of the excess H+ generated during light-enhanced shell formation can be excreted through the light-dependent βNHE-like of the seawater-facing epithelium to minimize the impact on the whole-body pH. Importantly, the excreted H+ could dehydrate exogenous HCO3-, and facilitate the absorption of inorganic carbon through the seawater-facing epithelium dedicated for light-enhanced shell formation due to its close proximity with the shell-facing epithelium. NUCLEOTIDE SYMBOL COMBINATIONS: Pairs: R = A/G; W = A/T; Y = C/T. Triples: D = A/G/T.}, } @article {pmid30763358, year = {2019}, author = {Abi Khattar, Z and Lanois, A and Hadchity, L and Gaudriault, S and Givaudan, A}, title = {Spatiotemporal expression of the putative MdtABC efflux pump of Phtotorhabdus luminescens occurs in a protease-dependent manner during insect infection.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212077}, doi = {10.1371/journal.pone.0212077}, pmid = {30763358}, issn = {1932-6203}, abstract = {Photorhabdus luminescens is an enterobacterium establishing a mutualistic symbiosis with nematodes, that also kills insects after septicaemia and connective tissue colonization. The role of the bacterial mdtABC genes encoding a putative multidrug efflux system from the resistance/nodulation/cell division family was investigated. We showed that a mdtA mutant and the wild type had similar levels of resistance to antibiotics, antimicrobial peptides, metals, detergents and bile salts. The mdtA mutant was also as pathogenic as the wild-type following intrahaemocoel injection in Locusta migratoria, but had a slightly attenuated phenotype in Spodoptera littoralis. A transcriptional fusion of the mdtA promoter (PmdtA) and the green fluorescent protein (gfp) encoding gene was induced by copper in bacteria cultured in vitro. The PmdtA-gfp fusion was strongly induced within bacterial aggregates in the haematopoietic organ during late stages of infection in L. migratoria, whereas it was only weakly expressed in insect plasma throughout infection. A medium supplemented with haematopoietic organ extracts induced the PmdtA-gfp fusion ex vivo, suggesting that site-specific mdtABC expression resulted from insect signals from the haematopoietic organ. Finally, we showed that protease inhibitors abolished ex vivo activity of the PmdtA-gfp fusion in the presence of haematopoietic organ extracts, suggesting that proteolysis by-products play a key role in upregulating the putative MdtABC efflux pump during insect infection with P. luminescens.}, } @article {pmid30761784, year = {2018}, author = {Kuzmin, MD and Pashkova, TM and Kartashova, OL and Pashinina, OA and Popova, LP}, title = {[Biological properties of microorganisms isolated from the urine of patients with urolithiasis].}, journal = {Urologiia (Moscow, Russia : 1999)}, volume = {}, number = {4}, pages = {14-18}, pmid = {30761784}, issn = {1728-2985}, abstract = {AIM: To define persistent properties and antibiotic resistance of microorganisms isolated from the urine of adult patient undergoing surgery for urolithiasis.

MATERIALS AND METHODS: Urine specimens were obtained from the renal pelvis and urinary bladder during percutaneous nephrolithotripsy. Microorganisms that were isolated from the urine were examined for their persistent properties (anti-lysozyme activity, the ability of biofilm formation) and antibiotic resistance using photometric and bacteriological methods.

RESULTS: Strains of microorganisms isolated from the urine of patients with urolithiasis have high anti-lysozyme activity and the ability of biofilm formation, and variable antibiotic resistance. These properties should be taken into account when selecting an empirical antibiotic therapy for preventing infectious-inflammatory complications after percutaneous nephrolithotripsy.

CONCLUSION: The high level of resistance of microorganisms isolated from the urine of patients with urolithiasis to the studied antibiotics, their ability to inactivate lysozyme and form biofilms may be the cause of the development of postoperative complications.}, } @article {pmid30761341, year = {2018}, author = {Pushpakumara, BLDU and Gunawardana, D}, title = {Preliminary data on the presence of an alternate vanadium nitrogenase in a culturable cyanobiont of Azolla pinnata R. Brown: Implications on Chronic Kidney Disease of an unknown etiology (CKDu).}, journal = {Data in brief}, volume = {21}, number = {}, pages = {2590-2597}, doi = {10.1016/j.dib.2018.11.073}, pmid = {30761341}, issn = {2352-3409}, abstract = {In a recent paper titled "How a taxonomically-ambiguous cyanobiont and vanadate assist in the phytoremediation of cadmium by Azolla pinnata: implications for CKDu" (Atugoda et al., 2018) [1] it was shown by us, that plant health and phytoremediation capacities, of Azolla pinnata R. Brown, were elevated in the presence of vanadate, a vanadium containing ion. This highlighted a possibility, that either the major or minor cyanobionts of Azolla pinnata, could possess a vanadium dependent nitrogenase enzyme, as an alternate nitrogenase, in addition to the molybdenum counterpart. In this data article, we report the isolation of a minor cyanobiont which we name as Fischerella uthpalarensis. We grew Fischerella uthpalarensis, exclusively in N-free media, with only molybdenum (Mo+ V-), with only vanadium (V+ Mo-) and with neither (negative control), to find out the growth patterns in the relevant media. While F. uthpalarensis grew as green colored consistencies, increasing gradually in turbidity, for 4 weeks in culture, both, in the presence of molybdenum (Mo+ V-), as well as vanadium (V+ Mo-), the negative control, showed no, or very little growth. This alludes to the presence of dual nitrogenases in Fischerella uthpalarensis. An attempt was also made by us to unravel the vnf genes, responsible for the V-nitrogenase. However, it was not possible to PCR amplify the vnf genes, from both, the unculturable major (using total DNA from the Azolla-Nostoc azollae symbiosis) and minor (DNA directly from the cultured F. uthpalarensis) cyanobionts. This is the first time, to our knowledge, that an endosymbiotic cyanobacterium inside a plant compartment, has been shown to contain two possible nitrogenase systems.}, } @article {pmid30760820, year = {2019}, author = {Karimi, E and Keller-Costa, T and Slaby, BM and Cox, CJ and da Rocha, UN and Hentschel, U and Costa, R}, title = {Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1999}, doi = {10.1038/s41598-019-38737-x}, pmid = {30760820}, issn = {2045-2322}, support = {PTDC/BIA-MIC/3865/2012//Ministry of Education and Science | Funda&#x00E7;&#x00E3;o para a Ci&#x00EA;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/ ; PTDC/MAR-BIO/1547/2014//Ministry of Education and Science | Funda&#x00E7;&#x00E3;o para a Ci&#x00EA;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/ ; }, abstract = {Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness - were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.}, } @article {pmid30760639, year = {2019}, author = {Liu, J and Liu, J and Liu, J and Cui, M and Huang, Y and Tian, Y and Chen, A and Xu, G}, title = {The potassium transporter SlHAK10 is involved in mycorrhizal potassium uptake.}, journal = {Plant physiology}, volume = {}, number = {}, pages = {}, doi = {10.1104/pp.18.01533}, pmid = {30760639}, issn = {1532-2548}, abstract = {Most terrestrial plants form a root symbiosis with arbuscular mycorrhizal (AM) fungi, which receive fixed carbon from the plant and enhance the plant's uptake of mineral nutrients. AM symbiosis improves the phosphorous and nitrogen nutrition of host plants; however, little is known about the role of AM symbiosis in potassium (K+) nutrition. Here, we report that inoculation with the AM fungus Rhizophagus irregularis improved tomato (Solanum lycopersicum) plant growth and K+ acquisition, and K+ deficiency has a negative effect on root growth and AM colonization. Based on its homology to a Lotus japonicus AM-induced K+ transporter, we identified a mycorrhiza-specific tomato K+ transporter, SlHAK10 (Solanum lycopersicum High-affinity Potassium Transporter 10), that was exclusively expressed in arbuscule-containing cells. SlHAK10 could restore a yeast K+ uptake-defective mutant in the low-affinity concentration range. Loss of function of SlHAK10 led to a significant decrease in mycorrhizal K+ uptake and AM colonization rate under low K+ conditions, but did not affect arbuscule development. Overexpressing SlHAK10 from the constitutive CaMV35S promoter or the AM-specific pSmPT4 promoter (Solanum melongena Phosphate Transporter 4) not only improved plant growth and K+ uptake, but also increased AM colonization efficiency and soluble sugar content in roots supplied with low K+. Our results indicate that tomato plants have a SlHAK10-mediated mycorrhizal K+ uptake pathway and that improved plant K+ nutrition could increase carbohydrate accumulation in roots, which facilitates AM fungal colonization.}, } @article {pmid30759832, year = {2019}, author = {Jia, T and Wang, J and Chang, W and Fan, X and Sui, X and Song, F}, title = {Proteomics Analysis of E. angustifolia Seedlings Inoculated with Arbuscular Mycorrhizal Fungi under Salt Stress.}, journal = {International journal of molecular sciences}, volume = {20}, number = {3}, pages = {}, doi = {10.3390/ijms20030788}, pmid = {30759832}, issn = {1422-0067}, support = {31570635//National Natural Science Foundation of China/ ; 201504409//Special Fund for Forest Scientific Research in the Public Welfare/ ; JC201306//Excellent Youth Foundation of Heilongjiang Scientific Committee/ ; 2016//100 Discipline Young Scholars Project of the Heilongjiang University/ ; }, abstract = {To reveal the mechanism of salinity stress alleviation by arbuscular mycorrhizal fungi (AMF), we investigated the growth parameter, soluble sugar, soluble protein, and protein abundance pattern of E. angustifolia seedlings that were cultured under salinity stress (300 mmol/L NaCl) and inoculated by Rhizophagus irregularis (RI). Furthermore, a label-free quantitative proteomics approach was used to reveal the stress-responsive proteins in the leaves of E. angustifolia. The result indicates that the abundance of 75 proteins in the leaves was significantly influenced when E. angustifolia was inoculated with AMF, which were mainly involved in the metabolism, signal transduction, and reactive oxygen species (ROS) scavenging. Furthermore, we identified chorismate mutase, elongation factor mitochondrial, peptidyl-prolyl cis-trans isomerase, calcium-dependent kinase, glutathione S-transferase, glutathione peroxidase, NADH dehydrogenase, alkaline neutral invertase, peroxidase, and other proteins closely related to the salt tolerance process. The proteomic results indicated that E. angustifolia seedlings inoculated with AMF increased the secondary metabolism level of phenylpropane metabolism, enhanced the signal transduction of Ca2+ and ROS scavenging ability, promoted the biosynthesis of protein, accelerated the protein folding, and inhibited the degradation of protein under salt stress. Moreover, AMF enhanced the synthesis of ATP and provided sufficient energy for plant cell activity. This study implied that symbiosis of halophytes and AMF has potential as an application for the improvement of saline-alkali soils.}, } @article {pmid30759803, year = {2019}, author = {Crespo-Rivas, JC and Navarro-Gómez, P and Alias-Villegas, C and Shi, J and Zhen, T and Niu, Y and Cuéllar, V and Moreno, J and Cubo, T and Vinardell, JM and Ruiz-Sainz, JE and Acosta-Jurado, S and Soto, MJ}, title = {Sinorhizobium fredii HH103 RirA Is Required for Oxidative Stress Resistance and Efficient Symbiosis with Soybean.}, journal = {International journal of molecular sciences}, volume = {20}, number = {3}, pages = {}, doi = {10.3390/ijms20030787}, pmid = {30759803}, issn = {1422-0067}, support = {P11-CVI-7500//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; BIO2013-42801-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; BIO2016-78409-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; }, abstract = {Members of Rhizobiaceae contain a homologue of the iron-responsive regulatory protein RirA. In different bacteria, RirA acts as a repressor of iron uptake systems under iron-replete conditions and contributes to ameliorate cell damage during oxidative stress. In Rhizobium leguminosarum and Sinorhizobium meliloti, mutations in rirA do not impair symbiotic nitrogen fixation. In this study, a rirA mutant of broad host range S. fredii HH103 has been constructed (SVQ780) and its free-living and symbiotic phenotypes evaluated. No production of siderophores could be detected in either the wild-type or SVQ780. The rirA mutant exhibited a growth advantage under iron-deficient conditions and hypersensitivity to hydrogen peroxide in iron-rich medium. Transcription of rirA in HH103 is subject to autoregulation and inactivation of the gene upregulates fbpA, a gene putatively involved in iron transport. The S. fredii rirA mutant was able to nodulate soybean plants, but symbiotic nitrogen fixation was impaired. Nodules induced by the mutant were poorly infected compared to those induced by the wild-type. Genetic complementation reversed the mutant's hypersensitivity to H₂O₂, expression of fbpA, and symbiotic deficiency in soybean plants. This is the first report that demonstrates a role for RirA in the Rhizobium-legume symbiosis.}, } @article {pmid30759337, year = {2016}, author = {Abdurashytov, SF and Volkohon, VV}, title = {NEW ARBUSCULAR MYCORRHIZAL FUNGI ASSOCIATIONS FROM SOILS OF CRIMEAN STEPPE.}, journal = {Mikrobiolohichnyi zhurnal (Kiev, Ukraine : 1993)}, volume = {78}, number = {1}, pages = {63-70}, pmid = {30759337}, issn = {1028-0987}, abstract = {The primary selection ofarbuscular mycorrhizal (AM)fungifrom soils of Crimean Steppe was conducted The most effective associations P3, P5, S1, S3, S8 and S9 were identified using morphological characteristics of Sorgum sudanense roots colonization and spores surface appearance. It was shown that AMfitngiform Arum-type symbiosis contain well- established spores' kinds specific to individual associations. The molecular identification was performed in addition to the morphological data. AMfungi associations P3, P5, S1, S3, S8 and S9 were identified as Rhizophagus genus while SI association as Funneliformis genus.}, } @article {pmid30276423, year = {2019}, author = {Abdelkrim, S and Jebara, SH and Saadani, O and Chiboub, M and Abid, G and Mannai, K and Jebara, M}, title = {Heavy metal accumulation in Lathyrus sativus growing in contaminated soils and identification of symbiotic resistant bacteria.}, journal = {Archives of microbiology}, volume = {201}, number = {1}, pages = {107-121}, doi = {10.1007/s00203-018-1581-4}, pmid = {30276423}, issn = {1432-072X}, mesh = {Bacillus/growth & development/isolation & purification/metabolism ; Biodegradation, Environmental ; Cadmium/metabolism ; Copper/metabolism ; Fabaceae/microbiology ; Lathyrus/*growth & development/*microbiology ; Lead/metabolism ; Metals, Heavy/*metabolism ; Plant Roots/microbiology ; Pseudomonas/growth & development/isolation & purification/metabolism ; Rhizobium/growth & development/isolation & purification/metabolism ; Root Nodules, Plant/*microbiology ; Sinorhizobium meliloti/growth & development/isolation & purification/metabolism ; Soil ; Soil Microbiology ; Soil Pollutants/*metabolism ; Symbiosis ; Zinc/metabolism ; }, abstract = {In this study, two populations of leguminous plants Lathyrus sativus were grown in four soils that were collected from sites differently contaminated by heavy metals. Evaluations included basic soil properties, concentrations of major nutrients and four metals (copper, zinc, lead and cadmium) in these soils. Investigation of Lathyrus sativus response to contamination showed that the increase of heavy metal concentration in soils affected biomass of plant, number of nodules and plant metal uptake. Heavy metal tolerance of 46 isolated bacteria from the root nodules was evaluated and demonstrated that the maximum concentration of Cd, Pb, Cu and Zn tolerated by strains were 0.8, 2.5, 0.2, and 0.5 mM, respectively. Twenty-two isolates were tested for their effects on plant biomass production and nodule formation and showed that only R. leguminosarum nodulated Lathyrus sativus, while some bacteria improved the shoot and root dry biomass. Sequences of their 16S rDNA gene fragments were also obtained and evaluated for tentative identification of the isolates which revealed different bacterial genera represented by Rhizobium sp, Rhizobium leguminosarum, Sinorhizobium meliloti, Pseudomonas sp, Pseudomonas fluorescens, Luteibacter sp, Variovorax sp, Bacillus simplex and Bacillus megaterium. The existence of Pb- and Cd-resistant genes (PbrA and CadA) in these bacteria was determined by PCR, and it showed high homology with PbrA and CadA genes from other bacteria. The tested resistant population was able to accumulate high concentrations of Pb and Cd in all plant parts and, therefore, can be classified as a strong metal accumulator with suitable potential for phytoremediation of Pb and Cd polluted sites. Heavy metal resistant and efficient bacteria isolated from root nodules were chosen with Lathyrus sativus to form symbiotic associations for eventual bioremediation program, which could be tested to remove pollutants from contaminated sites.}, } @article {pmid30759164, year = {2019}, author = {Hassing, B and Winter, D and Becker, Y and Mesarich, CH and Eaton, CJ and Scott, B}, title = {Analysis of Epichloë festucae small secreted proteins in the interaction with Lolium perenne.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0209463}, doi = {10.1371/journal.pone.0209463}, pmid = {30759164}, issn = {1932-6203}, abstract = {Epichloë festucae is an endophyte of the agriculturally important perennial ryegrass. This species systemically colonises the aerial tissues of this host where its growth is tightly regulated thereby maintaining a mutualistic symbiotic interaction. Recent studies have suggested that small secreted proteins, termed effectors, play a vital role in the suppression of host defence responses. To date only a few effectors with important roles in mutualistic interactions have been described. Here we make use of the fully assembled E. festucae genome and EffectorP to generate a suite of 141 effector candidates. These were analysed with respect to their genome location and expression profiles in planta and in several symbiosis-defective mutants. We found an association between effector candidates and a class of transposable elements known as MITEs, but no correlation with other dynamic features of the E. festucae genome, such as transposable element-rich regions. Three effector candidates and a small GPI-anchored protein were chosen for functional analysis based on their high expression in planta compared to in culture and their differential regulation in symbiosis defective E. festucae mutants. All three candidate effector proteins were shown to possess a functional signal peptide and two could be detected in the extracellular medium by western blotting. Localization of the effector candidates in planta suggests that they are not translocated into the plant cell, but rather, are localized in the apoplastic space or are attached to the cell wall. Deletion and overexpression of the effector candidates, as well as the putative GPI-anchored protein, did not affect the plant growth phenotype or restrict growth of E. festucae mutants in planta. These results indicate that these proteins are either not required for the interaction at the observed life stages or that there is redundancy between effectors expressed by E. festucae.}, } @article {pmid30744248, year = {1998}, author = {Schwencke, J and Bureau, JM and Crosnier, MT and Brown, S}, title = {Cytometric determination of genome size and base composition of tree species of three genera of Casuarinaceae.}, journal = {Plant cell reports}, volume = {18}, number = {3-4}, pages = {346-349}, doi = {10.1007/s002990050584}, pmid = {30744248}, issn = {1432-203X}, abstract = {The genome size and base composition of diploid plant species from three genera of the Casuarinaceae family were determined by flow cytometry. Casuarina glauca Sieb. ex Spring. and Gymnostoma deplancheana (Miq.) L. Johnson showed a small genome with 2C = 0.70 pg, 58.6% AT, 40.5% GC for the first species and 2C = 0.75 pg, 58.7% AT, 40.5% GC for the second. Allocasuarina verticillata (Lam.) L. Johnson had a larger genome: 2C = 1.90 pg, 59.3% AT, 41.1% GC. One haploid genome of C. glauca is therefore about 340×106 base pairs. In leaves, roots or bark of these three species, polysomaty was virtually absent: a maximum frequency of 4C nuclei of only 0.08 was found in bark of C. glauca. The genome sizes of C. glauca and G. deplancheana are among the smallest described for higher plants. Small genome size, diploidy and the absence of polysomaty are advantageous traits for facilitating molecular approaches to improvement of these actinorhizal plants and developing the study of their symbiotic interactions with Frankia.}, } @article {pmid30683856, year = {2019}, author = {Ellegaard, KM and Engel, P}, title = {Genomic diversity landscape of the honey bee gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {446}, doi = {10.1038/s41467-019-08303-0}, pmid = {30683856}, issn = {2041-1723}, mesh = {Age Factors ; Animals ; Bees/*microbiology ; Bifidobacterium/classification/*genetics/isolation & purification ; *Biological Variation, Individual ; DNA, Bacterial/genetics ; Firmicutes/classification/*genetics/isolation & purification ; Gammaproteobacteria/classification/*genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Metagenomics ; Microbial Consortia/genetics ; Phylogeny ; Symbiosis/physiology ; }, abstract = {The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis.}, } @article {pmid30129423, year = {2018}, author = {Woodruff, GC and Phillips, PC}, title = {Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps.}, journal = {BMC ecology}, volume = {18}, number = {1}, pages = {26}, pmid = {30129423}, issn = {1472-6785}, support = {R01 GM-102511/NH/NIH HHS/United States ; F32 GM115209/GM/NIGMS NIH HHS/United States ; 5F32GM115209-03/NH/NIH HHS/United States ; PE13557//Japan Society for the Promotion of Science/International ; R01 GM102511/GM/NIGMS NIH HHS/United States ; }, mesh = {*Animal Distribution ; Animals ; Caenorhabditis/*physiology ; Ficus/*physiology ; Fruit/physiology ; Japan ; *Pollination ; *Symbiosis ; Wasps/*physiology ; }, abstract = {BACKGROUND: Biotic interactions are ubiquitous and require information from ecology, evolutionary biology, and functional genetics in order to be understood. However, study systems that are amenable to investigations across such disparate fields are rare. Figs and fig wasps are a classic system for ecology and evolutionary biology with poor functional genetics; Caenorhabditis elegans is a classic system for functional genetics with poor ecology. In order to help bridge these disciplines, here we describe the natural history of a close relative of C. elegans, Caenorhabditis inopinata, that is associated with the fig Ficus septica and its pollinating Ceratosolen wasps.

RESULTS: To understand the natural context of fig-associated Caenorhabditis, fresh F. septica figs from four Okinawan islands were sampled, dissected, and observed under microscopy. C. inopinata was found in all islands where F. septica figs were found. C.i nopinata was routinely found in the fig interior and almost never observed on the outside surface. C. inopinata was only found in pollinated figs, and C. inopinata was more likely to be observed in figs with more foundress pollinating wasps. Actively reproducing C. inopinata dominated early phase figs, whereas late phase figs with emerging wasp progeny harbored C. inopinata dauer larvae. Additionally, C. inopinata was observed dismounting from Ceratosolen pollinating wasps that were placed on agar plates. C. inopinata was not found on non-pollinating, parasitic Philotrypesis wasps. Finally, C. inopinata was only observed in F. septica figs among five Okinawan Ficus species sampled.

CONCLUSION: These are the first detailed field observations of C. inopinata, and they suggest a natural history where this species proliferates in early phase F. septica figs and disperses from late phase figs on Ceratosolen pollinating fig wasps. While consistent with other examples of nematode diversification in the fig microcosm, the fig and wasp host specificity of C. inopinata is highly divergent from the life histories of its close relatives and frames hypotheses for future investigations. This natural co-occurrence of the fig/fig wasp and C. inopinata study systems sets the stage for an integrated research program that can help to explain the evolution of interspecific interactions.}, } @article {pmid30753553, year = {2019}, author = {Gautrat, P and Mortier, V and Laffont, C and De Keyser, A and Fromentin, J and Frugier, F and Goormachtig, S}, title = {Unraveling new molecular players involved in the autoregulation of nodulation in Medicago truncatula.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/ery465}, pmid = {30753553}, issn = {1460-2431}, abstract = {The number of legume root nodules resulting from a symbiosis with rhizobia is tightly controlled by the plant. Certain members of the CLAVATA3/Embryo Surrounding Region (CLE) peptide family, specifically MtCLE12 and MtCLE13 in Medicago truncatula, act in the systemic autoregulation of nodulation (AON) pathway that negatively regulates the number of nodules. Little is known about the molecular pathways that operate downstream of the AON-related CLE peptides. Here, by means of a transcriptome analysis, we show that roots ectopically expressing MtCLE13 deregulate only a limited number of genes, including three down-regulated genes encoding lysin motif receptor-like kinases (LysM-RLKs), among which are the nodulation factor (NF) receptor NF Perception gene (NFP) and two up-regulated genes, MtTML1 and MtTML2, encoding Too Much Love (TML)-related Kelch-repeat containing F-box proteins. The observed deregulation was specific for the ectopic expression of nodulation-related MtCLE genes and depended on the Super Numeric Nodules (SUNN) AON RLK. Moreover, overexpression and silencing of these two MtTML genes demonstrated that they play a role in the negative regulation of nodule numbers. Hence, the identified MtTML genes are the functional counterpart of the Lotus japonicus TML gene shown to be central in the AON pathway. Additionally, we propose that the down-regulation of a subset of LysM-RLK-encoding genes, among which is NFP, might contribute to the restriction of further nodulation once the first nodules have been formed.}, } @article {pmid30753410, year = {2019}, author = {Plouznikoff, K and Asins, MJ and de Boulois, HD and Carbonell, EA and Declerck, S}, title = {Genetic analysis of tomato root colonization by arbuscular mycorrhizal fungi.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcy240}, pmid = {30753410}, issn = {1095-8290}, abstract = {Background and Aims: Arbuscular mycorrhizal fungi (AMF) play an important role in plant nutrition and protection against pests and diseases, as well as in soil structuration, nutrient cycling and, generally speaking, in sustainable agriculture, particularly under drought, salinity and low input or organic agriculture. However, little is known about the genetics of the AMF-plant association in tomato. The aim of this study was the genetic analysis of root AMF colonization in tomato via the detection of the quantitative trait loci (QTLs) involved.

Methods: A population of 130 recombinant inbred lines derived from the wild species Solanum pimpinellifolium, genotyped for 1899 segregating, non-redundant single nucleotide polymorphisms (SNPs) from the SolCAP tomato panel, was characterized for intensity, frequency and arbuscular abundance of AMF colonization to detect the QTLs involved and to analyse the genes within their peaks (2-2.6 Mbp).

Key Results: The three AMF colonization parameters were highly correlated (0.78-0.97) and the best one, with the highest heritability (0.23), corresponded to colonization intensity. A total of eight QTLs in chromosomes 1, 3, 4, 5, 6, 8, 9 and 10 were detected. Seven of them simultaneously affected intensity and arbuscule abundance. The allele increasing the expression of the trait usually came from the wild parent in accordance with the parental means, and several epistatic interactions were found relevant for breeding purposes. SlCCaMK and SlLYK13 were found among the candidate genes. Carbohydrate transmembrane transporter activity, lipid metabolism and transport, metabolic processes related to nitrogen and phosphate-containing compounds, regulation of carbohydrates, and other biological processes involved in the plant defence were found to be over-represented within the QTL peaks.

Conclusions: Intensity is genetically the best morphological measure of tomato root AMF colonization. Wild alleles can improve AMF colonization, and the gene contents of AMF colonization QTLs might be important for explaining the establishment and functioning of the AMF-plant symbiosis.}, } @article {pmid29906776, year = {2018}, author = {Trinh, CS and Jeong, CY and Lee, WJ and Truong, HA and Chung, N and Han, J and Hong, SW and Lee, H}, title = {Paenibacillus pabuli strain P7S promotes plant growth and induces anthocyanin accumulation in Arabidopsis thaliana.}, journal = {Plant physiology and biochemistry : PPB}, volume = {129}, number = {}, pages = {264-272}, doi = {10.1016/j.plaphy.2018.06.001}, pmid = {29906776}, issn = {1873-2690}, mesh = {Anthocyanins/*metabolism ; Arabidopsis/*growth & development/metabolism/microbiology ; Chlorophyll/metabolism ; Gene Expression Regulation, Plant ; Paenibacillus/*metabolism ; Plant Roots/*microbiology ; Reverse Transcriptase Polymerase Chain Reaction ; Seedlings/growth & development ; Symbiosis ; }, abstract = {In this study, a novel plant growth-promoting rhizobacteria (PGPR), the bacterial strain Paenibacillus pabuli P7S (PP7S), showed promising plant growth-promoting effects. Furthermore, it induced anthocyanin accumulation in Arabidopsis. When co-cultivated with PP7S, there was a significant increase in anthocyanin content and biomass of Arabidopsis seedlings compared with those of the control. The quantitative reverse transcription-polymerase chain reaction analysis revealed higher expression of many key genes regulating anthocyanin and flavonoid biosynthesis pathways in PP7S-treated seedlings when compared with that of the control. Furthermore, higher expression of pathogen-related genes and microbe-associated molecular pattern genes was also observed in response to PP7S, indicating that the PGPR triggered the induced systemic response (ISR) in A. thaliana. These results suggest that PP7S promotes plant growth in A. thaliana and increases anthocyanin biosynthesis by triggering specific ISRs in plant.}, } @article {pmid29105020, year = {2018}, author = {Pentimone, I and Lebrón, R and Hackenberg, M and Rosso, LC and Colagiero, M and Nigro, F and Ciancio, A}, title = {Identification of tomato miRNAs responsive to root colonization by endophytic Pochonia chlamydosporia.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {2}, pages = {907-919}, doi = {10.1007/s00253-017-8608-7}, pmid = {29105020}, issn = {1432-0614}, mesh = {Apoptosis ; Endophytes/physiology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Hypocreales/*physiology ; Lycopersicon esculentum/*genetics/microbiology ; MicroRNAs/*genetics ; Plant Roots/*microbiology ; Real-Time Polymerase Chain Reaction ; Symbiosis/*genetics ; }, abstract = {The molecular mechanisms active during the endophytic phase of the fungus Pochonia chlamydosporia are still poorly understood. In particular, few data are available on the links between the endophyte and the root response, as modulated by noncoding small RNAs. In this study, we describe the microRNAs (miRNAs) that are differentially expressed (DE) in the roots of tomato, colonized by P. chlamydosporia. A genome-wide NGS expression profiling of small RNAs in roots, either colonized or not by the fungus, showed 26 miRNAs upregulated in inoculated roots. Their predicted target genes are involved in the plant information processing system, which recognizes, percepts, and transmits signals, with higher representations in processes such as apoptosis and plant defense regulation. RNAseq data showed that predicted miRNA target genes were downregulated in tomato roots after 4, 7, 10, and 21 days post P. chlamydosporia inoculation. The differential expression of four miRNAs was further validated using qPCR analysis. The P. chlamydosporia endophytic lifestyle in tomato roots included an intricate network of miRNAs and targets. Data provide a first platform of DE tomato miRNAs after P. chlamydosporia colonization. They indicated that several miRNAs are involved in the host response to the fungus, playing important roles for its recognition as a symbiotic microorganism, allowing endophytism by modulating the host defense reaction. Data also indicated that endophytism affects tRNA fragmentation. This is the first study on miRNAs induced by P. chlamydosporia endophytism and related development regulation effects in Solanum lycopersicum.}, } @article {pmid30742016, year = {2019}, author = {Ohbayashi, T and Futahashi, R and Terashima, M and Barrière, Q and Lamouche, F and Takeshita, K and Meng, XY and Mitani, Y and Sone, T and Shigenobu, S and Fukatsu, T and Mergaert, P and Kikuchi, Y}, title = {Comparative cytology, physiology and transcriptomics of Burkholderia insecticola in symbiosis with the bean bug Riptortus pedestris and in culture.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0361-8}, pmid = {30742016}, issn = {1751-7370}, support = {15H05638//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 14J03996//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20170267//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {In the symbiosis of the bean bug Riptortus pedestris with Burkholderia insecticola, the bacteria occupy an exclusive niche in the insect midgut and favor insect development and reproduction. In order to understand how the symbiotic bacteria stably colonize the midgut crypts and which services they provide to the host, we compared the cytology, physiology, and transcriptomics of free-living and midgut-colonizing B. insecticola. The analyses revealed that midgut-colonizing bacteria were smaller in size and had lower DNA content, they had increased stress sensitivity, lost motility, and an altered cell surface. Transcriptomics revealed what kinds of nutrients are provided by the bean bug to the Burkholderia symbiont. Transporters and metabolic pathways of diverse sugars such as rhamnose and ribose, and sulfur compounds like sulfate and taurine were upregulated in the midgut-colonizing symbionts. Moreover, pathways enabling the assimilation of insect nitrogen wastes, i.e. allantoin and urea, were also upregulated. The data further suggested that the midgut-colonizing symbionts produced all essential amino acids and B vitamins, some of which are scarce in the soybean food of the host insect. Together, these findings suggest that the Burkholderia symbiont is fed with specific nutrients and also recycles host metabolic wastes in the insect gut, and in return, the bacterial symbiont provides the host with essential nutrients limited in the insect food, contributing to the rapid growth and enhanced reproduction of the bean bug host.}, } @article {pmid30740571, year = {2018}, author = {Wang, Y and Li, N and Chen, T and Gong, Y}, title = {Generation and characterization of expressed sequence tags (ESTs) from coralloid root cDNA library of Cycas debaoensis.}, journal = {Plant diversity}, volume = {40}, number = {5}, pages = {245-252}, doi = {10.1016/j.pld.2018.09.002}, pmid = {30740571}, issn = {2468-2659}, abstract = {A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN (duplex-specific nuclease) normalization method combined with the SMART (Switching Mechanism At 5' end of the RNA Transcript) technique. The titer of the original cDNA library was about 1.5 × 106 cfu·mL-1 and the average insertion size was about 1 kb with a high recombination rate (97%). The 5011 high-quality expressed sequence tags (ESTs) were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 (50.1%) unigenes were associated with 4082 Gene Ontology (GO) terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups (COG) functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase (RLK) genes were screened. Furthermore, a total of 94 simple sequence repeats (SSRs) were discovered, of which 20 loci were successfully amplified in C. debaoensis. This study is the first EST analysis for the coralloid roots of C. debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C. debaoensis and related cycad species.}, } @article {pmid30740120, year = {2018}, author = {Nogales, A and Santos, ES and Abreu, MM and Arán, D and Victorino, G and Pereira, HS and Lopes, CM and Viegas, W}, title = {Mycorrhizal Inoculation Differentially Affects Grapevine's Performance in Copper Contaminated and Non-contaminated Soils.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1906}, doi = {10.3389/fpls.2018.01906}, pmid = {30740120}, issn = {1664-462X}, abstract = {Plant inoculation with arbuscular mycorrhizal fungi (AMF) is increasingly employed to enhance productivity and sustainability in agricultural ecosystems. In the present study, the potential benefits of AMF inoculation on young grapevines replanted in pots containing vineyard soil with high Cu concentration were evaluated. For this purpose, one-year-old cv. Touriga Nacional grapevines grafted onto 1103P rootstocks were further inoculated with Rhizoglomus irregulare or Funneliformis mosseae, or left non-inoculated, and maintained in a sterilized substrate under greenhouse conditions for three months. After this time, half of the plants were transplanted to containers filled with an Arenosol from a vineyard which had been artificially contaminated or not with 300 mg kg-1 of Cu. At the end of the growing season, soil nutrient concentration, soil dehydrogenase activity and mycorrhizal colonization rate were analyzed. Grapevine performance was assessed by measuring several vegetative growth and physiological parameters as well as nutrient concentrations in leaves and roots. In the non-contaminated soil, R. irregulare- and F. mosseae-inoculated plants had significantly greater root biomass than the non-inoculated ones. However, the opposite effect was observed in the Cu-contaminated soil, where non-inoculated plants performed better regarding shoot and root development. Concerning nutrient levels, an increase in Cu, Mg and Mn concentrations was observed in the roots of plants growing in the contaminated soil, although only Mn was translocated to leaves. This led to a large increase in leaf Mn concentrations, which was significantly higher in non-inoculated and F. mosseae- inoculated plants than in the R. irregulare- inoculated ones. Copper contamination induced a general decrease in leaf N, P and Fe concentrations as well as chlorosis symptoms. The largest decrease in N and P was observed in F. mosseae- inoculated plants, with 73 and 31.2%, respectively. However, these plants were the ones with the least decrease in Fe concentration (10% vs. almost 30% in the other two inoculation treatments). In conclusion, this study indicates that soil Cu levels can modify the outcome of AMF inoculations in young grapevines, disclosing new AMF-plant associations potentially relevant in vineyards with a tradition of Cu-based fungicide application.}, } @article {pmid30321327, year = {2018}, author = {Chouvenc, T and Elliott, ML and Šobotník, J and Efstathion, CA and Su, NY}, title = {The Termite Fecal Nest: A Framework for the Opportunistic Acquisition of Beneficial Soil Streptomyces (Actinomycetales: Streptomycetaceae).}, journal = {Environmental entomology}, volume = {47}, number = {6}, pages = {1431-1439}, doi = {10.1093/ee/nvy152}, pmid = {30321327}, issn = {1938-2936}, mesh = {Animals ; Antifungal Agents/analysis ; Feces/microbiology ; Female ; Isoptera/*microbiology ; Male ; *Soil Microbiology ; Streptomyces/chemistry/*isolation & purification ; Symbiosis ; }, abstract = {Mutualistic associations between insects and microorganisms must imply gains for both partners, and the emphasis has mostly focused on coevolved host-symbiont systems. However, some insect hosts may have evolved traits that allow for various means of association with opportunistic microbial communities, especially when the microbes are omnipresent in their environment. It was previously shown that colonies of the subterranean termite Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) build nests out of fecal material that host a community of Streptomyces Waksman and Henrici (Actinomycetales: Streptomycetaceae). These Actinobacteria produce an array of bioactive metabolites that provides a level of protection for termites against certain entomopathogenic fungi. How C. formosanus acquires and maintains this association remains unknown. This study shows that the majority of Streptomyces isolates found in field termite fecal nest materials are identical to Streptomyces isolates from soils surrounding the nests and are not vertically inherited. A survey of Streptomyces communities from C. formosanus fecal nest materials sampled at 20 locations around the world revealed that all nests are reliably associated with a diverse Streptomyces community. The C. formosanus fecal nest material therefore provides a nutritional framework that can recruit beneficial Streptomyces from the soil environment, in the absence of long-term coevolutionary processes. A diverse Streptomyces community is reliably present in soils, and subterranean termite colonies can acquire such facultative symbionts each social cycle into their fecal nest. This association probably emerged as an exaptation from the existing termite nest structure and benefits both the termite and the opportunistic colonizing bacteria.}, } @article {pmid30178231, year = {2018}, author = {Morel, F and Jacquier, H and Desroches, M and Fihman, V and Kumanski, S and Cambau, E and Decousser, JW and Berçot, B}, title = {Use of Andromas and Bruker MALDI-TOF MS in the identification of Neisseria.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {12}, pages = {2273-2277}, pmid = {30178231}, issn = {1435-4373}, mesh = {Biological Specimen Banks ; Humans ; Neisseria/*classification/isolation & purification ; Neisseria gonorrhoeae/isolation & purification ; Neisseria meningitidis/isolation & purification ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*instrumentation/*methods ; Symbiosis ; }, abstract = {Through the past decade, MALDI-TOF MS has been recognized as a fast and robust tool for identification of most bacteria in clinical microbiology. However, the accuracy of this method to identify Neisseria species is still debated, and few data are available about commensal Neisseria species identification. In this study, we assessed two MALDI-TOF MS systems (Bruker Biotyper and Andromas) for the identification of 88, 18, and 29 isolates of Neisseria gonorrhoeae, Neisseria meningitidis, and commensal Neisseria species, respectively. All 88 isolates of N. gonorrhoeae were correctly identified using both systems, and most N. meningitidis and commensal Neisseria species were well identified: only 1/18 isolates of N. meningitidis was misidentified using Bruker Biotyper, and 1 isolate of Neisseria polysaccharea was misidentified as N. meningitidis using both systems. These results strengthen the possibility to use MALDI-TOF MS as a single method for Neisseria identification in routine, with excellent performance for N. gonorrhoeae identification. However, results should be interpreted prudently for N. meningitdis and commensal Neisseria species when isolated from genital and oropharyngeal samples where these both species can coexist.}, } @article {pmid29479025, year = {2018}, author = {}, title = {[Symposium].}, journal = {Nihon saikingaku zasshi. Japanese journal of bacteriology}, volume = {73}, number = {1}, pages = {6-20}, doi = {10.3412/jsb.73.6}, pmid = {29479025}, issn = {1882-4110}, mesh = {Animals ; Antibiosis ; Clostridium ; Fungi/pathogenicity ; *Gastrointestinal Microbiome/genetics/physiology ; Gastrointestinal Tract/metabolism/*microbiology ; Host Microbial Interactions/physiology ; Humans ; Infant, Newborn ; Microbiology/*organization & administration ; Parkinson Disease ; Societies, Scientific/*organization & administration ; Symbiosis ; alpha-Synuclein ; }, } @article {pmid29479020, year = {2018}, author = {}, title = {[Luncheon Seminar].}, journal = {Nihon saikingaku zasshi. Japanese journal of bacteriology}, volume = {73}, number = {1}, pages = {154-155}, doi = {10.3412/jsb.73.154}, pmid = {29479020}, issn = {1882-4110}, mesh = {Bacteria/genetics ; Gastrointestinal Microbiome ; Genome, Bacterial/genetics ; Humans ; Japan/epidemiology ; Microbiology/*organization & administration ; Phylogeny ; Publishing ; Research Personnel ; Serotyping ; Societies, Scientific/*organization & administration ; Symbiosis ; Syphilis/epidemiology ; Whole Genome Sequencing ; }, } @article {pmid29330177, year = {2018}, author = {Zhu, YX and Song, YL and Zhang, YK and Hoffmann, AA and Zhou, JC and Sun, JT and Hong, XY}, title = {Incidence of Facultative Bacterial Endosymbionts in Spider Mites Associated with Local Environments and Host Plants.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {6}, pages = {}, pmid = {29330177}, issn = {1098-5336}, mesh = {Animals ; Bacteroidetes/*physiology ; China ; Environment ; Lycopersicon esculentum/growth & development ; Soybeans/growth & development ; Spiroplasma/*physiology ; *Symbiosis ; Tetranychidae/*microbiology/physiology ; Wolbachia/*physiology ; Zea mays/growth & development ; }, abstract = {Spider mites are frequently associated with multiple endosymbionts whose infection patterns often exhibit spatial and temporal variation. However, the association between endosymbiont prevalence and environmental factors remains unclear. Here, we surveyed endosymbionts in natural populations of the spider mite, Tetranychus truncatus, in China, screening 935 spider mites from 21 localities and 12 host plant species. Three facultative endosymbiont lineages, Wolbachia, Cardinium, and Spiroplasma, were detected at different infection frequencies (52.5%, 26.3%, and 8.6%, respectively). Multiple endosymbiont infections were observed in most local populations, and the incidence of individuals with the Wolbachia-Spiroplasma coinfection was higher than expected from the frequency of each infection within a population. Endosymbiont infection frequencies exhibited associations with environmental factors: Wolbachia infection rates increased at localities with higher annual mean temperatures, while Cardinium and Spiroplasma infection rates increased at localities from higher altitudes. Wolbachia was more common in mites from Lycopersicon esculentum and Glycine max compared to those from Zea mays This study highlights that host-endosymbiont interactions may be associated with environmental factors, including climate and other geographically linked factors, as well as the host's food plant.IMPORTANCE The aim of this study was to examine the incidence of endosymbiont distribution and the infection patterns in spider mites. The main findings are that multiple endosymbiont infections were more common than expected and that endosymbiont infection frequencies were associated with environmental factors. This work highlights that host-endosymbiont interactions need to be studied within an environmental and geographic context.}, } @article {pmid29250734, year = {2018}, author = {Martín-Vivaldi, M and Soler, JJ and Martínez-García, Á and Arco, L and Juárez-García-Pelayo, N and Ruiz-Rodríguez, M and Martínez-Bueno, M}, title = {Acquisition of Uropygial Gland Microbiome by Hoopoe Nestlings.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {285-297}, pmid = {29250734}, issn = {1432-184X}, support = {CGL2009-14006//Ministerio de Ciencia e Innovación/ ; CGL2010-19233-C03-01//Ministerio de Ciencia e Innovación/ ; CGL2010-19233-C03-03//Ministerio de Ciencia e Innovación/ ; CGL2013-48193-C3-1-P//Ministerio de Ciencia e Innovación/ ; CGL2013-48193-C3-2-P//Ministerio de Ciencia e Innovación/ ; P09-RNM-4557//Agencia de Innovación y Desarrollo de Andalucía/ ; Predoctoral grant P09-RNM-4557//Agencia de Innovación y Desarrollo de Andalucía/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Load ; Bacterial Physiological Phenomena ; Biodiversity ; Biological Coevolution ; Birds/*microbiology/physiology ; DNA, Bacterial/genetics ; Exocrine Glands/*microbiology ; Female ; Microbiota/*physiology ; Molecular Typing ; Nesting Behavior/*physiology ; Phylogeny ; Spain ; Symbiosis ; }, abstract = {Mutualistic symbioses between animals and bacteria depend on acquisition of appropriate symbionts while avoiding exploitation by non-beneficial microbes. The mode of acquisition of symbionts would determine, not only the probability of encountering but also evolutionary outcomes of mutualistic counterparts. The microbiome inhabiting the uropygial gland of the European hoopoe (Upupa epops) includes a variety of bacterial strains, some of them providing antimicrobial benefits. Here, the mode of acquisition and stability of this microbiome is analyzed by means of Automated rRNA Intergenic Spacer Analysis and two different experiments. The first experiment impeded mothers' access to their glands, thus avoiding direct transmission of microorganisms from female to offspring secretions. The second experiment explored the stability of the microbiomes by inoculating glands with secretions from alien nests. The first experiment provoked a reduction in similarity of microbiomes of mother and nestlings. Interestingly, some bacterial strains were more often detected when females had not access to their glands, suggesting antagonistic effects among bacteria from different sources. The second experiment caused an increase in richness of the microbiome of receivers in terms of prevalence of Operational Taxonomic Units (OTUs) that reduced differences in microbiomes of donors and receivers. That occurred because OTUs that were present in donors but not in receivers incorporated to the microbiome of the latter, which provoked that cross-inoculated nestlings got similar final microbiomes that included the most prevalent OTUs. The results are therefore consistent with a central role of vertical transmission in bacterial acquisition by nestling hoopoes and support the idea that the typical composition of the hoopoe gland microbiome is reached by the incorporation of some bacteria during the nestling period. This scenario suggests the existence of a coevolved core microbiome composed by a mix of specialized vertically transmitted strains and facultative symbionts able to coexist with them. The implications of this mixed mode of transmission for the evolution of the mutualism are discussed.}, } @article {pmid28320556, year = {2017}, author = {Gutierrez, AC and Tornesello-Galván, J and Manfrino, RG and Hipperdinger, M and Falvo, M and D'Alessandro, C and López Lastra, CC}, title = {[Organization and preservation of the collection of pathogenic and fungal symbionts of insects and other arthropods from CEPAVE (CONICET-UNLP), La Plata, Argentina].}, journal = {Revista Argentina de microbiologia}, volume = {49}, number = {2}, pages = {183-188}, doi = {10.1016/j.ram.2016.09.007}, pmid = {28320556}, issn = {0325-7541}, mesh = {Animals ; Argentina ; *Arthropods/microbiology ; *Ascomycota/isolation & purification ; *Insecta/microbiology ; Preservation, Biological ; *Symbiosis ; }, abstract = {The collection of fungal pathogens and symbionts of insects and other arthropods of the Centro de Estudios Parasitológicos y de Vectores, La Plata, Argentina, is unique because it preserves in vivo and in vitro cultures of fungal pathogens. This culture collection is open for research, teaching, consulting services, and strain deposit. It contains 421 strains belonging to 23 genera (16 Ascomycota, 4 Entomophthoromycotina, 2 Glomeromycota and 1 Oomycota), and the cultures are preserved by different methods such as cryopreservation in freezer at -20°C and -70°C, paper, distilled water and lyophilization. Fungi were isolated from insects, other arthropods, and soil (by using insect baits and selective media). Species were identified by morphological features and in a few strains by molecular taxonomy (PCR of rDNA). This collection is a reference center for species identification/certifications, research and teaching purposes, strain deposit, transference and consultancy services, and its overall goal is to preserve the fungal germplasm and ex situ diversity. Most of the strains are native of Argentina. The collection was originated in 1988 and is registered in the Latin American Federation for Culture Collections and in the World Federation of Culture Collections.}, } @article {pmid30737512, year = {2019}, author = {Ivanov, S and Austin, J and Berg, RH and Harrison, MJ}, title = {Extensive membrane systems at the host-arbuscular mycorrhizal fungus interface.}, journal = {Nature plants}, volume = {5}, number = {2}, pages = {194-203}, doi = {10.1038/s41477-019-0364-5}, pmid = {30737512}, issn = {2055-0278}, abstract = {During arbuscular mycorrhizal (AM) symbiosis, cells within the root cortex develop a matrix-filled apoplastic compartment in which differentiated AM fungal hyphae called arbuscules reside. Development of the compartment occurs rapidly, coincident with intracellular penetration and rapid branching of the fungal hypha, and it requires much of the plant cell's secretory machinery to generate the periarbuscular membrane that delimits the compartment. Despite recent advances, our understanding of the development of the periarbuscular membrane and the transfer of molecules across the symbiotic interface is limited. Here, using electron microscopy and tomography, we reveal that the periarbuscular matrix contains two types of membrane-bound compartments. We propose that one of these arises as a consequence of biogenesis of the periarbuscular membrane and may facilitate movement of molecules between symbiotic partners. Additionally, we show that the arbuscule contains massive arrays of membrane tubules located between the protoplast and the cell wall. We speculate that these tubules may provide the absorptive capacity needed for nutrient assimilation and possibly water absorption to enable rapid hyphal expansion.}, } @article {pmid30737510, year = {2019}, author = {Limpens, E}, title = {Extracellular membranes in symbiosis.}, journal = {Nature plants}, volume = {5}, number = {2}, pages = {131-132}, doi = {10.1038/s41477-019-0370-7}, pmid = {30737510}, issn = {2055-0278}, } @article {pmid30734808, year = {2019}, author = {Abreu, I and Mihelj, P and Raimunda, D}, title = {Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles.}, journal = {Metallomics : integrated biometal science}, volume = {}, number = {}, pages = {}, doi = {10.1039/c8mt00372f}, pmid = {30734808}, issn = {1756-591X}, abstract = {A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.}, } @article {pmid30733794, year = {2018}, author = {Satyanarayana, SDV and Krishna, MSR and Pavan Kumar, P and Jeereddy, S}, title = {In silico structural homology modeling of nif A protein of rhizobial strains in selective legume plants.}, journal = {Journal, genetic engineering & biotechnology}, volume = {16}, number = {2}, pages = {731-737}, doi = {10.1016/j.jgeb.2018.06.006}, pmid = {30733794}, issn = {2090-5920}, abstract = {Symbiosis is a complex genetic regulatory biological evolution which is highly specific pertaining to plant species and microbial strains. Biological nitrogen fixation in legumes is a functional combination of nodulation by nod genes and regulation by nif, fix genes. Three rhizobial strains (Rhizobium leguminosarum, Bradyrhizobium japonicum, and Mesorhizobium ciceri) that we considered for in silico analysis of nif A are proved to be the best isolates with respect to N2 fixing for ground nut, chick pea and soya bean (in vitro) out of 47 forest soil samples. An attempt has been made to understand the structural characteristics and variations of nif genes that may reveal the factors influencing the nitrogen fixation. The primary, secondary and tertiary structure of nif A protein was analyzed by using multiple bioinformatics tools such as chou-Fasman, GOR, ExPasy ProtParam tools, Prosa -web. Literature shows that the homology modeling of nif A protein have not been explored yet which insisted the immediate development for better understanding of nif A structure and its influence on biological nitrogen fixation. In the present predicted 3D structure, the nif A protein was analyzed by three different software tools (Phyre2, Swiss model, Modeller) and validated accordingly which can be considered as an acceptable model. However further in silico studies are suggested to determine the specific factors responsible for nitrogen fixing in the present three rhizobial strains.}, } @article {pmid30727226, year = {2012}, author = {Eskalen, A and Gonzalez, A and Wang, DH and Twizeyimana, M and Mayorquin, JS and Lynch, SC}, title = {First Report of a Fusarium sp. and Its Vector Tea Shot Hole Borer (Euwallacea fornicatus) Causing Fusarium Dieback on Avocado in California.}, journal = {Plant disease}, volume = {96}, number = {7}, pages = {1070}, doi = {10.1094/PDIS-03-12-0276-PDN}, pmid = {30727226}, issn = {0191-2917}, abstract = {Per capita consumption of avocado in the United States has nearly doubled between 2000 and 2010. The California avocado industry supplies almost 40% of U.S. demand and the remaining 60% is supplied by imports from Latin America and New Zealand. The Tea Shot Hole Borer (TSHB) is an ambrosia beetle from Asia that forms a symbiosis with a new, yet undescribed Fusarium sp. and is a serious problem for the Israeli avocado industry (3). The beetle also causes severe damage on the branches of tea (Camelia sinensis) in Sri Lanka and India (1). In California, TSHB was first reported on black locust (Robinia pseudoacacia) in 2003, but there are no records of fungal damage (4). In 2012, nine backyard avocado trees (cvs. Hass, Bacon, Fuerte, and Nabal) exhibiting branch dieback were observed throughout the residential neighborhoods of South Gate, Downey, and Pico Rivera in Los Angeles County. Upon inspection, symptoms of white powdery exudate, either dry or surrounded by wet discoloration of the outer bark in association with a single beetle exit hole, were found on the trunk and main branches of the tree. Examination of the cortex and wood under the exit hole revealed brown discolored necrosis. The TSHB was also found within galleries that were 1 to 4 cm long going against the grain. Symptomatic cortex and sapwood tissues were plated onto potato dextrose agar amended with 0.01% tetracycline (PDA-tet). The TSHB was dissected and plated onto PDA-tet after surface disinfestation following methods described by Kajimura and Hijii (2). After 5 days of incubation at room temperature, regular fungal colonies with aerial mycelia and reddish brown margins were produced. Single spore isolations were used to establish pure culture of the fungus. Fifty conidia were hyaline, clavate with a rounded apex, and initially aseptate (4.1 to 12.0 × 2.4 to 4.1 μm) becoming one- to three-septate (7.6 to 15.1 × 2.8 to 4.5 μm, 9.2 to 17.2 × 3.4 to 4.8 μm, and 13.5 to 17.6 × 4.3 to 4.7 μm, respectively). Identity of the fungal isolates was determined by amplification of the rDNA genes with primers ITS4/5 and EF1/2, respectively. Sequences were deposited into GenBank under Accession Nos. JQ723753, JQ723760, JQ723756, and JQ723763. A BLASTn search revealed 100% similarity to Fusarium sp. (Accession Nos. JQ038020 and JQ038013). Detached green shoots of healthy 1-year-old avocado were wounded to a depth of 1 to 2 mm and 5-mm mycelial plugs from 5-day-old cultures (UCR 1781 and UCR 1837) were placed mycelial side down onto the freshly wounded surfaces and then wrapped with Parafilm. Control shoots were inoculated with sterile agar plugs and five replicates per treatment were used. Shoots were incubated at 25 ± 1°C in moist chambers for 3 weeks. Lesions were observed on all inoculated shoots except for the control. Mean lesion lengths were 10.7 and 12.8 cm for UCR1781 and UCR1837, respectively, and were significantly different (P ≤ 0.05) from the control. Both isolates were reisolated from 100% of symptomatic tissues of inoculated shoots to complete Koch's postulates. This experiment was conducted twice and similar results were obtained. To our knowledge, this is the first report of Fusarium sp. and its vector E. fornicatus causing Fusarium dieback on Avocado in California. References: (1) W. Danthanarayana. Tea Quarterly 39:61, 1968. (2) H. Kajimura and N. Hijii. Ecol. Res. 7:107, 1992; (3) Mendel et al., Phytoparasitica, DOI 10.1007/s12600-012-0223-7, 2012. (4) R. J. Rabaglia. Annals Entomol. Soc. Amer. 99:1034, 2006.}, } @article {pmid30731202, year = {2019}, author = {Chujo, T and Lukito, Y and Eaton, CJ and Dupont, PY and Johnson, LJ and Winter, D and Cox, MP and Scott, B}, title = {Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis.}, journal = {Fungal genetics and biology : FG & B}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fgb.2019.02.001}, pmid = {30731202}, issn = {1096-0937}, abstract = {Epichloë festucae forms mutualistic symbiotic interactions with grasses of the Lolium and Festuca genera. Protection from insect and mammalian herbivory are the best-documented host benefits of these associations. The two main classes of anti-mammalian alkaloids synthesized by E. festucae are the ergot alkaloids and indole diterpenes, of which ergovaline and lolitrems are the principal terminal products. Synthesis of both metabolites require multiple gene products encoded by clusters of 11 genes located at the subtelomeric regions of chromosomes I and III respectively. These loci are essentially unexpressed in axenic culture but among the most highly expressed genes in planta. We show here that heterochromatin 1 protein (HepA) is an important component of the regulatory machinery that maintains these loci in a silent state in culture. Deletion of this gene led to derepression of eas and ltm gene expression under non-symbiotic culture conditions. Although there was no obvious culture phenotype, RNAseq analysis revealed that around 1000 genes were differentially expressed in the ΔhepA mutant compared to wild type with just one-third upregulated. Inoculation of the ΔhepA mutants into seedlings of Lolium perenne led to a severe host interaction phenotype characterized by a reduction in tiller length but an increase in tiller number. Hyphae within the leaves of these associations were much more abundant in the intercellular spaces of the leaves and aberrantly colonized the vascular bundles. This physiological change was accompanied by a dramatic change in the transcriptome with around 900 genes differentially expressed, with two thirds of these upregulated. This major physiological change was accompanied by a decrease in ltm gene expression and loss of the ability to synthesize lolitrems. These results show that HepA has an important role in controlling the chromatin state of these sub-telomeric secondary metabolite genes, including their symbiosis-specific regulation.}, } @article {pmid30730567, year = {2019}, author = {Li, C and Zhou, J and Wang, X and Liao, H}, title = {A purple acid phosphatase, GmPAP33, participates in arbuscule degeneration during AM symbiosis in soybean.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13530}, pmid = {30730567}, issn = {1365-3040}, abstract = {Arbuscules are the central structures of the symbiotic association between terrestrial plants and arbuscular mycorrhizal (AM) fungi. However, arbuscules are also ephemeral structures, and following development, these structures are soon digested and ultimately disappear. Currently, little is known regarding the mechanism underlying the digestion of senescent arbuscules. Here, biochemical and functional analyses were integrated to test the hypothesis that a purple acid phosphatase, GmPAP33, controls the hydrolysis of phospholipids during arbuscule degeneration. The expression of GmPAP33 was enhanced by AM fungal inoculation independent of the P conditions in soybean roots. Promoter-GUS reporter assays revealed that the expression of GmPAP33 was mainly localized to arbuscule-containing cells during symbiosis. The recombinant GmPAP33 exhibited high hydrolytic activity toward phospholipids, phosphatidylcholine and phosphatidic acid. Furthermore, soybean plants overexpressing GmPAP33 exhibited increased percentages of large arbuscules and improved yield and P content compared to wild-type plants when inoculated with AM fungi. Mycorrhizal RNAi plants had high phospholipid levels and a large percentage of small arbuscules. These results in combination with the subcellular localization of GmPAP33 at the plasma membrane indicate that GmPAP33 participates in arbuscule degeneration during AM symbiosis via involvement in phospholipid hydrolysis.}, } @article {pmid30729580, year = {2019}, author = {}, title = {Kalliope Papadopoulou.}, journal = {The New phytologist}, volume = {221}, number = {4}, pages = {1701-1702}, doi = {10.1111/nph.15622}, pmid = {30729580}, issn = {1469-8137}, } @article {pmid30727955, year = {2019}, author = {Détrée, C and Haddad, I and Demey-Thomas, E and Vinh, J and Lallier, FH and Tanguy, A and Mary, J}, title = {Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {109}, doi = {10.1186/s12864-019-5456-0}, pmid = {30727955}, issn = {1471-2164}, abstract = {BACKGROUND: Colonization of deep-sea hydrothermal vents by most invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers in these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts loss on the deep-sea mussel Bathymodiolus azoricus' molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels.

RESULTS: Global proteomic and transcriptomic results evidenced a global disruption of host machinery in aposymbiotic organisms. We observed that the total number of proteins identified decreased from 1118 in symbiotic mussels to 790 in partially depleted mussels and 761 in aposymbiotic mussels. Using microarrays we identified 4300 transcripts differentially expressed between symbiont-depleted and symbiotic mussels. Among these transcripts, 799 were found differentially expressed in aposymbiotic mussels and almost twice as many in symbiont-depleted mussels as compared to symbiotic mussels. Regarding apoptotic and immune system processes - known to be largely involved in symbiotic interactions - an overall up-regulation of associated proteins and transcripts was observed in symbiont-depleted mussels.

CONCLUSION: Overall, our study showed a global impairment of host machinery and an activation of both the immune and apoptotic system following symbiont-depletion. One of the main assumptions is the involvement of symbiotic bacteria in the inhibition and regulation of immune and apoptotic systems. As such, symbiotic bacteria may increase their lifespan in gill cells while managing the defense of the holobiont against putative pathogens.}, } @article {pmid30722538, year = {2013}, author = {Eskalen, A and Stouthamer, R and Lynch, SC and Rugman-Jones, PF and Twizeyimana, M and Gonzalez, A and Thibault, T}, title = {Host Range of Fusarium Dieback and Its Ambrosia Beetle (Coleoptera: Scolytinae) Vector in Southern California.}, journal = {Plant disease}, volume = {97}, number = {7}, pages = {938-951}, doi = {10.1094/PDIS-11-12-1026-RE}, pmid = {30722538}, issn = {0191-2917}, abstract = {The polyphagous shot hole borer (PSHB) is an invasive ambrosia beetle that forms a symbiosis with a new, as-yet-undescribed Fusarium sp., together causing Fusarium dieback on avocado and other host plants in California and Israel. In California, PSHB was first reported on black locust in 2003 but there were no records of fungal damage until 2012, when a Fusarium sp. was recovered from the tissues of several backyard avocado trees infested with PSHB in Los Angeles County. The aim of this study was to determine the plant host range of the beetle-fungus complex in two heavily infested botanical gardens in Los Angeles County. Of the 335 tree species observed, 207 (62%), representing 58 plant families, showed signs and symptoms consistent with attack by PSHB. The Fusarium sp. was recovered from 54% of the plant species attacked by PSHB, indicated by the presence of the Fusarium sp. at least at the site of the entry hole. Trees attacked by PSHB included 11 species of California natives, 13 agriculturally important species, and many common street trees. Survey results also revealed 19 tree species that function as reproductive hosts for PSHB. Additionally, approximately a quarter of all tree individuals planted along the streets of southern California belong to a species classified as a reproductive host. These data suggest the beetle-disease complex potentially may establish in a variety of plant communities locally and worldwide.}, } @article {pmid30648935, year = {2019}, author = {Soto, W and Travisano, M and Tolleson, AR and Nishiguchi, MK}, title = {Symbiont evolution during the free-living phase can improve host colonization.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {2}, pages = {174-187}, doi = {10.1099/mic.0.000756}, pmid = {30648935}, issn = {1465-2080}, abstract = {For micro-organisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether evolution during the free-living stage can be positively pleiotropic to microbial fitness in a host environment. To address this topic, the squid host Euprymna tasmanica and the marine bioluminescent bacterium Vibrio fischeri were utilized. Microbial ecological diversification in static liquid microcosms was used to simulate symbiont evolution during the free-living stage. Thirteen genetically distinct V. fischeri strains from a broad diversity of ecological sources (e.g. squid light organs, fish light organs and seawater) were examined to see if the results were reproducible in many different genetic settings. Genetic backgrounds that are closely related can be predisposed to considerable differences in how they respond to similar selection pressures. For all strains examined, new mutations with striking and facilitating effects on host colonization arose quickly during microbial evolution in the free-living stage, regardless of the ecological context under consideration for a strain's genetic background. Microbial evolution outside a host environment promoted host range expansion, improved host colonization for a micro-organism, and diminished the negative correlation between biofilm formation and motility.}, } @article {pmid30420273, year = {2019}, author = {Ueki, T and Fujie, M and Romaidi, and Satoh, N}, title = {Symbiotic bacteria associated with ascidian vanadium accumulation identified by 16S rRNA amplicon sequencing.}, journal = {Marine genomics}, volume = {43}, number = {}, pages = {33-42}, doi = {10.1016/j.margen.2018.10.006}, pmid = {30420273}, issn = {1876-7478}, mesh = {Animals ; Bacteria/*classification/genetics ; Japan ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; Species Specificity ; *Symbiosis ; Urochordata/microbiology/*physiology ; Vanadium/metabolism ; }, abstract = {Ascidians belonging to Phlebobranchia accumulate vanadium to an extraordinary degree (≤ 350 mM). Vanadium levels are strictly regulated and vary among ascidian species; thus, they represent well-suited models for studies on vanadium accumulation. No comprehensive study on metal accumulation and reduction in marine organisms in relation to their symbiotic bacterial communities has been published. Therefore, we performed comparative 16S rRNA amplicon sequence analyses on samples from three tissues (branchial sac, intestine, and intestinal lumen) involved in vanadium absorption, isolated from two vanadium-rich (Ascidia ahodori and Ascidia sydneiensis samea) and one vanadium-poor species (Styela plicata). For each sample, the abundance of every bacteria and an abundance value normalized to their abundance in seawater were calculated and compared. Two bacterial genera, Pseudomonas and Ralstonia, were extremely abundant in the branchial sacs of vanadium-rich ascidians. Two bacterial genera, Treponema and Borrelia, were abundant and enriched in the intestinal content of vanadium-rich ascidians. The results suggest that specific selective forces maintain the bacterial population in the three ascidian tissues examined, which contribute to successful vanadium accumulation. This study furthers the understanding of the relationship between bacterial communities and metal accumulation in marine life.}, } @article {pmid30398151, year = {2018}, author = {Rolig, AS and Sweeney, EG and Kaye, LE and DeSantis, MD and Perkins, A and Banse, AV and Hamilton, MK and Guillemin, K}, title = {A bacterial immunomodulatory protein with lipocalin-like domains facilitates host-bacteria mutualism in larval zebrafish.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30398151}, issn = {2050-084X}, support = {P01 HD022486/HD/NICHD NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; P01HD22486//Eunice Kennedy Shriver National Institute of Child Health and Human Development/International ; P50GM098911/GM/NIGMS NIH HHS/United States ; F32DK098884/DK/NIDDK NIH HHS/United States ; }, mesh = {Aeromonas/*genetics ; Animals ; Host-Pathogen Interactions/*genetics/immunology ; Immunity, Innate/*genetics ; Intestines/immunology/microbiology ; Larva/immunology/microbiology ; Lipocalins/genetics/immunology ; Protein Domains/genetics ; Symbiosis/*genetics/immunology ; Zebrafish/immunology/microbiology ; }, abstract = {Stable mutualism between a host and its resident bacteria requires a moderated immune response to control bacterial population size without eliciting excessive inflammation that could harm both partners. Little is known about the specific molecular mechanisms utilized by bacterial mutualists to temper their hosts' responses and protect themselves from aggressive immune attack. Using a gnotobiotic larval zebrafish model, we identified an Aeromonas secreted immunomodulatory protein, AimA. AimA is required during colonization to prevent intestinal inflammation that simultaneously compromises both bacterial and host survival. Administration of exogenous AimA prevents excessive intestinal neutrophil accumulation and protects against septic shock in models of both bacterially and chemically induced intestinal inflammation. We determined the molecular structure of AimA, which revealed two related calycin-like domains with structural similarity to the mammalian immune modulatory protein, lipocalin-2. As a secreted bacterial protein required by both partners for optimal fitness, AimA is an exemplar bacterial mutualism factor.}, } @article {pmid30223906, year = {2018}, author = {Bredon, M and Dittmer, J and Noël, C and Moumen, B and Bouchon, D}, title = {Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {162}, pmid = {30223906}, issn = {2049-2618}, mesh = {Animals ; Bacteria/enzymology/genetics/isolation & purification ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; Isopoda/*metabolism/*microbiology/physiology ; Lignin/*metabolism ; Phylogeny ; Soil/parasitology ; *Symbiosis ; }, abstract = {BACKGROUND: Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts.

RESULTS: To test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare.

CONCLUSIONS: Our results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.}, } @article {pmid30223892, year = {2018}, author = {Sitaraman, R}, title = {Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {163}, pmid = {30223892}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bacterial Physiological Phenomena ; *Biological Evolution ; *Gene Transfer, Horizontal ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.}, } @article {pmid30153277, year = {2018}, author = {Diplock, N and Johnston, K and Mellon, A and Mitchell, L and Moore, M and Schneider, D and Taylor, A and Whitney, J and Zegar, K and Kioko, J and Kiffner, C}, title = {Large mammal declines and the incipient loss of mammal-bird mutualisms in an African savanna ecosystem.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202536}, pmid = {30153277}, issn = {1932-6203}, mesh = {Animals ; *Birds ; *Ecosystem ; Grassland ; Humans ; *Mammals ; Symbiosis/*physiology ; Tanzania/epidemiology ; }, abstract = {Over the past half-century, large mammal populations have declined substantially throughout East Africa, mainly due to habitat loss and unsustainable direct exploitation. While it has been acknowledged that the loss of large mammals can have direct and cascading effects on community composition and ecosystem characteristics, limited quantitative work has been done on how declines of large herbivore populations impacts the abundance of mutualistic symbionts. Using a space-for-time observational approach, we quantified the large mammal community alongside the densities, host preferences and behaviors of mutualistic red-billed oxpeckers (Buphagus erythrorhynchus), and yellow-billed oxpeckers (Buphagus africanus) in northern Tanzania. At the landscape scale, mammal community composition was substantially less diverse in highly human-dominated areas when compared with more protected areas, with an observed complete loss of large wild mammal species in two study areas. Mirroring this trend, oxpecker densities were lowest in the least protected areas, and highest in fully protected areas. Using resource selection functions implemented via generalized linear models at different scales, we found that oxpeckers (1) were predominantly (67% of red-billed oxpeckers; 70% of yellow-billed oxpeckers) feeding on larger (between 500kg and 1500kg) ungulate host species within the mammal community, (2) usually preferred feeding on larger individuals (adults and males) within a specific host species population, and (3) preferred hosts that were more tolerant of their presence. In particular, cattle were especially intolerant of oxpecker presence and were relatively effective in displacing oxpeckers. We found little evidence that oxpecker feeding was parasitic across all host species; wound feeding was only observed on giraffe, comprising 6% and 4% of feeding behavior in red-billed and yellow-billed oxpeckers respectively. Thus, a loss of large-bodied and oxpecker tolerant host species is a likely explanation for declines of oxpecker populations in human dominated landscapes, which may have further cascading effects.}, } @article {pmid29297160, year = {2018}, author = {Janashia, I and Choiset, Y and Jozefiak, D and Déniel, F and Coton, E and Moosavi-Movahedi, AA and Chanishvili, N and Haertlé, T}, title = {Beneficial Protective Role of Endogenous Lactic Acid Bacteria Against Mycotic Contamination of Honeybee Beebread.}, journal = {Probiotics and antimicrobial proteins}, volume = {10}, number = {4}, pages = {638-646}, pmid = {29297160}, issn = {1867-1314}, mesh = {Animals ; Antibiosis ; Bees/*microbiology ; Fungi/classification/growth & development/*isolation & purification/physiology ; Lactobacillales/genetics/*physiology ; Symbiosis ; }, abstract = {The purpose of this article is to reveal the role of the lactic acid bacteria (LAB) in the beebread transformation/preservation, biochemical properties of 25 honeybee endogenous LAB strains, particularly: antifungal, proteolytic, and amylolytic activities putatively expressed in the beebread environment have been studied. Seventeen fungal strains isolated from beebread samples were identified and checked for their ability to grow on simulated beebread substrate (SBS) and then used to study mycotic propagation in the presence of LAB. Fungal strains identified as Aspergillus niger (Po1), Candida sp. (BB01), and Z. rouxii (BB02) were able to grow on SBS. Their growth was partly inhibited when co-cultured with the endogenous honeybee LAB strains studied. No proteolytic or amylolytic activities of the studied LAB were detected using pollen, casein starch based media as substrates. These findings suggest that some honeybee LAB symbionts are involved in maintaining a safe microbiological state in the host honeybee colonies by inhibiting beebread mycotic contaminations, starch, and protein predigestion in beebread by LAB is less probable. Honeybee endogenous LAB use pollen as a growth substrate and in the same time restricts fungal propagation, thus showing host beneficial action preserving larval food. This study also can have an impact on development of novel methods of pollen preservation and its processing as a food ingredient.}, } @article {pmid29249193, year = {2017}, author = {Schwartz, WJ}, title = {Embodied Clocks.}, journal = {Journal of biological rhythms}, volume = {32}, number = {6}, pages = {503-504}, doi = {10.1177/0748730417748381}, pmid = {29249193}, issn = {1552-4531}, mesh = {Animals ; Circadian Clocks/*physiology ; Decapodiformes/*microbiology/*physiology/radiation effects ; Light ; Models, Biological ; *Symbiosis ; Vibrio/*physiology ; }, } @article {pmid29228264, year = {2018}, author = {Porter, SS and Faber-Hammond, JJ and Friesen, ML}, title = {Co-invading symbiotic mutualists of Medicago polymorpha retain high ancestral diversity and contain diverse accessory genomes.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {1}, pages = {}, doi = {10.1093/femsec/fix168}, pmid = {29228264}, issn = {1574-6941}, mesh = {Animals ; Biological Evolution ; California ; Ecosystem ; Europe ; Genome, Bacterial/genetics ; *Introduced Species ; Medicago/*microbiology ; Rhizobium/genetics ; Root Nodules, Plant/*microbiology ; Sinorhizobium/*classification/genetics/*isolation & purification ; Symbiosis/genetics ; }, abstract = {Exotic, invasive plants and animals can wreak havoc on ecosystems by displacing natives and altering environmental conditions. However, much less is known about the identities or evolutionary dynamics of the symbiotic microbes that accompany invasive species. Most leguminous plants rely upon symbiotic rhizobium bacteria to fix nitrogen and are incapable of colonizing areas devoid of compatible rhizobia. We compare the genomes of symbiotic rhizobia in a portion of the legume's invaded range with those of the rhizobium symbionts from across the legume's native range. We show that in an area of California the legume Medicago polymorpha has invaded, its Ensifer medicae symbionts: (i) exhibit genome-wide patterns of relatedness that together with historical evidence support host-symbiont co-invasion from Europe into California, (ii) exhibit population genomic patterns consistent with the introduction of the majority of deep diversity from the native range, rather than a genetic bottleneck during colonization of California and (iii) harbor a large set of accessory genes uniquely enriched in binding functions, which could play a role in habitat invasion. Examining microbial symbiont genome dynamics during biological invasions is critical for assessing host-symbiont co-invasions whereby microbial symbiont range expansion underlies plant and animal invasions.}, } @article {pmid29192362, year = {2018}, author = {Bidartondo, MI and Hijri, M}, title = {The Ninth International Conference on Mycorrhiza in Prague: across mycorrhizal symbioses from molecules to global scales.}, journal = {Mycorrhiza}, volume = {28}, number = {2}, pages = {203-205}, doi = {10.1007/s00572-017-0804-x}, pmid = {29192362}, issn = {1432-1890}, mesh = {Congresses as Topic ; Czech Republic ; Mycorrhizae/*physiology ; *Symbiosis ; }, } @article {pmid30726794, year = {2019}, author = {Matsuoka, JI and Ishizuna, F and Ogawa, T and Hidaka, M and Siarot, L and Aono, T}, title = {Localization of the reb operon expression is inconsistent with that of the R-body production in the stem nodules formed by Azorhizobium caulinodans mutants having a deletion of praR.}, journal = {The Journal of general and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2323/jgam.2018.09.003}, pmid = {30726794}, issn = {1349-8037}, abstract = {Azorhizobium caulinodans, a kind of rhizobia, has a reb operon encoding pathogenic R-body components, whose expression is usually repressed by a transcription factor PraR. Mutation on praR induced a high expression of reb operon and the formation of aberrant nodules, in which both morphologically normal and shrunken host cells were observed. Histochemical GUS analyses of praR mutant expressing reb operon-uidA fusion revealed that the bacterial cells within the normal host cells highly expressed the reb operon, but rarely produced R-bodies. On the other hand, the bacterial cells within the shrunken host cells frequently produced R-bodies but rarely expressed the reb operon. This suggests that R-body production is not only regulated at the transcriptional level, but by other regulatory mechanisms as well.}, } @article {pmid30726789, year = {2019}, author = {Hashami, SZ and Nakamura, H and Ohkama-Ohtsu, N and Kojima, K and Djedidi, S and Fukuhara, I and Haidari, MD and Sekimoto, H and Yokoyama, T}, title = {Evaluation of Immune Responses Induced by Simultaneous Inoculations of Soybean (Glycine max [L.] Merr.) with Soil Bacteria and Rhizobia.}, journal = {Microbes and environments}, volume = {}, number = {}, pages = {}, doi = {10.1264/jsme2.ME18110}, pmid = {30726789}, issn = {1347-4405}, abstract = {Legumes form root nodules and fix atmospheric nitrogen by establishing symbiosis with rhizobia. However, excessive root nodules are harmful to plants because of the resulting overconsumption of energy from photosynthates. The delay of an inoculation of the soybean super-nodulation mutant NOD1-3 with Bradyrhizobium diazoefficiens USDA110T by 5 d after an inoculation with several soil bacteria confirmed that one bacterial group significantly decreased root nodules throughout the study period. Moreover, no significant changes were observed in nitrogen fixation by root nodules between an inoculation with USDA 110T only and co-inoculation treatments. To clarify the potential involvement of PR proteins in the restriction of nodule formation in the plants tested, the relative expression levels of PR-1, PR-2, PR-5, and PDF1.2 in NOD1-3 roots were measured using real-time PCR. One group of soil bacteria (Gr.3), which markedly reduced nodule numbers, significantly induced the expression of PR-1, PR-5 and PDF1.2 genes by day 5 after the inoculation. By days 7, 10, and 20 after the inoculation, the expression levels of PR-2 and PR-5 were lower than those with the uninoculated treatment. Inoculations with this group of soil bacteria resulted in lower root nodule numbers than with other tested soil bacteria exerting weak inhibitory effects on nodulation, and were accompanied by the induction of plant defense-related genes. Thus, PR genes appear to play important roles in the mechanisms that suppresses nodule formation on soybean roots.}, } @article {pmid30723470, year = {2019}, author = {Cohen, IR and Efroni, S}, title = {The Immune System Computes the State of the Body: Crowd Wisdom, Machine Learning, and Immune Cell Reference Repertoires Help Manage Inflammation.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {10}, doi = {10.3389/fimmu.2019.00010}, pmid = {30723470}, issn = {1664-3224}, abstract = {Here, we outline an overview of the mammalian immune system that updates and extends the classical clonal selection paradigm. Rather than focusing on strict self-not-self discrimination, we propose that the system orchestrates variable inflammatory responses that maintain the body and its symbiosis with the microbiome while eliminating the threat from pathogenic infectious agents and from tumors. The paper makes four points: The immune system classifies healthy and pathologic states of the body-including both self and foreign elements-by deploying individual lymphocytes as cellular computing machines; immune cells transform input signals from the body into an output of specific immune reactions.Rather than independent clonal responses, groups of individually activated immune-system cells co-react in lymphoid organs to make collective decisions through a type of self-organizing swarm intelligence or crowd wisdom.Collective choices by swarms of immune cells, like those of schools of fish, are modified by relatively small numbers of individual regulators responding to shifting conditions-such collective inflammatory responses are dynamically responsive.Self-reactive autoantibody and T-cell receptor (TCR) repertoires shared by healthy individuals function in a biological version of experience-based supervised machine learning. Immune system decisions are primed by formative experience with training sets of self-antigens encountered during lymphocyte development; these initially trained T cell and B cell repertoires form a Wellness Profile that then guides immune responses to test sets of antigens encountered later. This experience-based machine learning strategy is analogous to that deployed by supervised machine-learning algorithms. We propose experiments to test these ideas. This overview of the immune system bears clinical implications for monitoring wellness and for treating autoimmune disease, cancer, and allograft reactions.}, } @article {pmid30517219, year = {2018}, author = {Farias, CP and Carvalho, RC and Resende, FML and Azevedo, LCB}, title = {Consortium of five fungal isolates conditioning root growth and arbuscular mycorrhiza in soybean, corn, and sugarcane.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {90}, number = {4}, pages = {3649-3660}, doi = {10.1590/0001-3765201820180161}, pmid = {30517219}, issn = {1678-2690}, mesh = {Mycorrhizae/*physiology ; Plant Roots/*growth & development/microbiology ; Saccharum/*growth & development/microbiology ; Soybeans/*growth & development/microbiology ; Symbiosis ; Zea mays/*growth & development/microbiology ; }, abstract = {Plant growth and arbuscular mycorrhizal colonization were studied in sugarcane, corn and soybean by applying five plant growth promoting fungi: Beauveria bassiana, Metarhizium anisopliae, Pochonia chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperella. Sugarcane, corn and soybean were grown in pots under two treatments: (1) inoculation with the fungal consortium and (2) control without inoculation. In the inoculated treatment, fungal spore suspension were applied to the seeds and shoots were sprayed every 28 days. Means were analyzed by analysis of variance and Tukey's test at 5% probability level. The experiment was arranged in a completely randomized design, with six replications. Fungi consortium mediate root growth in soybean and corn, and arbuscular mycorrhizal colonization in soybean and sugarcane. These findings are probably caused by the fungi producing phytohormones and inducing the plants to synthesize phytohormones: auxins for root growth; and jasmonic, abscisic, and salicylic acids with a role in the regulation of mycorrhizal colonization. These effects are important when seeking conservation strategies in agriculture and livestock production, since Fungi consortium can better mediate soil resource acquisition, promoting greater absorption of nutrients and water.}, } @article {pmid30195930, year = {2019}, author = {St John, E and Liu, Y and Podar, M and Stott, MB and Meneghin, J and Chen, Z and Lagutin, K and Mitchell, K and Reysenbach, AL}, title = {A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {1}, pages = {94-106}, doi = {10.1016/j.syapm.2018.08.005}, pmid = {30195930}, issn = {1618-0984}, mesh = {Desulfurococcaceae/*classification/genetics ; Genome, Archaeal ; Hot Springs/*microbiology ; New Zealand ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Three thermophilic Nanoarchaeota-Crenarchaeota symbiotic systems have been described. We obtained another stable anaerobic enrichment culture at 80°C, pH 6.0 from a New Zealand hot spring. The nanoarchaeote (Ncl-1) and its host (NZ3T) were isolated in co-culture and their genomes assembled. The small (∼200nm) flagellated cocci were often attached to larger cocci. Based on 16S rRNA gene similarity (88.4%) and average amino acid identity (52%), Ncl-1 is closely related to Candidatus Nanopusillus acidilobi. Their genomes both encode for archaeal flagella and partial glycolysis and gluconeogenesis pathways, but lack ATP synthase genes. Like Nanoarchaeum equitans, Ncl-1 has a CRISPR-Cas system. Ncl-1 also relies on its crenarchaeotal host for most of its biosynthetic needs. The host NZ3T was isolated and grows on proteinaceous substrates but not on sugars, alcohols, or fatty acids. NZ3T requires thiosulfate and grows best at 82°C, pH 6.0. NZ3T is most closely related to the Desulfurococcaceae, Ignisphaera aggregans (∼92% 16S rRNA gene sequence similarity, 45% AAI). Based on phylogenetic, physiological and genomic data, Ncl-1 and NZ3T represent novel genera in the Nanoarchaeota and the Desulfurococcaceae, respectively, with the proposed names Candidatus Nanoclepta minutus and Zestosphaera tikiterensis gen. nov., sp. nov., type strain NZ3T (=DSMZ 107634T=OCM 1213T).}, } @article {pmid29924971, year = {2018}, author = {Gefen, T and Geva-Zatorsky, N}, title = {What Came First: The Microbiota or the Tr(egg) Cells?.}, journal = {Immunity}, volume = {48}, number = {6}, pages = {1072-1074}, doi = {10.1016/j.immuni.2018.06.005}, pmid = {29924971}, issn = {1097-4180}, mesh = {Bacteria ; Immunity ; *Microbiota ; Symbiosis ; *T-Lymphocytes, Regulatory ; }, abstract = {Studies have shown that gut commensals facilitate the differentiation of peripheral regulatory T cells (pTregs) via their metabolic products. In this issue of Immunity, Campbell et al. (2018) demonstrate a reciprocal effect of pTregs on the metabolic functions of specific gut commensals that affects their overall energy harvest capacity.}, } @article {pmid29536599, year = {2018}, author = {Correia, M and Heleno, R and Vargas, P and Rodríguez-Echeverría, S}, title = {Should I stay or should I go? Mycorrhizal plants are more likely to invest in long-distance seed dispersal than non-mycorrhizal plants.}, journal = {Ecology letters}, volume = {21}, number = {5}, pages = {683-691}, doi = {10.1111/ele.12936}, pmid = {29536599}, issn = {1461-0248}, mesh = {*Mycorrhizae ; Plants ; *Seed Dispersal ; Seeds ; Symbiosis ; }, abstract = {Seed dispersal and mycorrhizal associations are key mutualisms for the functioning and regeneration of plant communities; however, these processes have seldom been explored together. We hypothesised that obligatory mycorrhizal plants will be less likely to have long-distance dispersal (LDD) syndromes since the probability of finding suitable mycorrhizal partners is likely to decrease with distance to the mother plant. We contrasted the mycorrhizal status and LDD syndromes for 1960 European plant species, using phylogenetically corrected log-linear models. Contrary to our expectation, having specialised structures for LDD is more frequent in obligate mycorrhizal plants than in non-mycorrhizal plants, revealing that lack of compatible mutualists does not constrain investment in LDD structures in the European Flora. Ectomycorrhizal plants associated with wind-dispersing fungi are also more likely to have specialised structures for wind dispersal. Habitat specificity and narrower niche of non-mycorrhizal plants might explain the smaller investment in specialised structures for seed dispersal.}, } @article {pmid29234159, year = {2018}, author = {Zug, R and Hammerstein, P}, title = {Evolution of reproductive parasites with direct fitness benefits.}, journal = {Heredity}, volume = {120}, number = {3}, pages = {266-281}, pmid = {29234159}, issn = {1365-2540}, mesh = {Animals ; Biological Evolution ; Female ; Fertility ; *Genetic Fitness ; Male ; *Models, Genetic ; Parasites/*physiology ; *Reproduction ; *Symbiosis ; }, abstract = {Maternally inherited symbionts such as Wolbachia have long been seen mainly as reproductive parasites, with deleterious effects on host fitness. It is becoming clear, however, that, frequently, these symbionts also have beneficial effects on host fitness, either along with reproductive parasitism or not. Using the examples of cytoplasmic incompatibility (CI) and male-killing (MK), we here analyze the effect of direct fitness benefits on the evolution of reproductive parasites. By means of a simple theoretical framework, we synthesize and extend earlier modeling approaches for CI and MK, which usually ignore fitness benefits. Moreover, our framework is not restricted to a particular mechanism underlying the fitness benefit (e.g., protection against pathogens). We derive invasion conditions and equilibrium frequencies for the different infection scenarios. Our results demonstrate the importance of a symbiont's "effective fecundity" (i.e., the product of the relative fecundity of an infected female and her transmission efficiency) for a symbiont's invasion success. In particular, we adopt the concept of effective fecundity to scenarios where CI and MK co-occur in one host population. We confirm that direct fitness benefits substantially facilitate the invasion and spread of infections (for example, by lowering or removing the invasion threshold) or even make invasion possible in the first place (for example, if reproductive parasitism is weak or absent). Finally, we discuss the role of direct fitness benefits in long-term evolutionary dynamics of reproductive phenotypes and highlight their potential to resolve genetic conflicts between maternally inherited symbionts and their hosts.}, } @article {pmid28611430, year = {2017}, author = {Tsao, HF and Scheikl, U and Volland, JM and Köhsler, M and Bright, M and Walochnik, J and Horn, M}, title = {'Candidatus Cochliophilus cryoturris' (Coxiellaceae), a symbiont of the testate amoeba Cochliopodium minus.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3394}, pmid = {28611430}, issn = {2045-2322}, support = {I 1628//Austrian Science Fund FWF/Austria ; }, mesh = {Amebiasis/*microbiology ; Amoebida/*classification/isolation & purification ; Coxiellaceae/*physiology ; *Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S ; *Symbiosis ; }, abstract = {Free-living amoebae are well known for their role in controlling microbial community composition through grazing, but some groups, namely Acanthamoeba species, also frequently serve as hosts for bacterial symbionts. Here we report the first identification of a bacterial symbiont in the testate amoeba Cochliopodium. The amoeba was isolated from a cooling tower water sample and identified as C. minus. Fluorescence in situ hybridization and transmission electron microscopy revealed intracellular symbionts located in vacuoles. 16S rRNA-based phylogenetic analysis identified the endosymbiont as member of a monophyletic group within the family Coxiellaceae (Gammaprotebacteria; Legionellales), only moderately related to known amoeba symbionts. We propose to tentatively classify these bacteria as 'Candidatus Cochliophilus cryoturris'. Our findings add both, a novel group of amoeba and a novel group of symbionts, to the growing list of bacteria-amoeba relationships.}, } @article {pmid30721680, year = {2019}, author = {Jenkins, B and Richards, TA}, title = {Symbiosis: Wolf Lichens Harbour a Choir of Fungi.}, journal = {Current biology : CB}, volume = {29}, number = {3}, pages = {R88-R90}, doi = {10.1016/j.cub.2018.12.034}, pmid = {30721680}, issn = {1879-0445}, abstract = {Identification of the fungus Tremella as a consistent fourth component of wolf lichens further challenges the conventional view of lichen symbiosis as a mutualistic interaction between two players.}, } @article {pmid30721677, year = {2019}, author = {King, KC}, title = {Defensive symbionts.}, journal = {Current biology : CB}, volume = {29}, number = {3}, pages = {R78-R80}, doi = {10.1016/j.cub.2018.11.028}, pmid = {30721677}, issn = {1879-0445}, abstract = {Interactions in nature vary from competitive to neutral to symbiotic. An interesting case of symbiosis is seen when one organism provides protection to the other-a relationship termed 'defensive symbiosis'. Kayla King highlights this interesting type of relationship, which can be found throughout the tree of life.}, } @article {pmid30719639, year = {2019}, author = {Cornejo Ulloa, P and van der Veen, MH and Krom, BP}, title = {Review: modulation of the oral microbiome by the host to promote ecological balance.}, journal = {Odontology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10266-019-00413-x}, pmid = {30719639}, issn = {1618-1255}, abstract = {The indivisible relationship between the human host and its oral microbiome has been shaped throughout the millennia, by facing various changes that have forced the adaptation of oral microorganisms to new environmental conditions. In this constant crosstalk between the human host and its microbiome, a bidirectional relationship has been established. The microorganisms provide the host with functions it cannot perform on its own and at the same time the host provides its microbes with a suitable environment for their growth and development. These host factors can positively affect the microbiome, promoting diversity and balance between different species, resulting in a state of symbiosis and absence of pathology. In contrast, other host factors can negatively influence the composition of the oral microbiome and drive the interaction towards a dysbiotic state, where the balance tilts towards a harmful relationship between the host and its microbiome. The aim of this review is to describe the role host factors play in cultivating and maintaining a healthy oral ecology and discuss mechanisms that can prevent its drift towards dysbiosis.}, } @article {pmid30716127, year = {2019}, author = {Piquet, B and Shillito, B and Lallier, FH and Duperron, S and Andersen, AC}, title = {High rates of apoptosis visualized in the symbiont-bearing gills of deep-sea Bathymodiolus mussels.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0211499}, doi = {10.1371/journal.pone.0211499}, pmid = {30716127}, issn = {1932-6203}, abstract = {Symbiosis between Bathymodiolus and Gammaproteobacteria allows these deep-sea mussels to live in toxic environments such as hydrothermal vents and cold seeps. The quantity of endosymbionts within the gill-bacteriocytes appears to vary according to the hosts environment; however, the mechanisms of endosymbiont population size regulation remain obscure. We investigated the possibility of a control of endosymbiont density by apoptosis, a programmed cell death, in three mussel species. Fluorometric TUNEL and active Caspase-3-targeting antibodies were used to visualize and quantify apoptotic cells in mussel gills. To control for potential artefacts due to depressurization upon specimen recovery from the deep-sea, the apoptotic rates between mussels recovered unpressurised, versus mussels recovered in a pressure-maintaining device, were compared in two species from hydrothermal vents on the Mid-Atlantic Ridge: Bathymodiolus azoricus and B. puteoserpentis. Results show that pressurized recovery had no significant effect on the apoptotic rate in the gill filaments. Apoptotic levels were highest in the ciliated zone and in the circulating hemocytes, compared to the bacteriocyte zone. Apoptotic gill-cells in B. aff. boomerang from cold seeps off the Gulf of Guinea show similar distribution patterns. Deep-sea symbiotic mussels have much higher rates of apoptosis in their gills than the coastal mussel Mytilus edulis, which lacks chemolithoautotrophic symbionts. We discuss how apoptosis might be one of the mechanisms that contribute to the adaptation of deep-sea mussels to toxic environments and/or to symbiosis.}, } @article {pmid30715218, year = {2019}, author = {Schoenherr, AP and Rizzo, E and Jackson, N and Manosalva, P and Gomez, SK}, title = {Mycorrhiza-Induced Resistance in Potato Involves Priming of Defense Responses Against Cabbage Looper (Noctuidae: Lepidoptera).}, journal = {Environmental entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/ee/nvy195}, pmid = {30715218}, issn = {1938-2936}, abstract = {Most plants form mutualistic associations with arbuscular mycorrhizal (AM) fungi that are ubiquitous in soils. Through this symbiosis, plants can withstand abiotic and biotic stresses. The underlying molecular mechanisms involved in mediating mycorrhiza-induced resistance against insects needs further research, and this is particularly true for potato (Solanum tuberosum L. (Solanales: Solanaceae)), which is the fourth most important crop worldwide. In this study, the tripartite interaction between potato, the AM fungus Rhizophagus irregularis (Glomerales: Glomeraceae), and cabbage looper (Trichoplusia ni Hübner) (Lepidoptera: Noctuidae) was examined to determine whether potato exhibits mycorrhiza-induced resistance against this insect. Plant growth, insect fitness, AM fungal colonization of roots, and transcript levels of defense-related genes were measured in shoots and roots after 5 and 8 d of herbivory on mycorrhizal and nonmycorrhizal plants. AM fungal colonization of roots did not have an effect on potato growth, but root colonization levels increased by herbivory. Larval weight gain was reduced after 8 d of feeding on mycorrhizal plants compared with nonmycorrhizal plants. Systemic upregulation of Allene Oxide Synthase 1 (AOS1), 12-Oxo-Phytodienoate Reductase 3 (OPR3) (jasmonic acid pathway), Protease Inhibitor Type I (PI-I) (anti-herbivore defense), and Phenylalanine Ammonia Lyase (PAL) transcripts (phenylpropanoid pathway) was found during the tripartite interaction. Together, these findings suggest that potato may exhibit mycorrhiza-induced resistance to cabbage looper by priming anti-herbivore defenses aboveground. This study illustrates how mycorrhizal potato responds to herbivory by a generalist-chewing insect and serves as the basis for future studies involving tripartite interactions with other pests.}, } @article {pmid30712873, year = {2019}, author = {Kobayashi, T and Voisin, B and Kim, DY and Kennedy, EA and Jo, JH and Shih, HY and Truong, A and Doebel, T and Sakamoto, K and Cui, CY and Schlessinger, D and Moro, K and Nakae, S and Horiuchi, K and Zhu, J and Leonard, WJ and Kong, HH and Nagao, K}, title = {Homeostatic Control of Sebaceous Glands by Innate Lymphoid Cells Regulates Commensal Bacteria Equilibrium.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2018.12.031}, pmid = {30712873}, issn = {1097-4172}, abstract = {Immune cells and epithelium form sophisticated barrier systems in symbiotic relationships with microbiota. Evidence suggests that immune cells can sense microbes through intact barriers, but regulation of microbial commensalism remain largely unexplored. Here, we uncovered spatial compartmentalization of skin-resident innate lymphoid cells (ILCs) and modulation of sebaceous glands by a subset of RORγt+ ILCs residing within hair follicles in close proximity to sebaceous glands. Their persistence in skin required IL-7 and thymic stromal lymphopoietin, and localization was dependent on the chemokine receptor CCR6. ILC subsets expressed TNF receptor ligands, which limited sebocyte growth by repressing Notch signaling pathway. Consequently, loss of ILCs resulted in sebaceous hyperplasia with increased production of antimicrobial lipids and restricted commensalism of Gram-positive bacterial communities. Thus, epithelia-derived signals maintain skin-resident ILCs that regulate microbial commensalism through sebaceous gland-mediated tuning of the barrier surface, highlighting an immune-epithelia circuitry that facilitates host-microbe symbiosis.}, } @article {pmid30626871, year = {2019}, author = {Pacheco, AR and Moel, M and Segrè, D}, title = {Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {103}, doi = {10.1038/s41467-018-07946-9}, pmid = {30626871}, issn = {2041-1723}, support = {5R01DE024468/NH/NIH HHS/United States ; R01GM121950/NH/NIH HHS/United States ; P30DK036836/NH/NIH HHS/United States ; }, mesh = {*Computer Simulation ; *Microbial Consortia ; *Microbial Interactions ; Microbiota ; *Models, Biological ; Species Specificity ; Symbiosis ; }, abstract = {Metabolic exchange mediates interactions among microbes, helping explain diversity in microbial communities. As these interactions often involve a fitness cost, it is unclear how stable cooperation can emerge. Here we use genome-scale metabolic models to investigate whether the release of "costless" metabolites (i.e. those that cause no fitness cost to the producer), can be a prominent driver of intermicrobial interactions. By performing over 2 million pairwise growth simulations of 24 species in a combinatorial assortment of environments, we identify a large space of metabolites that can be secreted without cost, thus generating ample cross-feeding opportunities. In addition to providing an atlas of putative interactions, we show that anoxic conditions can promote mutualisms by providing more opportunities for exchange of costless metabolites, resulting in an overrepresentation of stable ecological network motifs. These results may help identify interaction patterns in natural communities and inform the design of synthetic microbial consortia.}, } @article {pmid30205594, year = {2018}, author = {Wu, Q and Sun, J and Chen, J and Zhang, H and Guo, YW and Wang, H}, title = {Terpenoids from Marine Soft Coral of the Genus Lemnalia: Chemistry and Biological Activities.}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30205594}, issn = {1660-3397}, support = {No. 81773628, No. 81741165, No. 41776139//National Natural Science Foundation of China/ ; No. 2017YFE0103100//National Key Research and Development Program/ ; No. LY16H300008, No. LY16H300007//National Natural Science Foundation of Zhejiang Province/ ; Jianwei Chen//Zhejiang Postdoctoral Foundation/ ; 2017M620254//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Anthozoa/genetics/*metabolism/microbiology ; Anti-Inflammatory Agents/chemistry/isolation & purification/metabolism/*pharmacology ; Antineoplastic Agents/chemistry/isolation & purification/metabolism/*pharmacology ; Biological Products/chemistry/isolation & purification/metabolism/*pharmacology ; Biosynthetic Pathways/genetics ; Cell Line, Tumor/drug effects ; Humans ; Molecular Structure ; Oceans and Seas ; Symbiosis ; Terpenes/chemistry/isolation & purification/metabolism/*pharmacology ; }, abstract = {Lemnalia is one of the most widely-distributed marine soft coral in tropical oceans and is known to produce novel terpenoids with a broad spectrum of biological activities. This review provides the first comprehensive overview of terpenoids produced by soft coral Lemnalia since their first discovery in 1974.}, } @article {pmid30198488, year = {2018}, author = {Krapivin, VA and Bagrov, SV and Varfolomeeva, MA}, title = {Effect of tidal level on abundance of symbionts in the White Sea blue mussel.}, journal = {Diseases of aquatic organisms}, volume = {130}, number = {2}, pages = {131-144}, doi = {10.3354/dao03259}, pmid = {30198488}, issn = {0177-5103}, mesh = {Animals ; *Mytilus edulis/parasitology ; *Symbiosis ; *Tidal Waves ; *Trematoda ; }, abstract = {In the White Sea, the blue mussel Mytilus edulis occupies a wide range of biotopes and is associated with numerous symbiotic organisms. At some sites, mussel cover spreads continuously from the intertidal to the subtidal zone. We checked whether the patterns of infection by different associated organisms differed among the upper subtidal, zero-depth and lower intertidal zones at 3 sites in the Kandalaksha Gulf and the Onega Bay of the White Sea. Organisms belonging to 13 taxa were found in mantle cavities and tissues of blue mussels. Parasitic green algae, a sporocyst and metacercariae of 5 species of digenean trematodes occupied mussel tissues; commensal ciliates, rhabdocoelans and some free-living invertebrates were found in mantle cavities. Quantitative composition of symbiotic communities of mussels was not the same at different tidal levels: Urastoma cyprinae (commensal rhabdocoelans) were more abundant in the subtidal and zero-depth zones, while encysted metacercariae of Renicola roscovita and Himasthla sp. were more abundant at the zero-depth and intertidal zones. We suggested several hypotheses to explain this heterogeneity.}, } @article {pmid30189599, year = {2018}, author = {Gemperlein, K and Zaburannyi, N and Garcia, R and La Clair, JJ and Müller, R}, title = {Metabolic and Biosynthetic Diversity in Marine Myxobacteria.}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30189599}, issn = {1660-3397}, support = {German Center for Infection Research//Deutsches Zentrum für Infektionsforschung/ ; X//Xenobe Research Institute/ ; }, mesh = {Animals ; Aquatic Organisms/*metabolism ; *Biodiversity ; Biological Products/isolation & purification/metabolism/*pharmacology ; Biosynthetic Pathways/genetics ; Computer Simulation ; Genome, Bacterial/genetics ; Myxococcales/genetics/*metabolism ; Phylogeny ; Porifera/*microbiology ; Soil Microbiology ; Symbiosis ; }, abstract = {Prior to 2005, the vast majority of characterized myxobacteria were obtained from terrestrial habitats. Since then, several species of halotolerant and even obligate marine myxobacteria have been described. Chemical analyses of extracts from these organisms have confirmed their ability to produce secondary metabolites with unique chemical scaffolds. Indeed, new genera of marine-derived myxobacteria, particularly Enhygromyxa, have been shown to produce novel chemical scaffolds that differ from those observed in soil myxobacteria. Further studies have shown that marine sponges and terrestrial myxobacteria are capable of producing similar or even identical secondary metabolites, suggesting that myxobacterial symbionts may have been the true producers. Recent in silico analysis of the genome sequences available from six marine myxobacteria disclosed a remarkably versatile biosynthetic potential. With access to ever-advancing tools for small molecule and genetic evaluation, these studies suggest a bright future for expeditions into this yet untapped resource for secondary metabolites.}, } @article {pmid30110359, year = {2018}, author = {Moir, ML and Renton, M and Hoffmann, BD and Leng, MC and Lach, L}, title = {Development and testing of a standardized method to estimate honeydew production.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0201845}, pmid = {30110359}, issn = {1932-6203}, mesh = {Animals ; *Hemiptera/anatomy & histology/growth & development ; Introduced Species ; *Models, Biological ; North America ; Species Specificity ; Symbiosis ; }, abstract = {Honeydew production by Hemiptera is an ecologically important process that facilitates mutualisms and increases nutrient cycling. Accurate estimates of the amount of honeydew available in a system are essential for quantifying food web dynamics, energy flow, and the potential growth of sooty mould that inhibits plant growth. Despite the importance of honeydew, there is no standardized method to estimate its production when intensive laboratory testing is not feasible. We developed two new models to predict honeydew production, one based on insect body mass and taxonomic family, and one based on body mass and life stage. We tested the accuracy of both models' predictions for a diverse range of honeydew-producing hemipteran families (Aphididae, Pseudococcidae, Coccidae, Psyllidae, Aleyrodidae, Delphacidae, Cicadellidae). The method based on body mass and family provided more accurate estimates of honeydew production, due to large variation in honeydew production among families. We apply our methodology to a case study, the recalculation of honeydew available to invasive red imported fire ant (Solenopsis invicta) in the United States. We find that the amount of honeydew may be an order of magnitude lower than that previously estimated (2.16 versus 21.6 grams of honeydew per day) and discuss possible reasons for the difference. We anticipate that being able to estimate honeydew production based on minimal biological information will have applications to agriculture, invasion biology, forestry, and carbon farming.}, } @article {pmid30102395, year = {2018}, author = {Manzano-Marín, A and Coeur d'acier, A and Clamens, AL and Orvain, C and Cruaud, C and Barbe, V and Jousselin, E}, title = {A Freeloader? The Highly Eroded Yet Large Genome of the Serratia symbiotica Symbiont of Cinara strobi.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2178-2189}, pmid = {30102395}, issn = {1759-6653}, mesh = {Animals ; Aphids/*microbiology/physiology ; Biological Evolution ; Buchnera/*genetics/isolation & purification/physiology ; Enterobacteriaceae/*genetics/isolation & purification/physiology ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Serratia/*genetics/isolation & purification/physiology ; *Symbiosis ; }, abstract = {Genome reduction is pervasive among maternally inherited bacterial endosymbionts. This genome reduction can eventually lead to serious deterioration of essential metabolic pathways, thus rendering an obligate endosymbiont unable to provide essential nutrients to its host. This loss of essential pathways can lead to either symbiont complementation (sharing of the nutrient production with a novel co-obligate symbiont) or symbiont replacement (complete takeover of nutrient production by the novel symbiont). However, the process by which these two evolutionary events happen remains somewhat enigmatic by the lack of examples of intermediate stages of this process. Cinara aphids (Hemiptera: Aphididae) typically harbor two obligate bacterial symbionts: Buchnera and Serratia symbiotica. However, the latter has been replaced by different bacterial taxa in specific lineages, and thus species within this aphid lineage could provide important clues into the process of symbiont replacement. In the present study, using 16S rRNA high-throughput amplicon sequencing, we determined that the aphid Cinara strobi harbors not two, but three fixed bacterial symbionts: Buchnera aphidicola, a Sodalis sp., and S. symbiotica. Through genome assembly and genome-based metabolic inference, we have found that only the first two symbionts (Buchnera and Sodalis) actually contribute to the hosts' supply of essential nutrients while S. symbiotica has become unable to contribute towards this task. We found that S. symbiotica has a rather large and highly eroded genome which codes only for a few proteins and displays extensive pseudogenization. Thus, we propose an ongoing symbiont replacement within C. strobi, in which a once "competent" S. symbiotica does no longer contribute towards the beneficial association. These results suggest that in dual symbiotic systems, when a substitute cosymbiont is available, genome deterioration can precede genome reduction and a symbiont can be maintained despite the apparent lack of benefit to its host.}, } @article {pmid30078596, year = {2018}, author = {Mowbray, CA and Niranji, SS and Cadwell, K and Bailey, R and Watson, KA and Hall, J}, title = {Gene expression of AvBD6-10 in broiler chickens is independent of AvBD6, 9, and 10 peptide potency.}, journal = {Veterinary immunology and immunopathology}, volume = {202}, number = {}, pages = {31-40}, doi = {10.1016/j.vetimm.2018.06.007}, pmid = {30078596}, issn = {1873-2534}, mesh = {Animals ; Avian Proteins/*genetics/immunology ; Bacteria ; Chickens/*immunology ; Gastrointestinal Tract/*immunology/microbiology ; Interleukin-1beta/immunology ; Interleukin-6/immunology ; Kidney/immunology ; Liver/immunology ; Symbiosis/immunology ; Transcriptome ; beta-Defensins/*genetics/immunology ; }, abstract = {The Avian β-defensin (AvBD) gene cluster contains fourteen genes; within this, two groups (AvBD6/7 and AvBD8 -10) encode charged peptides of >+5 (AvBD6/7), indicative of potent microbial killing activities, and ≤+4 (AvBD8-10), suggestive of reduced antimicrobial activities. Chicken broiler gut tissues are constantly exposed to microbes in the form of commensal bacteria. This study examined whether tissue expression patterns of AvBD6-10 reflected microbial exposure and the encoded peptides a functional antimicrobial hierarchy. Gut AvBD6-10 gene expression was observed in hatch to day 21 birds, although the AvBD8-10 profiles were eclipsed by those detected in the liver and kidney tissues. In vitro challenges of chicken CHCC-OU2 cells using the gut commensal Lactobacillus johnsonii (104 CFU) did not significantly affect AvBD8-10 gene expression patterns, although upregulation (P < 0.05) of IL-Iβ gene expression was observed. Similarly, in response to Bacteriodes doreii, IL-Iβ and IL-6 gene upregulation were detected (P < 0.05), but AvBD10 gene expression remained unaffected. These data suggested that AvBD8-10 gene expression was not induced by commensal gut bacteria. Bacterial time-kill assays employing recombinant (r)AvBD6, 9 and 10 peptides (0.5μM - 12μM), indicated an antimicrobial hierarchy, linked to charge, of AvBD6 > AvBD9 > AvBD10 against Escherichia coli, but AvBD10 > AvBD9 > AvBD6 using Enterococcus faecalis. rAvBD10, selected due to its reduced cationic charge was, using CHCC-OU2 cells, investigated for cell proliferation and wound healing properties, but none were observed. These data suggest that in healthy broiler chicken tissues AvBD6/7 and AvBD8-10 gene expression profiles are independent of the in vitro antimicrobial hierarchies of the encoded AvBD6, 9 and 10 peptides.}, } @article {pmid30060189, year = {2018}, author = {Río Bártulos, C and Rogers, MB and Williams, TA and Gentekaki, E and Brinkmann, H and Cerff, R and Liaud, MF and Hehl, AB and Yarlett, NR and Gruber, A and Kroth, PG and van der Giezen, M}, title = {Mitochondrial Glycolysis in a Major Lineage of Eukaryotes.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2310-2325}, pmid = {30060189}, issn = {1759-6653}, support = {//Wellcome Trust/United Kingdom ; 078566/A/05/Z//Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; Blastocystis/cytology/enzymology/genetics/*metabolism ; Diatoms/cytology/enzymology/genetics/*metabolism ; Energy Metabolism ; Genome, Mitochondrial ; *Glycolysis ; Mitochondria/genetics/*metabolism ; Symbiosis ; Transformation, Genetic ; }, abstract = {The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host's metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.}, } @article {pmid29929338, year = {2018}, author = {Che, R and Deng, Y and Wang, F and Wang, W and Xu, Z and Hao, Y and Xue, K and Zhang, B and Tang, L and Zhou, H and Cui, X}, title = {Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils.}, journal = {The Science of the total environment}, volume = {639}, number = {}, pages = {997-1006}, doi = {10.1016/j.scitotenv.2018.05.238}, pmid = {29929338}, issn = {1879-1026}, mesh = {*Grassland ; Nitrogen ; *Nitrogen Fixation ; Soil ; *Soil Microbiology ; Symbiosis/*physiology ; Tibet ; }, abstract = {Biological nitrogen fixation, conducted by soil diazotrophs, is the primary nitrogen source for natural grasslands. However, the diazotrophs in grassland soils are still far from fully investigated. Particularly, their regional-scale distribution patterns have never been systematically examined. Here, soils (0-5 cm) were sampled from 54 grasslands on the Tibetan Plateau to examine the diazotroph abundance, diversity, and community composition, as well as their distribution patterns and driving factors. The diazotroph abundance was expressed as nifH gene copies, measured using real-time PCR. The diversity and community composition of diazotrophs were analyzed through MiSeq sequencing of nifH genes. The results showed that Cyanobacteria (47.94%) and Proteobacteria (45.20%) dominated the soil diazotroph communities. Most Cyanobacteria were classified as Nostocales which are main components of biological crusts. Rhizobiales, most of which were identified as potential symbiotic diazotrophs, were also abundant in approximately half of the soil samples. The soil diazotroph abundance, diversity, and community composition followed the distribution patterns in line with mean annual precipitation. Moreover, they also showed significant correlations with prokaryotic abundance, plant biomass, vegetation cover, soil pH values, and soil nutrient contents. Among these environmental factors, the soil moisture, organic carbon, available phosphorus, and inorganic nitrogen contents could be the main drivers of diazotroph distribution due to their strong correlations with diazotroph indices. These findings suggest that autotrophic and symbiotic diazotrophs are the predominant nitrogen fixers in Tibetan grassland soils, and highlight the key roles of water and nutrient availability in determining the soil diazotroph distribution on the Tibetan Plateau.}, } @article {pmid29119317, year = {2018}, author = {Woodhams, DC and LaBumbard, BC and Barnhart, KL and Becker, MH and Bletz, MC and Escobar, LA and Flechas, SV and Forman, ME and Iannetta, AA and Joyce, MD and Rabemananjara, F and Gratwicke, B and Vences, M and Minbiole, KPC}, title = {Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {1049-1062}, pmid = {29119317}, issn = {1432-184X}, support = {DEB-1136662//Division of Environmental Biology/ ; }, mesh = {Animals ; Antifungal Agents/pharmacology ; Anura/microbiology ; Bacteria/classification/isolation & purification/*metabolism ; Biological Control Agents/antagonists & inhibitors ; Chytridiomycota/*drug effects/growth & development/pathogenicity ; Indoles/*antagonists & inhibitors/chemistry/*metabolism ; Microbial Sensitivity Tests ; Panama ; Phylogeny ; Prodigiosin/*antagonists & inhibitors/chemistry/*metabolism ; Serratia/classification/isolation & purification/metabolism ; Skin/microbiology ; Switzerland ; Symbiosis ; United States ; Volatile Organic Compounds/*antagonists & inhibitors/chemistry/*metabolism ; }, abstract = {Symbiotic bacteria can produce secondary metabolites and volatile compounds that contribute to amphibian skin defense. Some of these symbionts have been used as probiotics to treat or prevent the emerging disease chytridiomycosis. We examined 20 amphibian cutaneous bacteria for the production of prodigiosin or violacein, brightly colored defense compounds that pigment the bacteria and have characteristic spectroscopic properties making them readily detectable, and evaluated the antifungal activity of these compounds. We detected violacein from all six isolates of Janthinobacterium lividum on frogs from the USA, Switzerland, and on captive frogs originally from Panama. We detected prodigiosin from five isolates of Serratia plymuthica or S. marcescens, but not from four isolates of S. fonticola or S. liquefaciens. All J. lividum isolates produced violacein when visibly purple, while prodigiosin was only detected on visibly red Serratia isolates. When applied to cultures of chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), prodigiosin caused significant growth inhibition, with minimal inhibitory concentrations (MIC) of 10 and 50 μM, respectively. Violacein showed a MIC of 15 μM against both fungi and was slightly more active against Bsal than Bd at lower concentrations. Although neither violacein nor prodigiosin showed aerosol activity and is not considered a volatile organic compound (VOC), J. lividum and several Serratia isolates did produce antifungal VOCs. White Serratia isolates with undetectable prodigiosin levels could still inhibit Bd growth indicating additional antifungal compounds in their chemical arsenals. Similarly, J. lividum can produce antifungal compounds such as indole-3-carboxaldehyde in addition to violacein, and isolates are not always purple, or turn purple under certain growth conditions. When Serratia isolates were grown in the presence of cell-free supernatant (CFS) from the fungi, CFS from Bd inhibited growth of the prodigiosin-producing isolates, perhaps indicative of an evolutionary arms race; Bsal CFS did not inhibit bacterial growth. In contrast, growth of one J. lividum isolate was facilitated by CFS from both fungi. Isolates that grow and continue to produce antifungal compounds in the presence of pathogens may represent promising probiotics for amphibians infected or at risk of chytridiomycosis. In a global analysis, 89% of tested Serratia isolates and 82% of J. lividum isolates were capable of inhibiting Bd and these have been reported from anurans and caudates from five continents, indicating their widespread distribution and potential for host benefit.}, } @article {pmid29119316, year = {2018}, author = {Grigorescu, AS and Renoz, F and Sabri, A and Foray, V and Hance, T and Thonart, P}, title = {Accessing the Hidden Microbial Diversity of Aphids: an Illustration of How Culture-Dependent Methods Can Be Used to Decipher the Insect Microbiota.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {1035-1048}, doi = {10.1007/s00248-017-1092-x}, pmid = {29119316}, issn = {1432-184X}, support = {Grant FRFC 6886819//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Animals ; Aphids/*microbiology ; Bacteria/classification/genetics/growth & development/*isolation & purification ; *Biodiversity ; Culture Techniques/*methods ; DNA/isolation & purification ; Fungi/classification/genetics/growth & development/*isolation & purification ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics/*physiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Serratia/classification/isolation & purification/physiology ; Symbiosis ; }, abstract = {Microorganism communities that live inside insects can play critical roles in host development, nutrition, immunity, physiology, and behavior. Over the past decade, high-throughput sequencing reveals the extraordinary microbial diversity associated with various insect species and provides information independent of our ability to culture these microbes. However, their cultivation in the laboratory remains crucial for a deep understanding of their physiology and the roles they play in host insects. Aphids are insects that received specific attention because of their ability to form symbiotic associations with a wide range of endosymbionts that are considered as the core microbiome of these sap-feeding insects. But, if the functional diversity of obligate and facultative endosymbionts has been extensively studied in aphids, the diversity of gut symbionts and other associated microorganisms received limited consideration. Herein, we present a culture-dependent method that allowed us to successfully isolate microorganisms from several aphid species. The isolated microorganisms were assigned to 24 bacterial genera from the Actinobacteria, Firmicutes, and Proteobacteria phyla and three fungal genera from the Ascomycota and Basidiomycota phyla. In our study, we succeeded in isolating already described bacteria found associated to aphids (e.g., the facultative symbiont Serratia symbiotica), as well as microorganisms that have never been described in aphids before. By unraveling a microbial community that so far has been ignored, our study expands our current knowledge on the microbial diversity associated with aphids and illustrates how fast and simple culture-dependent approaches can be applied to insects in order to capture their diverse microbiota members.}, } @article {pmid29119315, year = {2018}, author = {DeLong, JP and Al-Ameeli, Z and Lyon, S and Van Etten, JL and Dunigan, DD}, title = {Size-dependent Catalysis of Chlorovirus Population Growth by A Messy Feeding Predator.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {847-853}, pmid = {29119315}, issn = {1432-184X}, mesh = {Animals ; Catalysis ; Chlorella/virology ; Ciliophora/*physiology ; DNA Viruses ; Food Chain ; Host-Pathogen Interactions/*physiology ; Paramecium/*virology ; Phycodnaviridae/growth & development/*physiology ; Population Dynamics ; *Predatory Behavior ; *Symbiosis ; }, abstract = {Many chloroviruses replicate in endosymbiotic zoochlorellae that are protected from infection by their symbiotic host. To reach the high virus concentrations that often occur in natural systems, a mechanism is needed to release zoochlorellae from their hosts. We demonstrate that the ciliate predator Didinium nasutum foraging on zoochlorellae-bearing Paramecium bursaria can release live zoochlorellae from the ruptured prey cell that can then be infected by chloroviruses. The catalysis process is very effective, yielding roughly 95% of the theoretical infectious virus yield as determined by sonication of P. bursaria. Chlorovirus activation is more effective with smaller Didinia, as larger Didinia typically consume entire P. bursaria cells without rupturing them, precluding the release of zoochlorellae. We also show that the timing of Chlorovirus growth is tightly linked to the predator-prey cycle between Didinium and Paramecium, with the most rapid increase in chloroviruses temporally linked to the peak foraging rate of Didinium, supporting the idea that predator-prey cycles can drive cycles of Chlorovirus abundance.}, } @article {pmid29110065, year = {2018}, author = {Li, J and Chen, D and Yu, B and He, J and Zheng, P and Mao, X and Yu, J and Luo, J and Tian, G and Huang, Z and Luo, Y}, title = {Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {821-829}, pmid = {29110065}, issn = {1432-184X}, support = {31301987//National Natural Science Foundation of China/ ; 3167131062//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Ascomycota/physiology ; Basidiomycota/physiology ; Biodiversity ; Candida/pathogenicity/physiology ; Chytridiomycota/physiology ; Diet ; Dysbiosis/microbiology ; Food ; Fungi/classification/*pathogenicity/*physiology ; Gastrointestinal Microbiome/immunology/*physiology ; Gastrointestinal Tract/immunology/*microbiology ; *Host-Pathogen Interactions/immunology/physiology ; Humans ; Inflammatory Bowel Diseases/immunology/microbiology ; Intestinal Mucosa/microbiology ; Lectins, C-Type/metabolism ; Mice ; Mycobiome/*physiology ; Mycoses ; Symbiosis ; Toll-Like Receptor 2/metabolism ; Toll-Like Receptor 4/metabolism ; }, abstract = {Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice. In the GIT of humans, fungi belonging to the phyla Ascomycota, Basidiomycota and Chytridiomycota are predominant. The murine intestines harbor a more diverse assemblage of fungi. Diet is one of the major factors influencing colonization of fungi in the GIT. Presence of the genus Candida is positively associated with dietary carbohydrates, but are negatively correlated with dietary amino acids, proteins, and fatty acids. However, the relationship between diet and the fungal community (and functions), as well as the underlying mechanisms remains unclear. Dysbiosis of intestinal fungi can cause invasive infections and inflammatory bowel diseases (IBD). However, it is not clear whether dysbiosis of the mycobiome is a cause, or a result of IBD. Compared to non-inflamed intestinal mucosa, the abundance and diversity of fungi is significantly increased in the inflamed mucosa. The commonly observed commensal fungal species Candida albicans might contribute to occurrence and development of IBD. Limited studies show that Candida albicans might interact with immune cells of the host intestines through the pathways associated with Dectin-1, Toll-like receptor 2 (TLR2), and TLR4. This review is expected to provide new thoughts for future studies on intestinal fungi and for new therapies to fungal infections in the GIT of human and animals.}, } @article {pmid29071368, year = {2018}, author = {Theron-De Bruin, N and Dreyer, LL and Ueckermann, EA and Wingfield, MJ and Roets, F}, title = {Birds Mediate a Fungus-Mite Mutualism.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {863-874}, pmid = {29071368}, issn = {1432-184X}, support = {na//Department of Science and Technology/National Research Foundation Centre of Excellence in Tree Health Biotechnology/ ; }, mesh = {Animals ; Arthropod Vectors/*microbiology ; Birds/*microbiology ; DNA, Fungal/analysis ; Fungi/isolation & purification/*physiology ; Mites/*microbiology ; Proteaceae/microbiology ; South Africa ; Spores, Fungal ; Symbiosis/*physiology ; Trees/microbiology ; }, abstract = {Mutualisms between ophiostomatoid fungi and arthropods have been well documented. These fungi commonly aid arthropod nutrition and, in turn, are transported to new niches by these arthropods. The inflorescences of Protea trees provide a niche for a unique assemblage of ophiostomatoid fungi. Here, mites feed on Sporothrix fungi and vector the spores to new niches. Protea-pollinating beetles transport the spore-carrying mites between Protea trees. However, many Protea species are primarily pollinated by birds that potentially play a central role in the Protea-Sporothrix-mite system. To investigate the role of birds in the movement of mites and/or fungal spores, mites were collected from Protea inflorescences and cape sugarbirds, screened for Sporothrix fungal spores and tested for their ability to feed and reproduce on the fungal associates. Two mite species where abundant in both Protea inflorescences and on cape sugarbirds and regularly carried Sporothrix fungal spores. One of these mite species readily fed and reproduced on its transported fungal partner. For dispersal, this mite (a Glycyphagus sp.) attached to a larger mite species (Proctolaelaps vandenbergi) which, in turn, were carried by the birds to new inflorescences. The results of this study provide compelling evidence for a new mite-fungus mutualism, new mite-mite commensalisms and the first evidence of birds transporting mites with Sporothrix fungal spores to colonise new Protea trees.}, } @article {pmid28864228, year = {2017}, author = {de León-Martínez, JA and Yañez-Ocampo, G and Wong-Villarreal, A}, title = {Burkholderia species associated with legumes of Chiapas, Mexico, exhibit stress tolerance and growth in aromatic compounds.}, journal = {Revista Argentina de microbiologia}, volume = {49}, number = {4}, pages = {394-401}, doi = {10.1016/j.ram.2017.04.009}, pmid = {28864228}, issn = {0325-7541}, mesh = {*Burkholderia/genetics/isolation & purification ; DNA, Bacterial ; *Fabaceae/microbiology ; Mexico ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Stress, Physiological ; Symbiosis ; }, abstract = {Leguminous plants have received special interest for the diversity of β-proteobacteria in their nodules and are promising candidates for biotechnological applications. In this study, 15 bacterial strains were isolated from the nodules of the following legumes: Indigofera thibaudiana, Mimosa diplotricha, Mimosa albida, Mimosa pigra, and Mimosa pudica, collected in 9 areas of Chiapas, Mexico. The strains were grouped into four profiles of genomic fingerprints through BOX-PCR and identified based on their morphology, API 20NE biochemical tests, sequencing of the 16S rRNA, nifH and nodC genes as bacteria of the Burkholderia genus, genetically related to Burkholderia phenoliruptrix, Burkholderia phymatum, Burkholderia sabiae, and Burkholderia tuberum. The Burkholderia strains were grown under stress conditions with 4% NaCl, 45°C, and benzene presence at 0.1% as the sole carbon source. This is the first report on the isolation of these nodulating species of the Burkholderia genus in legumes in Mexico.}, } @article {pmid28747779, year = {2017}, author = {Kotilínek, M and Hiiesalu, I and Košnar, J and Šmilauerová, M and Šmilauer, P and Altman, J and Dvorský, M and Kopecký, M and Doležal, J}, title = {Fungal root symbionts of high-altitude vascular plants in the Himalayas.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6562}, pmid = {28747779}, issn = {2045-2322}, mesh = {Altitude ; *Biodiversity ; Endophytes/*classification/cytology/genetics/*physiology ; India ; Microscopy ; Mycorrhizae/*classification/*physiology ; Phylogeny ; Plant Roots/*microbiology ; *Symbiosis ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) form symbiotic relationships with plants influencing their productivity, diversity and ecosystem functions. Only a few studies on these fungi, however, have been conducted in extreme elevations and none over 5500 m a.s.l., although vascular plants occur up to 6150 m a.s.l. in the Himalayas. We quantified AMF and DSE in roots of 62 plant species from contrasting habitats along an elevational gradient (3400-6150 m) in the Himalayas using a combination of optical microscopy and next generation sequencing. We linked AMF and DSE communities with host plant evolutionary history, ecological preferences (elevation and habitat type) and functional traits. We detected AMF in elevations up to 5800 m, indicating it is more constrained by extreme conditions than the host plants, which ascend up to 6150 m. In contrast, DSE were found across the entire gradient up to 6150 m. AMF diversity was unimodally related to elevation and positively related to the intensity of AMF colonization. Mid-elevation steppe and alpine plants hosted more diverse AMF communities than plants from deserts and the subnival zone. Our results bring novel insights to the abiotic and biotic filters structuring AMF and DSE communities in the Himalayas.}, } @article {pmid30709144, year = {2019}, author = {Owolabi, KM and Hammouch, Z}, title = {Mathematical modeling and analysis of two-variable system with noninteger-order derivative.}, journal = {Chaos (Woodbury, N.Y.)}, volume = {29}, number = {1}, pages = {013145}, doi = {10.1063/1.5086909}, pmid = {30709144}, issn = {1089-7682}, abstract = {The aim of this paper is to apply the newly trending Atangana-Baluanu derivative operator to model some symbiosis systems describing commmensalism and predator-prey processes. The choice of using this derivative is due to the fact that it combines nonlocal and nonsingular properties in its formulation, which are the essential ingredients when dealing with models of real-life applications. In addition, it is only the Atangana-Baleanu derivative that has both Markovian and non-Markovian properties. Also, its waiting time takes into account the power, exponential, and Mittag-Leffler laws in its formulation. Mathematical analysis of these dynamical models is considered to guide in the correct use of parameters therein, with chaotic and spatiotemporal results reported for some instances of fractional power α.}, } @article {pmid30708940, year = {2019}, author = {Mei, L and Yang, X and Cao, H and Zhang, T and Guo, J}, title = {Arbuscular Mycorrhizal Fungi Alter Plant and Soil C:N:P Stoichiometries Under Warming and Nitrogen Input in a Semiarid Meadow of China.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/ijerph16030397}, pmid = {30708940}, issn = {1660-4601}, support = {(No. 31470405) and (No. 31770359)//National Natural Science Foundation of China/ ; }, abstract = {Ecological stoichiometry has been widely used to determine how plant-soil systems respond to global change and to reveal which factors limit plant growth. Arbuscular mycorrhizal fungi (AMF) can increase plants' uptake of nutrients such as nitrogen (N) and phosphorus (P), thereby altering plant and soil stoichiometries. To understand the regulatory effect of AMF feedback on plants and soil stoichiometry under global change, a microcosm experiment was conducted with warming and N input. The C₄ grass Setaria viridis, C₃ grass Leymus chinensis, and Chenopodiaceae species Suaeda corniculata were studied. The results showed that the mycorrhizal benefits for the C₄ grass S. viridis were greater than those for the C₃ grass L. chinensis, whereas for the Chenopodiaceae species S. corniculata, AMF symbiosis was antagonistic. Under N input and a combination of warming and N input, AMF significantly decreased the N:P ratios of all three species. Under N input, the soil N content and the N:P ratio were decreased significantly in the presence of AMF, whereas the soil C:N ratio was increased. These results showed that AMF can reduce the P limitation caused by N input and improve the efficiency of nutrient utilization, slow the negative influence of global change on plant growth, and promote grassland sustainability.}, } @article {pmid30708045, year = {2019}, author = {Chen, J and Bai, X and Hua, Y and Zhang, H and Wang, H}, title = {Fusariumins C and D, two novel antimicrobial agents from Fusarium oxysporum ZZP-R1 symbiotic on Rumex madaio Makino.}, journal = {Fitoterapia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fitote.2019.01.016}, pmid = {30708045}, issn = {1873-6971}, abstract = {Bioassay-guided fractionation of the crude extract of fermentation broth of one symbiotic strain Fusarium oxysporum ZZP-R1 derived from coastal plant Rumex madaio Makino, one traditional Chinese medicine used as a treatment of inflammation and toxication, yielded two novel compounds, fusariumins C (1) and D (2). Chemical structures of 1 and 2 were respectively determined as one meroterpene with cyclohexanone moiety and a sesquiterpene ester with a conjugated triene and an unusual oxetene ring by a combination of spectroscopic methods, including 1D and 2D NMR, mass spectrometry, and optical rotation analysis, as well as by comparison with literature data. Bioassay results indicated that compound 1 displayed potent activity against Staphyloccocus aureus with an MIC value of 6.25 μM, and compound 2 had a moderate inhibitory effect on S. aureus with an MIC value of 25.0 μM. It was the first report that phytochemical investigation of Fusarium strain from R. madaio Makino led to isolation of new antimicrobial agents.}, } @article {pmid30707488, year = {2019}, author = {Popović-Djordjević, J and Marjanović, ŽS and Gršić, N and Adžić, T and Popović, B and Bogosavljević, J and Brčeski, I}, title = {Essential elements as a distinguishing factor between mycorrhizal potentials of two cohabiting truffle species in riparian forest habitat in Serbia.}, journal = {Chemistry & biodiversity}, volume = {}, number = {}, pages = {}, doi = {10.1002/cbdv.201800693}, pmid = {30707488}, issn = {1612-1880}, abstract = {True truffles (Tuber sp.) that establish ectomycorrhizal symbiosis (ECM) with trees in the Mediterranean and temporal regions have species specific abilities to assimilate soil born elements. Suitable habitats are usually inhabited by few truffle species, while distinguishing their symbiotic potentials appeared very difficult. Two species that commonly inhabit riparian forests in Serbia are the most prized one, Tuber magnatum Pico (Piedmont white truffle) and not so highly valued Tuber brumale Vitt. In order to assess potential differences between their assimilation and accumulation abilities, the differences between contents of elements that may be the subjects of the symbiotic trade between the host plant and fungi were evaluated in accumulation target (ascocarps) and their source (the soil). Essential macro (K, Na, Ca, Mg, Fe, P, S and Zn) and essential trace (Co, Cr, Cu, Mn and Se) elements in truffles and soil samples were determined by means of inductively coupled plasma with optical emission spectrometry (ICP-OES). Their concentrations (mg/kg) in ascocarps were in the range from 1.364±0.591 (Cr) to 10760.862±16.058 (K), while in soil ranged from 23.035±0.010 (Cr) to 20809.300±122.934 (Fe). Element accumulation potential (bioaccumulation factor) was calculated in the system truffle/soil. The statistical approaches were used for establishing the differences, while the possible differentiation between symbiotic potentials of two mycelia in the defined soil conditions was discussed.}, } @article {pmid30706343, year = {2019}, author = {Martínez-García, S and Ortiz-García, CI and Cruz-Aguilar, M and Zenteno, JC and Murrieta-Coxca, JM and Pérez-Tapia, SM and Rodríguez-Martínez, S and Cancino-Diaz, ME and Cancino-Diaz, JC}, title = {Competition/antagonism associations of biofilm formation among Staphylococcus epidermidis Agr groups I, II, and III.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {2}, pages = {143-153}, doi = {10.1007/s12275-019-8322-5}, pmid = {30706343}, issn = {1976-3794}, abstract = {Staphylococci have quorum-sensing (QS) systems that enable cell-to-cell communication, as well as the regulation of numerous colonization and virulence factors. The accessory gene regulator (Agr) operon is one of the Staphylococcus genus QS systems. Three groups (I, II, and III) are present in Staphylococcus epidermidis Agr operon. To date, it is unknown whether Agr groups can interact symbiotically during biofilm development. This study analyzed a symbiotic association among Agr groups during biofilm formation in clinical and commensal isolates. Different combinations among Agr group isolates was used to study biofilm formation in vitro and in vivo (using a mouse catheter-infection model). The analysis of Agr groups were also performed from samples of human skin (head, armpits, and nostrils). Different predominant coexistence was found within biofilms, suggesting symbiosis type. In vitro, Agr I had a competition with Agr II and Agr III. Agr II had a competition with Agr III, and Agr II was an antagonist to Agr I and III when the three strains were combined. In vivo, Agr II had a competition to Agr I, but Agr I and II were antagonists to Agr III. The associations found in vitro and in vivo were also found in different sites of the skin. Besides, other associations were observed: Agr III antagonized Agr I and II, and Agr III competed with Agr I and Agr II. These results suggest that, in S. epidermidis, a symbiotic association of competition and antagonism occurs among different Agr groups during biofilm formation.}, } @article {pmid30705119, year = {2019}, author = {Sivakumar, R and Ranjani, J and Vishnu, US and Jayashree, S and Lozano, GL and Miles, J and Broderick, NA and Guan, C and Gunasekaran, P and Handelsman, J and Rajendhran, J}, title = {Evaluation of InSeq To Identify Genes Essential for Pseudomonas aeruginosa PGPR2 Corn Root Colonization.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1534/g3.118.200928}, pmid = {30705119}, issn = {2160-1836}, abstract = {The reciprocal interaction between rhizosphere bacteria and their plant hosts results in a complex battery of genetic and physiological responses. In this study, we used insertion sequencing (INSeq) to reveal the genetic determinants responsible for the fitness of Pseudomonas aeruginosa PGPR2 during root colonization. We generated a random transposon mutant library of Pseudomonas aeruginosa PGPR2 comprising 39,500 unique insertions and identified genes required for growth in culture and on corn roots. A total of 108 genes were identified as contributing to the fitness of strain PGPR2 on roots. The importance in root colonization of four genes identified in the TnSeq screen was verified by constructing deletion mutants in the genes and testing them for the ability to colonize corn roots singly or in competition with the wild type. All four mutants were affected in corn root colonization, displaying 5- to 100-fold reductions in populations in single inoculations, and all were outcompeted by the wild type by almost 100-fold after seven days on corn roots in mixed inoculations of the wild type and mutant. The genes identified in the screen had homology to genes involved in amino acid catabolism, stress adaptation, detoxification, signal transduction, and transport. INSeq technology proved a successful tool to identify fitness factors in Paeruginosa PGPR2 for root colonization.}, } @article {pmid30602371, year = {2019}, author = {Buret, AG and Motta, JP and Allain, T and Ferraz, J and Wallace, JL}, title = {Pathobiont release from dysbiotic gut microbiota biofilms in intestinal inflammatory diseases: a role for iron?.}, journal = {Journal of biomedical science}, volume = {26}, number = {1}, pages = {1}, doi = {10.1186/s12929-018-0495-4}, pmid = {30602371}, issn = {1423-0127}, support = {183-681-2011, 413888-2012//Natural Sciences and Engineering Research Council of Canada/ ; 12033//Canadian Institutes of Health Research/Canada ; 20142017//Crohn's and Colitis Canada/ ; PCOFUND-GA-2013-609398//AgreenSkillsPlus/ ; }, mesh = {*Bacterial Physiological Phenomena ; *Biofilms ; Dysbiosis/immunology/microbiology/*physiopathology ; Gastrointestinal Microbiome/*physiology ; Homeostasis ; Humans ; Inflammatory Bowel Diseases/complications/*immunology/microbiology ; Iron/*metabolism ; Symbiosis ; }, abstract = {Gut microbiota interacting with an intact mucosal surface are key to the maintenance of homeostasis and health. This review discusses the current state of knowledge of the biofilm mode of growth of these microbiota communities, and how in turn their disruptions may cause disease. Beyond alterations of relative microbial abundance and diversity, the aim of the review is to focus on the disruptions of the microbiota biofilm structure and function, the dispersion of commensal bacteria, and the mechanisms whereby these dispersed commensals may become pathobionts. Recent findings have linked iron acquisition to the expression of virulence factors in gut commensals that have become pathobionts. Causal studies are emerging, and mechanisms common to enteropathogen-induced disruptions, as well as those reported for Inflammatory Bowel Disease and colo-rectal cancer are used as examples to illustrate the great translational potential of such research. These new observations shed new light on our attempts to develop new therapies that are able to protect and restore gut microbiota homeostasis in the many disease conditions that have been linked to microbiota dysbiosis.}, } @article {pmid30509793, year = {2018}, author = {Baquiran, JIP and Conaco, C}, title = {Sponge-microbe partnerships are stable under eutrophication pressure from mariculture.}, journal = {Marine pollution bulletin}, volume = {136}, number = {}, pages = {125-134}, doi = {10.1016/j.marpolbul.2018.09.011}, pmid = {30509793}, issn = {1879-3363}, mesh = {Animals ; Coral Reefs ; *Ecosystem ; Environmental Monitoring/*methods ; *Eutrophication ; Fisheries ; *Microbiota/genetics ; Philippines ; *Porifera/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Sponges harbor a great diversity of symbiotic microorganisms. However, environmental stresses can affect this partnership and influence the health and abundance of the host sponges. In Bolinao, Pangasinan, Philippines, chronic input of organic materials from mariculture activities contributes to a eutrophic coastal environment. To understand how these conditions might affect sponge-microbial partnerships, transplantation experiments were conducted with the marine sponge Gelliodes obtusa. High-throughput sequencing of 16S rRNA revealed that the associated microbial community of the sponges did not exhibit significant shifts after six weeks of transplantation at a eutrophic fish farm site compared to sponges grown at a coral reef or a seagrass area. However, sponges at the fish farm revealed higher abundance of the amoA gene, suggesting that microbiome members are responsive to increased ammonium levels at the site. The stable association between G. obtusa and its microbiome indicates that the sponge holobiont can withstand eutrophication pressure from mariculture.}, } @article {pmid30089146, year = {2018}, author = {Anjos, D and Dáttilo, W and Del-Claro, K}, title = {Unmasking the architecture of ant-diaspore networks in the Brazilian Savanna.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0201117}, pmid = {30089146}, issn = {1932-6203}, mesh = {Animals ; Ants/*physiology ; Brazil ; Ecology ; *Ecosystem ; Fruit/chemistry ; Grassland ; Plants/chemistry ; Seed Dispersal/*physiology ; Seeds/chemistry ; Symbiosis ; }, abstract = {Ant-diaspore interactions are directly related to fruit consumption, seed predation and dispersal, being determinant for the plant fitness. However, although abundant and diversified, these ecological interactions have been neglected in network studies. Understanding the structure of these networks is the first step in preserving these ecological functions. However, describing the network structure is not enough; we need to understand what mechanisms are behind the network patterns. In this study, for the first time, we describe the structure of the ant-diaspore network, considering only the interactions that can benefit plants, separating it into fruit consumption and diaspore removal networks in the Brazilian Savanna. We postulated that ant-diaspore interactions tend to be more specialized in the diaspore removal network compared to the fruit consumption network. Furthermore, we tested whether morphological features, such as size of mandibles of ants and diaspores, could modulate these ecological networks. Overall, we recorded 24 ant and 29 plant species interacting. We found that fruit consumption and diaspore removal networks exhibited similar patterns of interactions (i.e., non-modular), although only the diaspore removal network was nested. The diaspore removal network did not show a more specialized pattern than the fruit consumption network, since both networks consisted of opportunistic interactions. We found that ant mandible and diaspore size does not explain the structure of ecological networks, but in diaspore removal networks the relationship between these morphological traits may explain the pattern of interactions. Thus, we showed that mandible size of ants may have implications on seedling recruitment, suggesting that mandible size can predict possible effects on plant fitness within in diaspore removal networks. Overall, ant-diaspore networks maintain important ecological functions, such as fruit consumption and seed dispersal, which often implies an increase in reproductive success of the plants.}, } @article {pmid29306352, year = {2017}, author = {Reid, CJ and Wyrsch, ER and Roy Chowdhury, P and Zingali, T and Liu, M and Darling, AE and Chapman, TA and Djordjevic, SP}, title = {Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26.}, journal = {Microbial genomics}, volume = {3}, number = {12}, pages = {}, pmid = {29306352}, issn = {2057-5858}, mesh = {Animals ; Australia ; Drug Resistance, Multiple, Bacterial/*genetics ; Environmental Pollutants ; Escherichia coli/*classification/*genetics/isolation & purification/pathogenicity ; Feces/*microbiology ; *Food Microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Integrons/*genetics ; Mutagenesis, Insertional ; Swine/*microbiology ; Symbiosis ; Virulence/genetics ; Whole Genome Sequencing ; Zoonoses/microbiology ; }, abstract = {Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.}, } @article {pmid30703093, year = {2019}, author = {Suzaki, T and Takeda, N and Nishida, H and Hoshino, M and Ito, M and Misawa, F and Handa, Y and Miura, K and Kawaguchi, M}, title = {Correction: LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus.}, journal = {PLoS genetics}, volume = {15}, number = {1}, pages = {e1007966}, doi = {10.1371/journal.pgen.1007966}, pmid = {30703093}, issn = {1553-7404}, abstract = {[This corrects the article DOI: 10.1371/journal.pgen.1007865.].}, } @article {pmid30700990, year = {2018}, author = {Sogawa, A and Yamazaki, A and Yamasaki, H and Komi, M and Manabe, T and Tajima, S and Hayashi, M and Nomura, M}, title = {SNARE Proteins LjVAMP72a and LjVAMP72b Are Required for Root Symbiosis and Root Hair Formation in Lotus japonicus.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1992}, doi = {10.3389/fpls.2018.01992}, pmid = {30700990}, issn = {1664-462X}, abstract = {SNARE (soluble N-ethyl maleimide sensitive factor attachment protein receptor) proteins mediate membrane trafficking in eukaryotic cells. Both LjVAMP72a and LjVAMP72b are members of R-SNARE and belong to a symbiotic subgroup of VAMP72 in Lotus japonicus. Their sequences are closely related and both were induced in the root upon rhizobial inoculation. The expression level of LjVAMP72a in the nodules was higher than in the leaves or roots; however, LjVMAP72b was expressed constitutively in the leaves, roots, and nodules. Immunoblot analysis showed that not only LjVAMP72a but also LjVAMP72b were accumulated in a symbiosome-enriched fraction, suggesting its localization in the symbiosome membrane during nodulation. Since there was 89% similarity between LjVAMP72a and LjVAMP72b, knockdown mutant by RNAi suppressed both genes. The suppression of both genes impaired root nodule symbiosis (RNS). The number of bacteroids and the nitrogen fixation activity were severely curtailed in the nodules formed on knockdown roots (RNAi-LjVAMP72a/72b). Arbuscular mycorrhization (AM) was also attenuated in knockdown roots, indicating that LjVAMP72a and LjVAMP72b were required to establish not only RNS but also AM. In addition, transgenic hairy roots of RNAi-LjVAMP72a/72b suppressed the elongation of root hairs without infections by rhizobia or arbuscular mycorrhizal fungi. Amino acid alignment showed the symbiotic subclade of VAMP72s containing LjVAMP72a and LjVAMP72b were a conserved six amino acid region (HHQAQD) within the SNARE motif. Taken together, our data suggested that LjVAMP72a and LjVAMP72b positively controlled both symbioses and root hair formation by affecting the secretory pathway.}, } @article {pmid30468749, year = {2019}, author = {Moran, RA and Hall, RM}, title = {pBuzz: A cryptic rolling-circle plasmid from a commensal Escherichia coli has two inversely oriented oriTs and is mobilised by a B/O plasmid.}, journal = {Plasmid}, volume = {101}, number = {}, pages = {10-19}, doi = {10.1016/j.plasmid.2018.11.001}, pmid = {30468749}, issn = {1095-9890}, mesh = {ATP-Binding Cassette Transporters/*genetics/metabolism ; Ampicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Base Pairing ; Base Sequence ; *Conjugation, Genetic ; DNA Replication ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/growth & development ; Escherichia coli Proteins/*genetics/metabolism ; Humans ; Plasmids/*chemistry/metabolism ; Sequence Alignment ; Streptomycin/pharmacology ; Sulfamethoxazole/pharmacology ; Symbiosis/physiology ; }, abstract = {Ampicillin, streptomycin and sulphamethoxazole resistant commensal E. coli 838-3B contains five plasmids that range in size from >90 kb to <2 kb. The resistance genes blaTEM (ampicillin), strA (streptomycin) and sul2 (sulphamethoxazole) transferred along with a B/O plasmid named p838B-R. However, three plasmids smaller than 7 kb were also found in transconjugants, suggesting that they could be mobilised by the B/O plasmid. The complete sequences of p838B-R and pBuzz, a small plasmid mobilised by p838B-R with 70% efficiency, were determined. p838B-R is 94,803 bp and contains an 8400 bp resistance island that includes the three antibiotic resistance genes. The p838B-R backbone contains a complete conjugative transfer region, including an oriT site upstream of nikAB that resembles the experimentally-defined oriT of R64. The 1982 bp pBuzz contains a rep gene and sites associated with replication that resemble those of pC194/pUB110 family rolling-circle plasmids. It also contains two, inversely oriented copies of an 84 bp sequence that differs from the oriT region in p838B-R at just 6 positions. These oriT-like sites likely explain the ability of pBuzz to co-transfer with the B/O plasmid using the NikB relaxase and NikA accessory protein encoded by p838B-R, i.e. pBuzz utilises relaxase-in trans mobilisation. Several rolling-circle plasmids related to pBuzz were found in the GenBank non-redundant nucleotide database. They contain diverse potential oriTs, including sequences similar to known oriTs found in conjugative plasmids of I-complex (I1, B/O, K, Z and I2), L or M types.}, } @article {pmid30317530, year = {2019}, author = {Adak, A and Khan, MR}, title = {An insight into gut microbiota and its functionalities.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {76}, number = {3}, pages = {473-493}, doi = {10.1007/s00018-018-2943-4}, pmid = {30317530}, issn = {1420-9071}, support = {under Unit of Excellence Project (BT/550/NE/U-Excel/2014)//Department of Science and Technology, India/ ; }, mesh = {Computational Biology ; Gastrointestinal Microbiome/genetics/immunology/*physiology ; Gastrointestinal Tract/microbiology ; Humans ; Symbiosis ; }, abstract = {Gut microbiota has evolved along with their hosts and is an integral part of the human body. Microbiota acquired at birth develops in parallel as the host develops and maintains its temporal stability and diversity through adulthood until death. Recent developments in genome sequencing technologies, bioinformatics and culturomics have enabled researchers to explore the microbiota and in particular their functions at more detailed level than before. The accumulated evidences suggest that though a part of the microbiota is conserved, the dynamic members vary along the gastrointestinal tract, from infants to elderly, primitive tribes to modern societies and in different health conditions. Though the gut microbiota is dynamic, it performs some basic functions in the immunological, metabolic, structural and neurological landscapes of the human body. Gut microbiota also exerts significant influence on both physical and mental health of an individual. An in-depth understanding of the functioning of gut microbiota has led to some very exciting developments in therapeutics, such as prebiotics, probiotics, drugs and faecal transplantation leading to improved health.}, } @article {pmid29452714, year = {2018}, author = {Stefan, A and Van Cauwenberghe, J and Rosu, CM and Stedel, C and Labrou, NE and Flemetakis, E and Efrose, RC}, title = {Genetic diversity and structure of Rhizobium leguminosarum populations associated with clover plants are influenced by local environmental variables.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {3}, pages = {251-259}, doi = {10.1016/j.syapm.2018.01.007}, pmid = {29452714}, issn = {1618-0984}, mesh = {Altitude ; DNA, Bacterial/genetics ; Genes, Bacterial ; *Genetic Variation ; Genetics, Population ; Medicago/*microbiology ; Multilocus Sequence Typing ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobium leguminosarum/*genetics ; Romania ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil/chemistry ; Symbiosis ; Trifolium/*microbiology ; }, abstract = {The identification and conservation of indigenous rhizobia associated with legume plants and their application as biofertilizers is becoming an agricultural worldwide priority. However, little is known about the genetic diversity and phylogeny of rhizobia in Romania. In the present study, the genetic diversity and population composition of Rhizobium leguminosarum symbiovar trifolii isolates from 12 clover plants populations located across two regions in Romania were analyzed. Red clover isolates were phenotypically evaluated and genotyped by sequencing 16S rRNA gene, 16S-23S intergenic spacer, three chromosomal genes (atpD, glnII and recA) and two plasmid genes (nifH and nodA). Multilocus sequence typing (MLST) analysis revealed that red clover plants are nodulated by a wide genetic diversity of R. leguminosarum symbiovar trifolii sequence types (STs), highly similar to the ones previously found in white clover. Rhizobial genetic variation was found mainly within the two clover populations for both chromosomal and plasmid types. Many STs appear to be unique for this region and the genetic composition of rhizobia differs significantly among the clover populations. Furthermore, our results showed that both soil pH and altitude contributed to plasmid sequence type composition while differences in chromosomal composition were affected by the altitude and were strongly correlated with distance.}, } @article {pmid29426636, year = {2018}, author = {Schrallhammer, M and Castelli, M and Petroni, G}, title = {Phylogenetic relationships among endosymbiotic R-body producer: Bacteria providing their host the killer trait.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {3}, pages = {213-220}, doi = {10.1016/j.syapm.2018.01.005}, pmid = {29426636}, issn = {1618-0984}, mesh = {Alphaproteobacteria/*classification/genetics ; Bacterial Proteins/*genetics ; DNA, Bacterial/genetics ; Paramecium/*microbiology/physiology ; Phenotype ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {R-body producing bacterial endosymbionts of Paramecium spp. transform their hosts into "killer" paramecia and provide them a selective advantage. This killer trait is connected to the presence of R-bodies, which are peculiar, tightly coiled protein ribbons capable of rapid unrolling. Based mainly on those two characteristics the respective obligate intracellular bacteria have been comprised in the genus Caedibacter and additional traits such as host species, subcellular localization, and R-body dimensions and mode of unrolling were used for species discrimination. Previous studies applying the full-cycle rRNA approach demonstrated the polyphyly of this assemblage. Following this approach, we obtained new sequences and in situ hybridizations for five strains of Caedibacter taeniospiralis and four strains associated to Caedibacter varicaedens and Caedibacter caryophilus. Detailed phylogenetic reconstructions confirm the association of C. taeniospiralis to Fastidiosibacteraceae and to Holosporales in case of the others. Therefore, we critically revise the taxonomy of the latter group. The high 16S rRNA gene sequence similarity among the type strains of Caedibacter varicaedens and C. caryophilus indicate that they should be classified within a single species for which we propose Caedimonas varicaedens comb. nov. owing to the priority of Caedibacter varicaedens. Moreover, we propose to establish the new family Caedimonadaceae fam. nov. to encompass Caedimonas varicaedens, "Ca. Paracaedimonas acanthamoebae" comb. nov. and "Ca. Nucleicultrix amoebiphila" within the order Holosporales.}, } @article {pmid29310897, year = {2018}, author = {Belhadi, D and de Lajudie, P and Ramdani, N and Le Roux, C and Boulila, F and Tisseyre, P and Boulila, A and Benguedouar, A and Kaci, Y and Laguerre, G}, title = {Vicia faba L. in the Bejaia region of Algeria is nodulated by Rhizobium leguminosarum sv. viciae, Rhizobium laguerreae and two new genospecies.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {2}, pages = {122-130}, doi = {10.1016/j.syapm.2017.10.004}, pmid = {29310897}, issn = {1618-0984}, mesh = {Algeria ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Genes, Bacterial ; Multilocus Sequence Typing ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rhizobium/*classification/genetics/isolation & purification ; Rhizobium leguminosarum/*classification/genetics/isolation & purification ; Root Nodules, Plant/microbiology ; Sequence Analysis, DNA ; Symbiosis ; Vicia faba/*microbiology ; }, abstract = {Fifty-eight rhizobial strains were isolated from root nodules of Vicia faba cv. Equina and Vicia faba cv. Minor by the host-trapping method in soils collected from eleven sites in Bejaia, Eastern Algeria. Eleven genotypic groups were distinguished based on the combined PCR/RFLP of 16S rRNA, 16S-23S rRNA intergenic spacer and symbiotic (nodC and nodD-F) genes and further confirmed by multilocus sequence analysis (MLSA) of three housekeeping genes (recA, atpD and rpoB), the 16S rRNA gene and the nodulation genes nodC and nodD. Of the 11 genotypes, 5 were dominant and 2 were the most represented. Most of the strains shared high nodD gene sequence similarity with Rhizobium leguminosarum sv. viciae; their nodC sequences were similar to both Rhizobium leguminosarum and Rhizobium laguerreae. Sequence analyses of the 16S-23S rRNA intergenic spacer showed that all the new strains were phylogenetically related to those described from Vicia sativa and V. faba in several African, European, American and Asian countries, with which they form a group related to Rhizobium leguminosarum. Phylogenetic analysis based on MLSA of 16S rRNA, recA, atpD and rpoB genes allowed the affiliations of strain AM11R to Rhizobium leguminosarum sv. viciae and of strains EB1 and ES8 to Rhizobium laguerreae. In addition, two separate clades with <97% similarity may represent two novel genospecies within the genus Rhizobium.}, } @article {pmid29307475, year = {2018}, author = {Taha, K and Berraho, EB and El Attar, I and Dekkiche, S and Aurag, J and Béna, G}, title = {Rhizobium laguerreae is the main nitrogen-fixing symbiont of cultivated lentil (Lens culinaris) in Morocco.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {2}, pages = {113-121}, doi = {10.1016/j.syapm.2017.09.008}, pmid = {29307475}, issn = {1618-0984}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial ; Genes, Bacterial ; Genetic Variation ; Genetics, Population ; Lens Plant/*microbiology ; Morocco ; *Nitrogen Fixation ; *Phylogeny ; RNA, Ribosomal, 16S ; Rhizobium/*classification/genetics ; Root Nodules, Plant/microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Genetic diversity and population structure of 268 Lens culinaris symbiotic rhizobia collected from 40 cultivated fields in the main lentil production regions in Morocco were estimated. Three chromosomal housekeeping genes (recA, glnII and atpD) and one common symbiotic gene (nodC) were sequenced and analyzed in order to identify the local symbionts of lentil. The molecular phylogeny of the concatenated housekeeping genes clustered more than 95% of the isolates in one main clade together with Rhizobium laguerreae species. R. laguerreae represents the main symbiont of cultivated lentil in Morocco and, for the first time, a large sample of individuals is obtained for this species. There is a significant and high genetic differentiation of bacterial populations among the four regions for their symbiotic gene, and much lower for their housekeeping genes. The reasons why R. laguerreae is so frequently recovered in our study is discussed.}, } @article {pmid30697746, year = {2019}, author = {Gibert, A and Tozer, W and Westoby, M}, title = {Plant performance response to eight different types of symbiosis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15392}, pmid = {30697746}, issn = {1469-8137}, support = {//Australian Research Council/ ; }, abstract = {Almost all plant species interact with one or more symbioses somewhere within their distribution range. Bringing together plant trait data and growth responses to symbioses spanning 552 plant species, we provide for the first time on a large scale (597 studies) a quantitative synthesis on plant performance differences between eight major types of symbiosis, including mycorrhizas, N-fixing bacteria, fungal endophytes and ant-plant interactions. Frequency distributions of plant growth responses varied considerably between different types of symbiosis, in terms of both mean effect and 'risk', defined here as percentage of experiments reporting a negative effect of symbiosis on plants. Contrary to expectation, plant traits were poor predictors of growth response across and within all eight symbiotic associations. Our analysis showed no systematic additive effect when a host plant engaged in two functionally different symbioses. This synthesis suggests that plant species' ecological strategies have little effect in determining the influence of a symbiosis on host plant growth. Reliable quantification of differences in plant performance across symbioses will prove valuable for developing general hypotheses on how species become engaged in mutualisms without a guarantee of net returns.}, } @article {pmid30696553, year = {2019}, author = {Lynge Pedersen, AM and Belstrøm, D}, title = {The role of natural salivary defences in maintaining a healthy oral microbiota.}, journal = {Journal of dentistry}, volume = {80 Suppl 1}, number = {}, pages = {S3-S12}, doi = {10.1016/j.jdent.2018.08.010}, pmid = {30696553}, issn = {1879-176X}, abstract = {OBJECTIVES: To provide an update on our current understanding of how saliva and its various constituents directly and indirectly affect oral bacteria and thereby play a role in the modulation and maintenance of a healthy oral microbiota and also the associations with symbiosis and dysbiosis.

METHODS: The search for biomedical literature on saliva and its antimicrobial activities (years 1966 to 2017) was conducted in PubMed, Embase and Web of Science databases.

RESULTS: This review underlines that saliva plays an essential role in shaping and maintaining the ecological equilibrium of the resident oral microbiota. Saliva contributes to the formation of the salivary pellicle, which covers the oral hard and soft tissues, and thereby determines the initial adhesion and colonisation of microorganisms. Saliva facilitates clearance of dietary carbohydrates and microorganisms from the oral cavity, but also supplies bacteria with nutrients through enzymatic breakdown of dietary starch and proteins and salivary glycoproteins. In addition, saliva comprises proteins such as mucins, which block the adherence of certain microorganisms to oral surfaces through binding and aggregating mechanisms. Saliva also provides antimicrobial activity through numerous proteins and peptides including mucins, lactoferrin, lysozyme, lactoperoxidase, statherin, histatins and secretory immunoglobulin A.

CONCLUSIONS: A balanced oral microbiome is important for the maintenance of oral health and symbiosis. Conditions associated with salivary gland hypofunction, impaired oral clearance, low salivary pH and altered salivary composition, often lead to perturbation of the function and composition of the oral microbiome causing dysbiosis, and an associated risk of oral disease.

CLINICAL SIGNIFICANCE: Saliva plays a significant role in keeping the relationship between the host and oral microbiota in a symbiotic state. In conditions with salivary gland dysfunction, the natural balance of the oral microbiome is often disturbed, leading to dysbiosis and associated risks of gingivitis, caries and fungal infection.}, } @article {pmid30695562, year = {2016}, author = {Sidelnikov, GD and Valikhov, AR}, title = {[On the role of endogenous retroviruses in tumor growth biology].}, journal = {Voprosy onkologii}, volume = {62}, number = {6}, pages = {758-766}, pmid = {30695562}, issn = {0507-3758}, abstract = {Retrotransposons are the mobile part of the genetic material in mammals. Such a close proximity is a unique in its kind example of the genetic symbiosis. As a result of long-term co-evolution retroviruses purchased the actual immortality and protection from adverse factors, providing instead the recombinant opportunities of its genetic apparatus for the implementation of the evolutionary, adaptive and biological processes that are vital to the host organism. The consequence of the violation of the established biological balance is the pathological activity of retrotransposons that can affect the expression of any gene. This review examines the point of view on the key role of retrotrasposons in the biology of tumor development as a result of aggressive parasitism and speculates about the causes of the violations of adequate immune response in the process of tumor growth.}, } @article {pmid30341476, year = {2018}, author = {Li, J and Liu, S and Guo, K and Zhang, F and Qiao, H and Chen, J and Yang, M and Zhu, X and Xu, R and Xu, C and Chen, J}, title = {Plant-mediated competition facilitates a phoretic association between a gall mite and a psyllid vector.}, journal = {Experimental & applied acarology}, volume = {76}, number = {3}, pages = {325-337}, pmid = {30341476}, issn = {1572-9702}, support = {81673699//National Natural Science Foundation of China/ ; 81470168//National Natural Science Foundation of China/ ; 2016-I2 M-3-017//Chinese Academy of Medical Science Innovation Fund for Medical Science/ ; }, mesh = {Animals ; Female ; Hemiptera/growth & development/*physiology ; Larva/growth & development/physiology ; *Lycium/growth & development ; Male ; Mites/growth & development/*physiology ; Nymph/growth & development/physiology ; Plant Tumors/parasitology ; *Symbiosis ; }, abstract = {Phoretic associations between mites and insects commonly occur in patchy and ephemeral habitats. As plants provide stable habitats for herbivores, herbivorous mites are rarely dependent on other animals for phoretic dispersal. However, a phoretic gall mite, Aceria pallida, which is found on plants, seasonally attaches to a herbivorous insect, Bactericera gobica, for overwintering survival. After detachment, the gall mite shares a habitat with its vector and is likely to compete with this vector for plant resources. However, excessive competition works against the sustainability of the seasonal phoretic association. How the gall mite, as an obligate phoretic mite, balances this relationship with its vector during the growing season to achieve phoresy is unknown. Here, the plant-mediated interspecific interaction between the gall mite and the psyllid after detachment was studied in the laboratory and field. The laboratory results showed that infestation by the gall mite had detrimental effects on the survival and development of psyllid nymphs. Meanwhile, the mite population and the gall size were also adversely affected. The results from the field showed that the mean densities of the mite galls and psyllids were lower in the mixed-species infestation treatment than in the single-species infestation treatment across the investigation period. However, the interspecific interaction between the gall mite and the psyllid decreased rather than accelerated leaf abscission caused by the psyllid, which promoted the persistence of the psyllid population and then indirectly contributed to phoretic association. Our results suggest that the plant-mediated competition between the phoretic gall mite and its vector after detachment facilitates the maintenance of the phoretic association.}, } @article {pmid30169517, year = {2018}, author = {Borst, ACW and Verberk, WCEP and Angelini, C and Schotanus, J and Wolters, JW and Christianen, MJA and van der Zee, EM and Derksen-Hooijberg, M and van der Heide, T}, title = {Foundation species enhance food web complexity through non-trophic facilitation.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0199152}, pmid = {30169517}, issn = {1932-6203}, mesh = {Animals ; Behavior, Animal/*physiology ; *Biodiversity ; Dominance-Subordination ; *Ecosystem ; *Food Chain ; Founder Effect ; Predatory Behavior/*physiology ; Principal Component Analysis ; Species Specificity ; Symbiosis/*physiology ; }, abstract = {Food webs are an integral part of every ecosystem on the planet, yet understanding the mechanisms shaping these complex networks remains a major challenge. Recently, several studies suggested that non-trophic species interactions such as habitat modification and mutualisms can be important determinants of food web structure. However, it remains unclear whether these findings generalize across ecosystems, and whether non-trophic interactions affect food webs randomly, or affect specific trophic levels or functional groups. Here, we combine analyses of 58 food webs from seven terrestrial, freshwater and coastal systems to test (1) the general hypothesis that non-trophic facilitation by habitat-forming foundation species enhances food web complexity, and (2) whether these enhancements have either random or targeted effects on particular trophic levels, functional groups, and linkages throughout the food web. Our empirical results demonstrate that foundation species consistently enhance food web complexity in all seven ecosystems. Further analyses reveal that 15 out of 19 food web properties can be well-approximated by assuming that foundation species randomly facilitate species throughout the trophic network. However, basal species are less strongly, and carnivores are more strongly facilitated in foundation species' food webs than predicted based on random facilitation, resulting in a higher mean trophic level and a longer average chain length. Overall, we conclude that foundation species strongly enhance food web complexity through non-trophic facilitation of species across the entire trophic network. We therefore suggest that the structure and stability of food webs often depends critically on non-trophic facilitation by foundation species.}, } @article {pmid30130476, year = {2018}, author = {Czyzewska, U and Bartoszewicz, M and Siemieniuk, M and Tylicki, A}, title = {Genetic relationships and population structure of Malassezia pachydermatis strains isolated from dogs with otitis externa and healthy dogs.}, journal = {Mycologia}, volume = {110}, number = {4}, pages = {666-676}, doi = {10.1080/00275514.2018.1495981}, pmid = {30130476}, issn = {1557-2536}, mesh = {Animals ; DNA, Intergenic ; DNA, Ribosomal ; Dog Diseases/epidemiology/*microbiology ; Dogs/microbiology ; *Genetic Variation ; Genotype ; Malassezia/*genetics/isolation & purification/*pathogenicity/physiology ; Otitis Externa/epidemiology/microbiology/*veterinary ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Random Amplified Polymorphic DNA Technique ; Symbiosis ; Virulence ; }, abstract = {Malassezia pachydermatis causes infections of the skin and mucous membranes, especially in animals. It is commonly accepted that symptom manifestation depends on the physiological status of the host (different metabolic, hormonal, and immunological disorders). However, it should be considered whether distinct strains of M. pachydermatis could have different pathogenic potential and maintain opposite relations with the host, such as commensalism or parasitism. The scope of this study was to explore the population structure, genetic diversity, and phylogenetic relationships of M. pachydermatis strains isolated from dogs with clinical symptoms of otitis externa and from healthy dogs in order to investigate their relationships and evolutionary history. For all tests, a group of 30 strains derived from dogs with otitis externa and 34 strains from healthy dogs were used. The level of genetic diversity was initially assessed by polymerase chain reaction (PCR)-based random amplification of polymorphic DNA (RAPD-PCR), whereas evolutionary history was assessed by comparison of the nucleotide sequences of the internal transcribed spacer ITS1 region of nuclear rDNA. RAPD-PCR fingerprinting revealed a high level of genetic polymorphism in both tested groups (85% of unique profiles), but clinical isolates usually grouped together with other strains from otitis externa cases. Sequencing analysis identified 17 distinct genotypes with 59 polymorphic sites within both populations; however, putatively virulent strains were more closely related, indicating a probable correlation between the genotype and the virulence potential. Therefore, the hypothesis that M. pachydermatis virulence depends solely on the host's properties should be reconsidered including evolutionary and epidemiological data.}, } @article {pmid30016354, year = {2018}, author = {Adachi, S and Honma, T and Yasaka, R and Ohshima, K and Tokuda, M}, title = {Effects of infection by Turnip mosaic virus on the population growth of generalist and specialist aphid vectors on turnip plants.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200784}, pmid = {30016354}, issn = {1932-6203}, mesh = {Animals ; Aphids/*virology ; Brassica napus/*virology ; Hydrogen-Ion Concentration ; Insect Vectors/virology ; Japan ; Phylogeny ; Plant Diseases/*virology ; Population Growth ; *Potyvirus ; Raphanus ; Species Specificity ; *Symbiosis ; Viral Proteins/genetics ; }, abstract = {Recent studies have revealed that relationships between plant pathogens and their vectors differ depending on species, strains and associated host plants. Turnip mosaic virus (TuMV) is one of the most important plant viruses worldwide and is transmitted by at least 89 aphid species in a non-persistent manner. TuMV is fundamentally divided into six phylogenetic groups; among which Asian-BR, basal-BR and world-B groups are known to occur in Japan. In Kyushu Japan, basal-BR has invaded approximately 2000 and immediately replaced the predominant world-B virus group. To clarify the relationships between TuMV and vector aphids, we examined the effects of the TuMV phylogenetic group on the population growth of aphid vectors in turnip plants. The population growth of a generalist aphid, Myzus persicae, was not significantly different between non-infected and TuMV-infected treatments. The population growth of a specialist aphid, Lipaphis erysimi, was higher in TuMV-infected plants than non-infected ones. Similar results were obtained in experiments using world-B and basal-BR groups of TuMV. Therefore, we conclude that L. erysimi is more mutualistic with TuMV than M. persicae, and differences in TuMV phylogenetic groups do not affect the growth of aphid vectors on turnip plants.}, } @article {pmid30016257, year = {2018}, author = {Brouat, C and Diagne, CA and Ismaïl, K and Aroussi, A and Dalecky, A and Bâ, K and Kane, M and Niang, Y and Diallo, M and Sow, A and Galal, L and Piry, S and Dardé, ML and Mercier, A}, title = {Seroprevalence of Toxoplasma gondii in commensal rodents sampled across Senegal, West Africa.}, journal = {Parasite (Paris, France)}, volume = {25}, number = {}, pages = {32}, pmid = {30016257}, issn = {1776-1042}, mesh = {Africa, Western/epidemiology ; Agglutination Tests ; Animals ; Antibodies, Protozoan/*blood ; Female ; Humans ; Male ; Murinae/*parasitology ; Rodent Diseases ; Senegal/epidemiology ; *Seroepidemiologic Studies ; Symbiosis ; Toxoplasma/*immunology ; Toxoplasmosis, Animal/blood/*epidemiology/*immunology/parasitology ; }, abstract = {Risks related to Toxoplasma gondii infection in humans remain poorly known in Senegal. Although rodent surveys could help to assess the circulation of T. gondii, they have seldom been set up in sub-Saharan Africa. The aim of this study was to examine Toxoplasma seroprevalence in rodents from villages and towns across Senegal. Rodents were sampled in 40 localities using a standardised trapping protocol. Detection of T. gondii antibodies was performed on 1205 rodents, using a modified agglutination test (MAT) technique. Seroprevalence data were analysed depending on geography, the local rodent community, and individual characteristics of the rodent hosts. We found 44 seropositive rodents from four different species (Mastomys erythroleucus, Mastomys natalensis, Mus musculus domesticus, Rattus rattus). Toxoplasma seroprevalence was low, averaging 4% in the localities. Higher Toxoplasma seroprevalence (up to 24%) was found in northern Senegal, a region known to be the heart of pastoral herding in the country.}, } @article {pmid29990378, year = {2018}, author = {Vicente, CSL and Mondal, SI and Akter, A and Ozawa, S and Kikuchi, T and Hasegawa, K}, title = {Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200512}, pmid = {29990378}, issn = {1932-6203}, mesh = {Ammonia/chemistry ; Animals ; Bacteroidetes/*genetics ; Blattellidae/*microbiology ; DNA, Bacterial/genetics ; *Genome, Bacterial ; Male ; Nitrogen/chemistry ; Periplaneta/*microbiology ; Phylogeny ; Symbiosis ; Urea/chemistry ; Uric Acid/chemistry ; }, abstract = {The successful adaptation of cockroaches is, in part, dependent of the activity of their obligatory endosymbionts, Blattabacterium spp., which are involved in uric acid degradation, nitrogen assimilation and nutrient provisioning. Their strategic localization, within bacteriocytes in the proximities of uric acid storage cells (urocytes), highlights their importance in the recycling of nitrogen from urea and ammonia, end-products not secreted by their host insects. In this study, we present the complete genome sequence of two new Blattabacterium spp. from Periplaneta fuliginosa (BPfu) and P. japonica (BPja), and detailed comparison with other Blattabacterium strains from different cockroach species. The genomes of BPfu and BPja show a high degree of stability as showed with for other Blattabacterium representatives, only presenting a 19-kb fragment inversion between BPja and BPfu. In fact, the phylogenomics showed BPja as an ancestor species of BPfu, BPLAN (P. americana) and BBor (Blatta orientalis), in congruence with their host cockroach phylogeny. Their functional profile is similar and closest to the omnivorous strain BBge (Blattella germanica). Interesting, BPja possesses the complete set of enzymes involved sulfate assimilatory pathway only found in BBge and BMda (Mastotermes darwiniensis). The newly sequenced genomes of BPja and BPfu emphasise the remarkable stability of Blattabacterium genomes supported by their long-term coevolution and obligatory lifestyle in their host insect.}, } @article {pmid29950179, year = {2018}, author = {Rami, A and Raz, A and Zakeri, S and Dinparast Djadid, N}, title = {Isolation and identification of Asaia sp. in Anopheles spp. mosquitoes collected from Iranian malaria settings: steps toward applying paratransgenic tools against malaria.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {367}, pmid = {29950179}, issn = {1756-3305}, mesh = {Acetobacteraceae/cytology/genetics/*isolation & purification/*physiology ; Animals ; Anopheles/anatomy & histology/*microbiology ; Biological Control Agents ; Digestive System/microbiology ; Female ; Humans ; Iran/epidemiology ; Larva/physiology ; Malaria/*epidemiology/parasitology/prevention & control ; Male ; Microbiota ; Middle East/epidemiology ; Mosquito Control/methods ; Mosquito Vectors/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {BACKGROUND: In recent years, the genus Asaia (Rhodospirillales: Acetobacteraceae) has been isolated from different Anopheles species and presented as a promising tool to combat malaria. This bacterium has unique features such as presence in different organs of mosquitoes (midgut, salivary glands and reproductive organs) of female and male mosquitoes and vertical and horizontal transmission. These specifications lead to the possibility of introducing Asaia as a robust candidate for malaria vector control via paratransgenesis technology. Several studies have been performed on the microbiota of Anopheles mosquitoes (Diptera: Culicidae) in Iran and the Middle East to find a suitable candidate for controlling the malaria based on paratransgenesis approaches. The present study is the first report of isolation, biochemical and molecular characterization of the genus Asaia within five different Anopheles species which originated from different zoogeographical zones in the south, east, and north of Iran.

METHODS: Mosquitoes originated from field-collected and laboratory-reared colonies of five Anopheles spp. Adult mosquitoes were anesthetized; their midguts were isolated by dissection, followed by grinding the midgut contents which were then cultured in enrichment broth media and later in CaCO3 agar plates separately. Morphological, biochemical and physiological characterization were carried out after the appearance of colonies. For molecular confirmation, selected colonies were cultured, their DNAs were extracted and PCR was performed on the 16S ribosomal RNA gene using specific newly designed primers.

RESULTS: Morphological, biochemical, physiological and molecular results indicated that all isolates are members of the genus Asaia.

CONCLUSIONS: Contrary to previous opinions, our findings show that Asaia bacteria are present in both insectary-reared colonies and field-collected mosquitoes and can be isolated by simple and specific methods. Furthermore, with respect to the fact that we isolated Asaia within the different Anopheles specimens from distinct climatic and zoogeographical regions, it is promising and may be concluded that species of this genus can tolerate the complicated environmental conditions of the vector-borne diseases endemic regions. Therefore, it can be considered as a promising target in paratransgenesis and vector control programs. However, we suggest that introducing the new technologies such as next generation sequencing and robust in silico approaches may pave the way to find a unique biomarker for rapid and reliable differentiation of the Asaia species.}, } @article {pmid29776375, year = {2018}, author = {Kaufman, EL and Stone, NE and Scoles, GA and Hepp, CM and Busch, JD and Wagner, DM}, title = {Range-wide genetic analysis of Dermacentor variabilis and its Francisella-like endosymbionts demonstrates phylogeographic concordance between both taxa.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {306}, pmid = {29776375}, issn = {1756-3305}, support = {2010-65104-20386//National Institute of Food and Agriculture/International ; }, mesh = {Animals ; Arachnid Vectors/microbiology ; Canada ; Coxiella burnetii/genetics/pathogenicity ; DNA, Bacterial/genetics ; Dermacentor/classification/*genetics/*microbiology ; Disease Vectors ; Francisella/classification/*genetics/pathogenicity ; Genes, Mitochondrial/genetics ; Humans ; *Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Rickettsia/genetics/pathogenicity ; Sequence Analysis, DNA/methods ; Symbiosis/genetics ; United States ; }, abstract = {BACKGROUND: The American dog tick, Dermacentor variabilis, is an important vector of pathogens to humans, wildlife and domestic animals in North America. Although this tick species is widely distributed in the USA and Canada, knowledge of its range-wide phylogeographic patterns remains incomplete.

METHODS: We carried out a phylogenetic analysis of D. variabilis using samples collected from 26 USA states and five Canadian provinces. Tick samples (n = 1053 in total) originated from two main sources: existing archives (2000-2011), and new collections made from 2012 to 2013. We sequenced a 691 bp fragment of the cox1 gene from a subset (n = 332) of geographically diverse D. variabilis. DNA extracted from individual ticks (n = 1053) was also screened for a Francisella-like endosymbiont, using a targeted 16S rRNA sequencing approach, and important pathogens (Rickettsia spp. and Coxiella burnetii), using species-specific quantitative PCR assays.

RESULTS: Maximum parsimony analysis of cox1 sequences revealed two major groups within D. variabilis with distinct geographical distributions: one from the eastern USA/Canada (Group 1) and one from the west coast states of the USA (California and Washington; Group 2). However, genetic subdivisions within both of these two major groups were weak to moderate and not tightly correlated with geography. We found molecular signatures consistent with Francisella-like endosymbionts in 257 of the DNA extracts from the 1053 individual ticks, as well as Rickettsia spp. and Coxiella burnetii in a small number of ticks (n = 29 and 2, respectively). Phylogenetic patterns for Francisella-like endosymbionts, constructed using sequence data from the bacterial 16S rRNA locus, were similar to those for D. variabilis, with two major groups that had a nearly perfect one-to-one correlation with the two major groups within D. variabilis.

CONCLUSIONS: Our findings reveal a distinct phylogenetic split between the two major D. variabilis populations. However, high levels of genetic mixture among widely separated geographical localities occur within each of these two major groups. Furthermore, our phylogenetic analyses provide evidence of long-term tick-symbiont co-evolution. This work has implications for understanding the dispersal and evolutionary ecology of D. variabilis and associated vector-borne diseases.}, } @article {pmid29748120, year = {2018}, author = {Špitalská, E and Sparagano, O and Stanko, M and Schwarzová, K and Špitalský, Z and Škultéty, Ľ and Havlíková, SF}, title = {Diversity of Coxiella-like and Francisella-like endosymbionts, and Rickettsia spp., Coxiella burnetii as pathogens in the tick populations of Slovakia, Central Europe.}, journal = {Ticks and tick-borne diseases}, volume = {9}, number = {5}, pages = {1207-1211}, doi = {10.1016/j.ttbdis.2018.05.002}, pmid = {29748120}, issn = {1877-9603}, mesh = {Animals ; Arachnid Vectors/*microbiology ; Bacterial Infections/epidemiology/transmission ; Coxiella/cytology/genetics/isolation & purification/pathogenicity ; Coxiella burnetii/genetics/*isolation & purification/pathogenicity ; DNA, Bacterial/genetics ; Dermacentor/microbiology ; Female ; Francisella/classification/genetics/*isolation & purification/pathogenicity ; Ixodes/microbiology ; Ixodidae/*microbiology ; Male ; Phylogeny ; Public Health ; Rickettsia/genetics/*isolation & purification/pathogenicity ; Slovakia/epidemiology ; Symbiosis ; }, abstract = {Ticks are important vectors of pathogens affecting humans and animals worldwide. They do not only carry pathogens but diverse commensal and symbiotic microorganisms are also present in ticks. A molecular screening for tick-borne pathogens and endosymbionts was carried out in Ixodes ricinus, Dermacentor reticulatus and Haemaphysalis inermis questing ticks collected in Slovakia. The presence of Rickettsia spp., Coxiella burnetii, Coxiella-like and Francisella-like microorganisms was evaluated by PCR in 605 individuals and by randomly sequencing 66 samples. Four species of rickettsiae (R. raoultii, R. slovaca, R. helvetica and R. monacensis) were identified and reported with an overall prevalence range between 0.4 and 50.3% (±8.0) depending on tick species, sex and locality. Partial sequencing of the gltA gene of 5 chosen samples in H. inermis showed 99% identity with Candidatus Rickettsia hungarica. The total prevalence of C. burnetii in ticks was 2.2 ± 1.7%; bacteria were confirmed in I. ricinus and D. reticulatus ticks. The sequences from 2 D. reticulatus males and 1 I. ricinus female ticks were compared to GenBank submissions and a 99.8% match was obtained with the pathogenic C. burnetii. Coxiella-like endosymbionts were registered in all three species of ticks from all studied sites with an average prevalence of 32.7 ± 3.7%. A phylogenetic analysis of this Coxiella sp. showed that it does not group with the pathogenic C. burnetii. The prevalence of Francisella-like microorganisms in questing ticks was 47.9 ± 3.9%, however H. inermis (n = 108) were not infested. Obtained sequences were 98% identical with previously identified Francisella-like endosymbionts in D. reticulatus and I. ricinus. Coxiella-like and Francisella-like microorganisms were identified for the first time in Slovakia, they might be considered as a non-pathogenic endosymbiont of I. ricinus, D. reticulatus and H. inermis, and future investigations could aim to assess their role in these ticks. However, this work provided further data and broadened our knowledge on bacterial pathogens and endosymbionts present in ticks in Slovakia to help understanding co-infestations, combined treatments and public health issues linked to tick bites.}, } @article {pmid29653599, year = {2018}, author = {Li, LH and Zhang, Y and Zhu, D}, title = {Effects of antibiotic treatment on the fecundity of Rhipicephalus haemaphysaloides ticks.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {242}, pmid = {29653599}, issn = {1756-3305}, support = {2016YFC1202001 and No.2016YFC1200500//National Key Research and Development Program of China/International ; No. GWIV-29//the fourth round of Three-Year Public Health Action Plan 2015-2017/International ; No.201202019//the Special Fund for Health Research in the Public Interest China/International ; 2017BSQD52//the Scientific Research Foundation for Doctors of Weifang Medical College/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage/adverse effects/therapeutic use ; Coxiella/genetics ; DNA, Ribosomal/genetics ; Female ; Fertility/drug effects ; Male ; Microbial Consortia/drug effects/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhipicephalus/*drug effects/genetics/microbiology/*physiology ; Rickettsia/genetics ; Sequence Analysis, DNA ; Symbiosis/drug effects ; }, abstract = {BACKGROUND: Endosymbiotic bacteria inhabit a variety of arthropods including ticks and may have multiple effects on the host's survival, reproduction or pathogen acquisition and transmission. Rhipicephalus haemaphysaloides is one of the most widely distributed tick species in China. The symbiotic bacteria composition and their impacts to R. haemaphysaloides ticks have not been studied. The present study investigated the composition of microbial community in R. haemaphysaloides ticks and then assessed the effects of endosymbionts on the host's fecundity by antibiotic treatment experiments.

METHODS: The microbial population of female and male R. haemaphysaloides ticks was analyzed using Illumina Miseq sequencing of 16S rRNA gene. Thirty engorged female ticks were then randomly divided into five groups and injected with ampicillin, ciprofloxacin, kanamycin, tetracycline, or phosphate-buffered solution (PBS), respectively. Effects of antibiotic treatments on maternal oviposition, egg hatching and density of endosymbionts were evaluated.

RESULTS: Illumina Miseq sequencing showed that Coxiella and Rickettsia were the predominant bacterial genera inhabiting R. haemaphysaloides ticks. Antibiotic treatment experiments found that kanamycin reduced the density of Coxiella-like endosymbiont (Coxiella-LE hereafter) in eggs, ciprofloxacin reduced the density of Rickettsia-like endosymbiont (Rickettsia-LE), and tetracycline had effect on both endosymbionts, while ampicillin affected neither. Meanwhile hatching rates of eggs were observed to decrease greatly in the kanamycin or tetracycline-treated group but maintained in the ampicillin or ciprofloxacin-treated group. Furthermore, the reduced hatching rates were found to be associated with density of Coxiella-LE in eggs.

CONCLUSIONS: The findings indicate that Coxiella-LE is essential for the reproduction of R. haemaphysaloides ticks, and that kanamycin can be used to study the role of Coxiella-LE on ticks.}, } @article {pmid29558974, year = {2018}, author = {Altinli, M and Gunay, F and Alten, B and Weill, M and Sicard, M}, title = {Wolbachia diversity and cytoplasmic incompatibility patterns in Culex pipiens populations in Turkey.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {198}, pmid = {29558974}, issn = {1756-3305}, support = {ANR-16-CE02-0006-01//Agence Nationale de la Recherche/International ; }, mesh = {Animals ; Culex/*microbiology ; Cytoplasm/*microbiology/pathology ; DNA, Mitochondrial/genetics ; *Disease Vectors ; *Genetic Variation ; Gram-Negative Bacterial Infections/epidemiology ; Mosquito Vectors/*microbiology ; Polymerase Chain Reaction ; Reproduction ; Symbiosis ; Turkey/epidemiology ; Wolbachia/*genetics/isolation & purification/physiology ; }, abstract = {BACKGROUND: Wolbachia are maternally transmitted bacteria that can manipulate their hosts' reproduction causing cytoplasmic incompatibility (CI). CI is a sperm-egg incompatibility resulting in embryonic death. Due to this sterilising effect on mosquitoes, Wolbachia are considered for vector control strategies. Important vectors for arboviruses, filarial nematodes and avian malaria, mosquitoes of Culex pipiens complex are suitable for Wolbachia-based vector control. They are infected with Wolbachia wPip strains belonging to five genetically distinct groups (wPip-I to V) within the Wolbachia B supergroup. CI properties of wPip strongly correlate with this genetic diversity: mosquitoes infected with wPip strains from a different wPip group are more likely to be incompatible with each other. Turkey is a critical spot for vector-borne diseases due to its unique geographical position as a natural bridge between Asia, Europe and Africa. However, general wPip diversity, distribution and CI patterns in natural Cx. pipiens (s.l.) populations in the region are unknown. In this study, we first identified wPip diversity in Turkish Cx. pipiens (s.l.) populations, by assigning them to one of the five groups within wPip (wPip-Ito V). We further investigated CI properties between different wPip strains from this region.

RESULTS: We showed a wPip fixation in Cx. pipiens (s.l.) populations in Turkey by analysing 753 samples from 59 sampling sites. Three wPip groups were detected in the region: wPip-I, wPip-II and wPip-IV. The most dominant group was wPip-II. While wPip-IV was restricted to only two locations, wPip-I and wPip-II had wider distributions. Individuals infected with wPip-II were found co-existing with individuals infected with wPip-I or wPip-IV in some sampling sites. Two mosquito isofemale lines harbouring either a wPip-I or a wPip-II strain were established from a population in northwestern Turkey. Reciprocal crosses between these lines showed that they were fully compatible with each other but bidirectionally incompatible with wPip-IV Istanbul infected line.

CONCLUSION: Our findings reveal a high diversity of wPip and CI properties in Cx. pipiens (s.l.) populations in Turkey. Knowledge on naturally occurring CI patterns caused by wPip diversity in Turkey might be useful for Cx. pipiens (s.l.) control in the region.}, } @article {pmid29277086, year = {2018}, author = {Hagström, E and Andersson, SG}, title = {The challenges of integrating two genomes in one cell.}, journal = {Current opinion in microbiology}, volume = {41}, number = {}, pages = {89-94}, doi = {10.1016/j.mib.2017.12.003}, pmid = {29277086}, issn = {1879-0364}, mesh = {Bacteria/*genetics/metabolism/pathogenicity ; Cell Nucleus/genetics ; *Evolution, Molecular ; *Genome ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics ; Oxygen/metabolism ; Phylogeny ; Respiration ; Symbiosis/genetics ; }, abstract = {Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single genome. Functional gene transfers to the host nuclear genome is uncommon in mutualistic bacteria and lost gene functions are rather rescued by co-symbiotic bacteria. Recent findings suggest that the mitochondrial genome is retained to avoid conflicting signals between protein targeting pathways in the cell. However, if the selective pressure for oxygenic respiration is lost, the mitochondrial genome will start to deteriorate and soon be lost.}, } @article {pmid29183410, year = {2018}, author = {Goedknegt, MA and Shoesmith, D and Jung, AS and Luttikhuizen, PC and van der Meer, J and Philippart, CJM and van der Veer, HW and Thieltges, DW}, title = {Trophic relationship between the invasive parasitic copepod Mytilicola orientalis and its native blue mussel (Mytilus edulis) host.}, journal = {Parasitology}, volume = {145}, number = {6}, pages = {814-821}, doi = {10.1017/S0031182017001779}, pmid = {29183410}, issn = {1469-8161}, mesh = {Animals ; Copepoda/*physiology ; Ecosystem ; Feeding Behavior ; Food Chain ; *Host-Parasite Interactions ; Isotope Labeling/methods ; Mytilus edulis/parasitology/*physiology ; *Symbiosis ; }, abstract = {Invasive parasites can spill over to new hosts in invaded ecosystems with often unpredictable trophic relationships in the newly arising parasite-host interactions. In European seas, the intestinal copepod Mytilicola orientalis was co-introduced with Pacific oysters (Magallana gigas) and spilled over to native blue mussels (Mytilus edulis), with negative impacts on the condition of infected mussels. However, whether the parasite feeds on host tissue and/or stomach contents is yet unknown. To answer this question, we performed a stable isotope analysis in which we included mussel host tissue and the primary food sources of the mussels, microphytobenthos (MPB) and particulate organic matter (POM). The copepods were slightly enriched in δ15N (mean Δ15N ± s.d.; 1·22 ± 0·58‰) and δ13C (Δ13C 0·25 ± 0·32‰) with respect to their host. Stable isotope mixing models using a range of trophic fractionation factors indicated that host tissue was the main food resource with consistent additional contributions of MPB and POM. These results suggest that the trophic relationship of the invasive copepod with its mussel host is parasitic as well as commensalistic. Stable isotope studies such as this one may be a useful tool to unravel trophic relationships in new parasite-host associations in the course of invasions.}, } @article {pmid29112885, year = {2018}, author = {Neville, BA and Forster, SC and Lawley, TD}, title = {Commensal Koch's postulates: establishing causation in human microbiota research.}, journal = {Current opinion in microbiology}, volume = {42}, number = {}, pages = {47-52}, doi = {10.1016/j.mib.2017.10.001}, pmid = {29112885}, issn = {1879-0364}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Gastrointestinal Microbiome/genetics/physiology ; Humans ; Metagenomics/methods ; *Microbiota ; Research ; *Symbiosis ; }, abstract = {Advances in high-throughput sequencing technologies and the development of sophisticated bioinformatics analysis methods, algorithms, and pipelines to handle the large amounts of data generated have driven the field of human microbiome research forward. This specialist knowledge has been crucial to thoroughly mine the human gut microbiota, particularly in the absence of methods for the routine cultivation of most enteric microorganisms. In recent years, however, significant efforts have been made to address the 'great plate count anomaly' and to overcome the barriers to cultivation of the fastidious and mostly strictly anaerobic bacteria that reside in the human gut. As a result, many new species have been discovered, characterised, genome sequenced, and deposited in culture collections. These continually expanding resources enable experimental investigation of the human gut microbiota, validation of hypotheses made with sequence-based analyses, and phenotypic characterisation of its constituent microbes. Herein we propose a variant of Koch's postulates, aimed at providing a framework to establish causation in microbiome studies, with a particular focus on demonstrating the health-promoting role of the commensal gut microbiota.}, } @article {pmid29101189, year = {2018}, author = {Chidebe, IN and Jaiswal, SK and Dakora, FD}, title = {Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {2}, pages = {}, pmid = {29101189}, issn = {1098-5336}, mesh = {Bradyrhizobium/*genetics/isolation & purification/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Geography ; Mozambique ; Nitrogen Fixation ; *Phylogeny ; Plant Root Nodulation ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rhizobium/*genetics/isolation & purification/metabolism ; Root Nodules, Plant/microbiology ; Symbiosis/genetics ; Vigna/*microbiology ; }, abstract = {Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLASTn sequence analysis of 16S rRNA and four housekeeping genes (glnII, gyrB, recA, and rpoB) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, Bradyrhizobium yuanmingense, and a novel Bradyrhizobium sp., as well as Rhizobium tropici, Rhizobium pusense, and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes.IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea nodulation in Mozambique was found in this study. Future studies could prove useful in evaluating these bacterial isolates for symbiotic efficiency and strain competitiveness in Mozambican soils.}, } @article {pmid28786370, year = {2018}, author = {Zélé, F and Denoyelle, J and Duron, O and Rivero, A}, title = {Can Wolbachia modulate the fecundity costs of Plasmodium in mosquitoes?.}, journal = {Parasitology}, volume = {145}, number = {6}, pages = {775-782}, doi = {10.1017/S0031182017001330}, pmid = {28786370}, issn = {1469-8161}, mesh = {Animals ; Coinfection/microbiology/parasitology ; Culex/parasitology ; Culicidae/*microbiology/physiology ; Fertility ; *Host-Parasite Interactions ; Malaria/transmission ; Mosquito Vectors/*microbiology/physiology ; Plasmodium/pathogenicity ; Symbiosis ; Wolbachia/*pathogenicity ; }, abstract = {Vertically transmitted parasites (VTPs) such as Wolbachia are expected not only to minimize the damage they inflict on their hosts, but also to protect their hosts against the damaging effects of coinfecting parasites. By modifying the fitness costs of the infection, VTPs can therefore play an important role in the evolution and epidemiology of infectious diseases.Using a natural system, we explore the effects of a Wolbachia-Plasmodium co-infection on mosquito fecundity. While Plasmodium is known to frequently express its virulence by partially castrating its mosquito vectors, the effects of Wolbachia infections on mosquito fecundity are, in contrast, highly variable. Here, we show that Plasmodium drastically decreases the fecundity of mosquitoes by ca. 20%, and we provide the first evidence that this decrease is independent of the parasite's burden. Wolbachia, on the other hand, increases fecundity by roughly 10%, but does not alter the tolerance (fecundity-burden relationship) of mosquitoes to Plasmodium infection.Although Wolbachia-infected mosquitoes fare overall better than uninfected ones, Wolbachia does not confer a sufficiently high reproductive boost to mosquitoes to compensate for the reproductive losses inflicted by Plasmodium. We discuss the potential mechanisms and implications underlying the conflicting effects of these two parasites on mosquito reproduction.}, } @article {pmid28534452, year = {2018}, author = {Gauthier, J and Drezen, JM and Herniou, EA}, title = {The recurrent domestication of viruses: major evolutionary transitions in parasitic wasps.}, journal = {Parasitology}, volume = {145}, number = {6}, pages = {713-723}, doi = {10.1017/S0031182017000725}, pmid = {28534452}, issn = {1469-8161}, mesh = {Animals ; DNA, Viral/genetics ; *Domestication ; *Evolution, Molecular ; Genome, Insect ; Genomics ; *Host-Parasite Interactions ; Polydnaviridae/genetics ; Symbiosis ; Virulence ; Viruses/*genetics ; Wasps/genetics/*virology ; }, abstract = {Several lineages of endoparasitoid wasps, which develop inside the body of other insects, have domesticated viruses, used as delivery tools of essential virulence factors for the successful development of their progeny. Virus domestications are major evolutionary transitions in highly diverse parasitoid wasps. Much progress has recently been made to characterize the nature of these ancestrally captured endogenous viruses that have evolved within the wasp genomes. Virus domestication from different viral families occurred at least three times in parasitoid wasps. This evolutionary convergence led to different strategies. Polydnaviruses (PDVs) are viral gene transfer agents and virus-like particles of the wasp Venturia canescens deliver proteins. Here, we take the standpoint of parasitoid wasps to review current knowledge on virus domestications by different parasitoid lineages. Then, based on genomic data from parasitoid wasps, PDVs and exogenous viruses, we discuss the different evolutionary steps required to transform viruses into vehicles for the delivery of the virulence molecules that we observe today. Finally, we discuss how endoparasitoid wasps manipulate host physiology and ensure parasitism success, to highlight the possible advantages of viral domestication as compared with other virulence strategies.}, } @article {pmid28496167, year = {2017}, author = {Saravanakumar, K and Li, Y and Yu, C and Wang, QQ and Wang, M and Sun, J and Gao, JX and Chen, J}, title = {Effect of Trichoderma harzianum on maize rhizosphere microbiome and biocontrol of Fusarium Stalk rot.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1771}, pmid = {28496167}, issn = {2045-2322}, mesh = {Antibiosis ; Fusarium/*physiology ; Gene Expression Profiling ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Metabolome ; Metabolomics/methods ; *Microbiota ; Plant Diseases/*microbiology/*prevention & control ; Plant Roots/microbiology ; *Rhizosphere ; Symbiosis ; Trichoderma/*physiology ; Zea mays/*microbiology ; }, abstract = {Fusarium stalk rot (FSR) caused by Fusarium graminearum (FG) significantly affects the productivity of maize grain crops. Application of agrochemicals to control the disease is harmful to environment. In this regard, use of biocontrol agent (BCA) is an alternative to agrochemicals. Although Trichoderma species are known as BCA, the selection of host-pathogen specific Trichoderma is essential for the successful field application. Hence, we screened a total of 100 Trichoderma isolates against FG, selected Trichoderma harzianum (CCTCC-RW0024) for greenhouse experiments and studied its effect on changes of maize rhizosphere microbiome and biocontrol of FSR. The strain CCTCC-RW0024 displayed high antagonistic activity (96.30%), disease reduction (86.66%), biocontrol-related enzyme and gene expression. The root colonization of the strain was confirmed by eGFP tagging and qRT-PCR analysis. Pyrosequencing revealed that exogenous inoculation of the strain in maize rhizosphere increased the plant growth promoting acidobacteria (18.4%), decreased 66% of FG, and also increased the plant growth. In addition, metabolites of this strain could interact with pathogenicity related transcriptional cofactor FgSWi6, thereby contributing to its inhibition. It is concluded that T. harzianum strain CCTCC-RW0024 is a potential BCA against FSR.}, } @article {pmid30694431, year = {2019}, author = {Yin, J and Guan, X and Zhang, H and Wang, L and Li, H and Zhang, Q and Chen, T and Xu, Z and Hong, Z and Cao, Y and Zhang, Z}, title = {An MAP kinase interacts with LHK1 and regulates nodule organogenesis in Lotus japonicus.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11427-018-9444-9}, pmid = {30694431}, issn = {1869-1889}, abstract = {Symbiosis receptor-like kinase (SymRK) is a key protein mediating the legume-Rhizobium symbiosis. Our previous work has identified an MAP kinase kinase, SIP2, as a SymRK-interacting protein to positively regulate nodule organogenesis in Lotus japonicus, suggesting that an MAPK cascade might be involved in Rhizobium-legume symbiosis. In this study, LjMPK6 was identified as a phosphorylation target of SIP2. Stable transgenic L. japonicus with RNAi silencing of LjMPK6 decreased the numbers of nodule primordia (NP) and nodule, while plants overexpressing LjMPK6 increased the numbers of nodule, infection threads (ITs), and NP, indicating that LjMPK6 plays a positive role in nodulation. LjMPK6 could interact with a cytokinin receptor, LHK1 both in vivo and in vitro. LjMPK6 was shown to compete with LHP1 to bind to the receiver domain (RD) of LHK1and to downregulate the expression of two LjACS (1-aminocyclopropane-1-carboxylic acid synthase) genes and ethylene levels during nodulation. This study demonstrated an important role of LjMPK6 in regulation of nodule organogenesis and ethylene production in L. japonicus.}, } @article {pmid30541943, year = {2018}, author = {Kasbekar, DP}, title = {A cross-eyed geneticist's view II. Riddles, wrapped in mysteries, inside … mealybugs.}, journal = {Journal of biosciences}, volume = {43}, number = {5}, pages = {819-822}, pmid = {30541943}, issn = {0973-7138}, mesh = {Adaptation, Physiological/genetics ; Animals ; Betaproteobacteria/*physiology ; Chromosomes, Insect/chemistry/metabolism ; Citrus/parasitology ; Eukaryotic Cells/metabolism/microbiology ; Female ; Gammaproteobacteria/*physiology ; Genotype ; *Inheritance Patterns ; Male ; *Meiosis ; Phloem/parasitology ; Planococcus Insect/*genetics/microbiology ; Ploidies ; Reproduction ; Symbiosis/*genetics ; }, } @article {pmid30197044, year = {2018}, author = {Lin, Z and Wang, L and Chen, M and Chen, J}, title = {The acute transcriptomic response of coral-algae interactions to pH fluctuation.}, journal = {Marine genomics}, volume = {42}, number = {}, pages = {32-40}, doi = {10.1016/j.margen.2018.08.006}, pmid = {30197044}, issn = {1876-7478}, mesh = {Animals ; Anthozoa/genetics/*physiology ; China ; Dinoflagellida/genetics/*physiology ; Hydrogen-Ion Concentration ; *Symbiosis ; *Transcriptome ; }, abstract = {Little is known about how the coral host and its endosymbiont interactions change when they are exposed to a sudden nonlinear environmental transformation, yet this is crucial to coral survival in extreme events. Here, we present a study that investigates the transcriptomic response of corals and their endosymbionts to an abrupt change in pH (pH 7.60 and 8.35). The transcriptome indicates that the endosymbiont demonstrates a synchronized downregulation in carbon acquisition and fixation processes and may result in photosynthetic dysfunction in endosymbiotic Symbiodinium, suggesting that the mutualistic continuum of coral-algae interactions is compromised in response to high-CO2 exposure. Transcriptomic data also shows that corals are still capable of calcifying in response to the low pH but could experience a series of negative effects on their energy dynamics, which including protein damage, DNA repair, ion transport, cellular apoptosis, calcification acclimation and maintenance of intracellular pH homeostasis and stress tolerance to pH swing. This suggests enhanced energy costs for coral metabolic adaptation. This study provides a deeper understanding of the biological basis related to the symbiotic corals in response to extreme future climate change and environmental variability.}, } @article {pmid29218845, year = {2018}, author = {Antwis, RE and Harrison, XA}, title = {Probiotic consortia are not uniformly effective against different amphibian chytrid pathogen isolates.}, journal = {Molecular ecology}, volume = {27}, number = {2}, pages = {577-589}, doi = {10.1111/mec.14456}, pmid = {29218845}, issn = {1365-294X}, mesh = {Amphibians/genetics/*microbiology ; Animals ; Chytridiomycota/*pathogenicity ; Communicable Diseases/genetics/microbiology ; Host-Pathogen Interactions/*genetics ; Humans ; Microbiota/*genetics ; Probiotics/metabolism ; Symbiosis/genetics ; }, abstract = {Symbiotic bacterial communities can protect their hosts from infection by pathogens. Treatment of wild individuals with protective bacteria (probiotics) isolated from hosts can combat the spread of emerging infectious diseases. However, it is unclear whether candidate probiotic bacteria can offer consistent protection across multiple isolates of globally distributed pathogens. Here, we use the lethal amphibian fungal pathogen Batrachochytrium dendrobatidis to investigate whether probiotic richness (number of bacteria) or genetic distance among consortia members influences broad-scale in vitro inhibitory capabilities of probiotics across multiple isolates of the pathogen. We show that inhibition of multiple pathogen isolates by individual bacteria is rare, with no systematic pattern among bacterial genera in ability to inhibit multiple B. dendrobatidis isolates. Bacterial consortia can offer stronger protection against B. dendrobatidis compared to single strains, and this tended to be more pronounced for consortia containing multiple genera compared with those consisting of bacteria from a single genus (i.e., with lower genetic distance), but critically, this effect was not uniform across all B. dendrobatidis isolates. These novel insights have important implications for the effective design of bacterial probiotics to mitigate emerging infectious diseases.}, } @article {pmid28729739, year = {2017}, author = {Sun, ZJ and Li, ZX}, title = {Host plants and obligate endosymbionts are not the sources for biosynthesis of the aphid alarm pheromone.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6041}, pmid = {28729739}, issn = {2045-2322}, mesh = {Animals ; Aphids/*metabolism ; Buchnera ; Gas Chromatography-Mass Spectrometry ; *Host-Parasite Interactions ; Pheromones/analysis/*biosynthesis ; Plant Diseases/parasitology ; Plants/*microbiology/*parasitology ; *Symbiosis ; Volatile Organic Compounds/analysis ; }, abstract = {(E)-β-farnesene (EβF) is the major component of the alarm pheromone of many aphid species, but where EβF is synthesized in aphids is only partly understood. There are at least three most possible sources for the alarm pheromone: host plants, aphid obligate endosymbiont and aphids themselves. Here we eliminated the possibility of host plants and the obligate endosymbiont Buchnera aphidicola as the sources for EβF released by aphids. We excluded the possible effects of host plants on EβF biosynthesis by rearing aphids on non-plant diets. Both the diet-reared aphids, including the cotton aphid Aphis gossypii and the green peach aphid Myzus persicae, could still release EβF based on solid-phase micro-extraction combined with gas chromatography-mass spectrometer analysis. Meanwhile, we treated host aphids with antibiotics to fully eliminate Buchnera bacteria. Though the treatment seriously affected the development and fecundity of host aphids, the treated aphids could still release EβF, and there was no significant difference in the EβF concentration as per the aphid weight under different rearing conditions. Taken together, our experimental results suggest that host plants and obligate endosymbionts are not the sources for EβF released by aphids, indicating that it is most probably the aphid itself synthesizes the alarm pheromone.}, } @article {pmid30687830, year = {2019}, author = {Le Quéré, A and Gully, D and Teulet, A and Navarro, E and Gargani, D and Fardoux, J and Cruveiller, S and Neyra, M and Giraud, E and Krasova Wade, T}, title = {Complete Genome Sequence of Bradyrhizobium sp. Strain ORS3257, an Efficient Nitrogen-Fixing Bacterium Isolated from Cowpea in Senegal.}, journal = {Microbiology resource announcements}, volume = {8}, number = {3}, pages = {}, doi = {10.1128/MRA.01449-18}, pmid = {30687830}, issn = {2576-098X}, abstract = {Here, we report the complete genome sequence of Bradyrhizobium sp. strain ORS3257, which forms efficient symbioses with cowpea, peanut, or groundnut. These genomic data will be useful to identify genes associated with symbiotic performance and host compatibility on several legumes, including Aeschynomene species, with which a Nod-independent type III secretion system (T3SS)-dependent symbiosis can be established.}, } @article {pmid30687394, year = {2018}, author = {Schwab, DB and Casasa, S and Moczek, AP}, title = {On the Reciprocally Causal and Constructive Nature of Developmental Plasticity and Robustness.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {735}, doi = {10.3389/fgene.2018.00735}, pmid = {30687394}, issn = {1664-8021}, abstract = {Exposure to environmental variation is a characteristic feature of normal development, one that organisms can respond to during their lifetimes by actively adjusting or maintaining their phenotype in order to maximize fitness. Plasticity and robustness have historically been studied by evolutionary biologists through quantitative genetic and reaction norm approaches, while more recent efforts emerging from evolutionary developmental biology have begun to characterize the molecular and developmental genetic underpinnings of both plastic and robust trait formation. In this review, we explore how our growing mechanistic understanding of plasticity and robustness is beginning to force a revision of our perception of both phenomena, away from our conventional view of plasticity and robustness as opposites along a continuum and toward a framework that emphasizes their reciprocal, constructive, and integrative nature. We do so in three sections. Following an introduction, the first section looks inward and reviews the genetic, epigenetic, and developmental mechanisms that enable organisms to sense and respond to environmental conditions, maintaining and adjusting trait formation in the process. In the second section, we change perspective and look outward, exploring the ways in which organisms reciprocally shape their environments in ways that influence trait formation, and do so through the lens of behavioral plasticity, niche construction, and host-microbiota interactions. In the final section, we revisit established plasticity and robustness concepts in light of these findings, and highlight research opportunities to further advance our understanding of the causes, mechanisms, and consequences of these ubiquitous, and interrelated, phenomena.}, } @article {pmid30644356, year = {2019}, author = {Shaikevich, E and Bogacheva, A and Ganushkina, L}, title = {Dirofilaria and Wolbachia in mosquitoes (Diptera: Culicidae) in central European Russia and on the Black Sea coast.}, journal = {Parasite (Paris, France)}, volume = {26}, number = {}, pages = {2}, doi = {10.1051/parasite/2019002}, pmid = {30644356}, issn = {1776-1042}, mesh = {Animals ; Black Sea ; Culex/microbiology/parasitology ; Culicidae/*microbiology/*parasitology ; DNA, Helminth/isolation & purification ; Dirofilaria immitis/genetics/isolation & purification/physiology ; Dirofilaria repens/isolation & purification/physiology ; Dirofilariasis/*epidemiology/*transmission ; Dog Diseases/epidemiology ; Dogs ; Female ; Larva/microbiology/parasitology ; Mosquito Vectors/microbiology/parasitology ; Russia/epidemiology ; Symbiosis ; Wolbachia/genetics/*isolation & purification/physiology ; }, abstract = {Dirofilariasis is endemic in Russia, as well as in many other European countries. The aim of this study was to assess the ability of mosquitoes to transfer Dirofilaria immitis and Dirofilaria repens in regions with temperate and subtropical climates. The possible impact of the symbiotic bacterium Wolbachia on Dirofilaria transmission was also investigated. 5333 female mosquitoes were collected at 11 points in central European Russia and on the Black Sea coast during the period 2013-2017. Out of 20 mosquito species examined, 14 were infected with D. repens and 13 with D. immitis. Both species of Dirofilaria were found in different climatic regions. The total Dirofilaria spp. estimated infection rate (EIR) in the central part of Russia varied from 3.1% to 3.7% and, in the southern region, from 1.1% to 3.0%. The highest estimated infection rate was found in Anopheles messeae, the lowest in Culex pipiens. The greatest epidemiological danger was represented by Aedes aegypti, Ae. geniculatus, An. messeae and Ae. communis. Six out of 20 mosquito species were infected with Wolbachia. Pools of Aedes albopictus, Cx. pipiens and Coquillettidia richiardii were simultaneously infected with Dirofilaria and Wolbachia. After checking mosquitoes individually, it was found that there was no development of Dirofilaria to the infective larval stage in specimens infected with Wolbachia. Twenty-two Dirofilaria-infective pools were Wolbachia-free and only two mosquito pools were Wolbachia-infected. The potential for transmission of Dirofilaria in mosquito species naturally uninfected with the symbiotic bacterium Wolbachia is higher than in species infected with the bacterium.}, } @article {pmid30237040, year = {2018}, author = {Oborník, M}, title = {The Birth of Red Complex Plastids: One, Three, or Four Times?.}, journal = {Trends in parasitology}, volume = {34}, number = {11}, pages = {923-925}, doi = {10.1016/j.pt.2018.09.001}, pmid = {30237040}, issn = {1471-5007}, mesh = {Apicomplexa ; Cell Cycle ; *Plastids ; *Symbiosis ; }, } @article {pmid29970182, year = {2018}, author = {Starr, EP and Shi, S and Blazewicz, SJ and Probst, AJ and Herman, DJ and Firestone, MK and Banfield, JF}, title = {Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {122}, pmid = {29970182}, issn = {2049-2618}, mesh = {Avena/metabolism/*microbiology ; Bacteria/*genetics/*metabolism ; Carbon/metabolism ; Carbon Dioxide/analysis/*chemistry ; DNA, Bacterial/*biosynthesis/genetics ; Energy Metabolism/*genetics ; Genome, Bacterial/*genetics ; Isotope Labeling ; Metagenomics ; Plant Roots/microbiology ; RNA, Bacterial/*biosynthesis/genetics ; Rhizosphere ; Soil Microbiology ; Symbiosis ; }, abstract = {BACKGROUND: The transformation of plant photosynthate into soil organic carbon and its recycling to CO2 by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowledge gaps related to which soil-associated microorganisms take up plant carbon in the rhizosphere and the fate of that carbon.

RESULTS: We conducted an experiment in which common wild oats (Avena fatua) were grown in a 13CO2 atmosphere and the rhizosphere and non-rhizosphere soil was sampled for genomic analyses. Density gradient centrifugation of DNA extracted from soil samples enabled distinction of microbes that did and did not incorporate the 13C into their DNA. A 1.45-Mbp genome of a Saccharibacteria (TM7) was identified and, despite the microbial complexity of rhizosphere soil, curated to completion. The genome lacks many biosynthetic pathways, including genes required to synthesize DNA de novo. Rather, it requires externally derived nucleotides for DNA and RNA synthesis. Given this, we conclude that rhizosphere-associated Saccharibacteria recycle DNA from bacteria that live off plant exudates and/or phage that acquired 13C because they preyed upon these bacteria and/or directly from the labeled plant DNA. Isotopic labeling indicates that the population was replicating during the 6-week period of plant growth. Interestingly, the genome is ~ 30% larger than other complete Saccharibacteria genomes from non-soil environments, largely due to more genes for complex carbon utilization and amino acid metabolism. Given the ability to degrade cellulose, hemicellulose, pectin, starch, and 1,3-β-glucan, we predict that this Saccharibacteria generates energy by fermentation of soil necromass and plant root exudates to acetate and lactate. The genome also encodes a linear electron transport chain featuring a terminal oxidase, suggesting that this Saccharibacteria may respire aerobically. The genome encodes a hydrolase that could breakdown salicylic acid, a plant defense signaling molecule, and genes to interconvert a variety of isoprenoids, including the plant hormone zeatin.

CONCLUSIONS: Rhizosphere Saccharibacteria likely depend on other bacteria for basic cellular building blocks. We propose that isotopically labeled CO2 is incorporated into plant-derived carbon and then into the DNA of rhizosphere organisms capable of nucleotide synthesis, and the nucleotides are recycled into Saccharibacterial genomes.}, } @article {pmid29484603, year = {2018}, author = {Robledo, M and Matia-González, AM and García-Tomsig, NI and Jiménez-Zurdo, JI}, title = {Identification of Small RNA-Protein Partners in Plant Symbiotic Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1737}, number = {}, pages = {351-370}, doi = {10.1007/978-1-4939-7634-8_20}, pmid = {29484603}, issn = {1940-6029}, mesh = {Aptamers, Nucleotide/genetics/*metabolism ; Chromatography, Affinity/*methods ; Host Factor 1 Protein/genetics/*metabolism ; Mass Spectrometry ; Plants/microbiology ; RNA, Bacterial/genetics/*metabolism ; RNA, Small Untranslated/genetics/*metabolism ; Sinorhizobium meliloti/genetics/growth & development/*metabolism ; Symbiosis ; }, abstract = {The identification of the protein partners of bacterial small noncoding RNAs (sRNAs) is essential to understand the mechanistic principles and functions of riboregulation in prokaryotic cells. Here, we describe an optimized affinity chromatography protocol that enables purification of in vivo formed sRNA-protein complexes in Sinorhizobium meliloti, a genetically tractable nitrogen-fixing plant symbiotic bacterium. The procedure requires the tagging of the desired sRNA with the MS2 aptamer, which is affinity-captured by the MS2-MBP protein conjugated to an amylose resin. As proof of principle, we show recovery of the RNA chaperone Hfq associated to the strictly Hfq-dependent AbcR2 trans-sRNA. This method can be applied for the investigation of sRNA-protein interactions on a broad range of genetically tractable α-proteobacteria.}, } @article {pmid29330647, year = {2018}, author = {Brambilla, S and Frare, R and Soto, G and Jozefkowicz, C and Ayub, N}, title = {Absence of the Nitrous Oxide Reductase Gene Cluster in Commercial Alfalfa Inoculants Is Probably Due to the Extensive Loss of Genes During Rhizobial Domestication.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {299-302}, pmid = {29330647}, issn = {1432-184X}, support = {PICT-2014-3659//Fondo para la Investigación Científica y Tecnológica/ ; }, mesh = {Bacteria/*genetics/metabolism ; Denitrification/genetics ; Evolution, Molecular ; Genome Size ; Medicago sativa/*microbiology ; *Multigene Family ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen Fixation ; Nitrous Oxide/metabolism ; Oxidoreductases/*genetics ; Rhizobium/*genetics ; Symbiosis ; }, abstract = {As other legume crops, alfalfa cultivation increases the emission of the greenhouse gas nitrous oxide (N2O). Since legume-symbiotic nitrogen-fixing bacteria play a crucial role in this emission, it is important to understand the possible impacts of rhizobial domestication on the evolution of denitrification genes. In comparison with the genomes of non-commercial strains, those of commercial alfalfa inoculants exhibit low total genome size, low number of ORFs and high numbers of both frameshifted genes and pseudogenes, suggesting a dramatic loss of genes during bacterial domestication. Genomic analysis focused on denitrification genes revealed that commercial strains have perfectly conserved the nitrate (NAP), nitrite (NIR) and nitric (NOR) reductase clusters related to the production of N2O from nitrate but completely lost the nitrous oxide (NOS) reductase cluster (nosRZDFYLX genes) associated with the reduction of N2O to gas nitrogen. Based on these results, we propose future screenings for alfalfa-nodulating isolates containing both nitrogen fixation and N2O reductase genes for environmental sustainability of alfalfa production.}, } @article {pmid29327073, year = {2018}, author = {Choix, FJ and López-Cisneros, CG and Méndez-Acosta, HO}, title = {Azospirillum brasilense Increases CO2 Fixation on Microalgae Scenedesmus obliquus, Chlorella vulgaris, and Chlamydomonas reinhardtii Cultured on High CO2 Concentrations.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {430-442}, pmid = {29327073}, issn = {1432-184X}, support = {247006//Project SENER-CONACyT/ ; 2517//Programa Catedrás CONACyT/ ; }, mesh = {Azospirillum brasilense/growth & development/*metabolism ; Biomass ; *Carbon Cycle ; Carbon Dioxide/*metabolism ; Cell Count ; Cells, Immobilized ; Chlamydomonas reinhardtii/growth & development/*metabolism ; Chlorella vulgaris/growth & development/*metabolism ; Culture Media ; Indoleacetic Acids/metabolism ; Microalgae/growth & development/*metabolism ; Microbial Interactions/physiology ; Plant Growth Regulators/metabolism ; Scenedesmus/*metabolism ; Symbiosis ; Tryptophan/metabolism ; }, abstract = {Mutualism interactions of microalgae with other microorganisms are widely used in several biotechnological processes since symbiotic interaction improves biotechnological capabilities of the microorganisms involved. The interaction of the bacterium Azospirillum brasilense was assessed with three microalgae genus, Scenedesmus, Chlorella, and Chlamydomonas, during CO2 fixation under high CO2 concentrations. The results in this study have demonstrated that A. brasilense maintained a mutualistic interaction with the three microalgae assessed, supported by the metabolic exchange of indole-3-acetic acid (IAA) and tryptophan (Trp), respectively. Besides, CO2 fixation increased, as well as growth and cell compound accumulation, mainly carbohydrates, in each microalgae evaluated, interacting with the bacterium. Overall, these results propose the mutualism interaction of A. brasilense with microalgae for improving biotechnological processes based on microalgae as CO2 capture and their bio-refinery capacity.}, } @article {pmid29299617, year = {2018}, author = {Deignan, LK and Pawlik, JR and Erwin, PM}, title = {Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {459-466}, pmid = {29299617}, issn = {1432-184X}, support = {OCE-0095724//National Science Foundation/ ; OCE-0550468//National Science Foundation/ ; OCE-1029515//National Science Foundation/ ; OCE-1558580//National Science Foundation/ ; OCE-1558580//National Science Foundation/ ; }, mesh = {Agelas/*microbiology ; Animal Diseases/*microbiology ; Animals ; Archaea/classification/physiology ; Bacteria/classification ; Bacterial Physiological Phenomena ; Cachexia ; Caribbean Region ; Chloroflexi/physiology ; *Dysbiosis ; Florida ; Gammaproteobacteria/physiology ; Microbiota ; Phylogeny ; Porifera/microbiology ; Prokaryotic Cells/*physiology ; Proteobacteria/physiology ; Seawater/microbiology ; *Symbiosis ; Wasting Syndrome/epidemiology/*microbiology ; }, abstract = {The brown tube sponge Agelas tubulata (cf. Agelas conifera) is an abundant and long-lived sponge on Caribbean reefs. Recently, a disease-like condition, Agelas wasting syndrome (AWS), was described from A. tubulata in the Florida Keys, where prevalence of the syndrome increased from 7 to 35% of the sponge population between 2010 and 2015. In this study, we characterized the prokaryotic symbiont community of A. tubulata for the first time from individuals collected within the same monitoring plots where AWS was described. We also sampled tissue from A. tubulata exhibiting symptoms of AWS to determine its effect on the diversity and structure of prokaryotic symbiont communities. Bacteria from the phyla Chloroflexi and Proteobacteria, particularly the class Gammaproteobacteria, dominated the sponge microbiome in tissue samples of both healthy sponges and those exhibiting AWS. Prokaryotic community structure differed significantly between the diseased and healthy sponge samples, with greater variability among communities in diseased samples compared to healthy samples. These differences in prokaryotic community structure included a shift in relative abundance of the dominant, ammonia-oxidizing (Thaumarchaeota) symbionts present in diseased and healthy sponge samples. Further research is required to determine the functional consequences of this shift in microbial community structure and the causal relationship of dysbiosis and sponge disease in A. tubulata.}, } @article {pmid29290035, year = {2018}, author = {Angelella, G and Nalam, V and Nachappa, P and White, J and Kaplan, I}, title = {Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {453-458}, pmid = {29290035}, issn = {1432-184X}, support = {107483//U.S. Department of Agriculture - National Institute of Food and Agriculture (US) Predoctoral Fellowship/ ; 2014-67013-21576//U.S. Department of Agriculture - National Institute of Food and Agriculture (US)/ ; }, mesh = {Animals ; Aphids/*microbiology/physiology ; Bacteriophages ; Enterobacteriaceae/physiology/*virology ; Host-Pathogen Interactions ; Insect Vectors/physiology/*virology ; Medicago sativa/virology ; Plant Diseases/virology ; Plant Viruses/pathogenicity/*physiology ; Potyvirus/pathogenicity/physiology ; Robinia/virology ; *Symbiosis ; }, abstract = {Insect endosymbionts (hereafter, symbionts) can modify plant virus epidemiology by changing the physiology or behavior of vectors, but their role in nonpersistent virus pathosystems remains uninvestigated. Unlike propagative and circulative viruses, nonpersistent plant virus transmission occurs via transient contamination of mouthparts, making direct interaction between symbiont and virus unlikely. Nonpersistent virus transmission occurs during exploratory intracellular punctures with styletiform mouthparts when vectors assess potential host-plant quality prior to phloem feeding. Therefore, we used an electrical penetration graph (EPG) to evaluate plant probing of the cowpea aphid, Aphis craccivora Koch, an important vector of cucurbit viruses, in the presence and absence of two facultative, intracellular symbionts. We tested four isolines of A. craccivora: two isolines were from a clone from black locust (Robinia pseudoacacia L.), one infected with Arsenophonus sp. and one cured, and two derived from a clone from alfalfa (Medicago sativa L.), one infected with Hamiltonella defensa and one cured. We quantified exploratory intracellular punctures, indicated by a waveform potential drop recorded by the EPG, initiation speed and frequency within the initial 15 min on healthy and watermelon mosaic virus-infected pumpkins. Symbiont associations differentially modified exploratory intracellular puncture frequency by aphids, with H. defensa-infected aphids exhibiting depressed probing, and Arsenophonus-infected aphids an increased frequency of probing. Further, there was greater overall aphid probing on virus-infected plants, suggesting that viruses manipulate their vectors to enhance acquisition-transmission rates, independent of symbiont infection. These results suggest facultative symbionts differentially affect plant-host exploration behaviors and potentially nonpersistent virus transmission by vectors.}, } @article {pmid29285550, year = {2018}, author = {Kellner, K and Kardish, MR and Seal, JN and Linksvayer, TA and Mueller, UG}, title = {Symbiont-Mediated Host-Parasite Dynamics in a Fungus-Gardening Ant.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {530-543}, pmid = {29285550}, issn = {1432-184X}, support = {DEB-0919519//Division of Environmental Biology/ ; DEB-1354629//Division of Environmental Biology/ ; IOS-1552822//Division of Integrative Organismal Systems/ ; }, mesh = {Animal Diseases/microbiology ; Animals ; Ants/*microbiology ; *Biological Coevolution ; Disease Resistance/physiology ; Ecology ; Fungi/classification/genetics/isolation & purification/*pathogenicity ; *Gardening ; Genotype ; Host-Pathogen Interactions/*physiology ; Hypocreales/classification/genetics/isolation & purification/pathogenicity ; *Symbiosis ; }, abstract = {Group-living can promote the evolution of adaptive strategies to prevent and control disease. Fungus-gardening ants must cope with two sets of pathogens, those that afflict the ants themselves and those of their symbiotic fungal gardens. While much research has demonstrated the impact of specialized fungal pathogens that infect ant fungus gardens, most of these studies focused on the so-called higher attine ants, which are thought to coevolve diffusely with two clades of leucocoprinaceous fungi. Relatively few studies have addressed disease ecology of lower Attini, which are thought to occasionally recruit (domesticate) novel leucocoprinaceous fungi from free-living populations; coevolution between lower-attine ants and their fungi is therefore likely weaker (or even absent) than in the higher Attini, which generally have many derived modifications. Toward understanding the disease ecology of lower-attine ants, this study (a) describes the diversity in the microfungal genus Escovopsis that naturally infect fungus gardens of the lower-attine ant Mycocepurus smithii and (b) experimentally determines the relative contributions of Escovopsis strain (a possible garden disease), M. smithii ant genotype, and fungal cultivar lineage to disease susceptibility and colony fitness. In controlled in-vivo infection laboratory experiments, we demonstrate that the susceptibility to Escovopsis infection was an outcome of ant-cultivar-Escovopsis interaction, rather than solely due to ant genotype or fungal cultivar lineage. The role of complex ant-cultivar-Escovopsis interactions suggests that switching M. smithii farmers onto novel fungus types might be a strategy to generate novel ant-fungus combinations resistant to most, but perhaps not all, Escovopsis strains circulating in a local population of this and other lower-attine ants.}, } @article {pmid29113014, year = {2017}, author = {Glassman, SI and Wang, IJ and Bruns, TD}, title = {Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales.}, journal = {Molecular ecology}, volume = {26}, number = {24}, pages = {6960-6973}, doi = {10.1111/mec.14414}, pmid = {29113014}, issn = {1365-294X}, mesh = {California ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Forests ; Hydrogen-Ion Concentration ; Models, Biological ; Mycorrhizae/*classification ; Pinus/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; Symbiosis ; }, abstract = {Whether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree "islands" to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly related, congeneric pine trees established at varying distances from each other and the forest edge, allowing us to disentangle the effects of geographic distance vs. host and edaphic environment on associated fungal communities. We identified fungal community composition with Illumina sequencing of ITS amplicons, measured all relevant environmental parameters for each tree-including tree age, size and soil chemistry-and calculated geographic distances from each tree to all others and to the nearest forest edge. We applied generalized dissimilarity modelling to test whether total and ectomycorrhizal fungal (EMF) communities were primarily structured by geographic or environmental filtering. Our results provide strong evidence that as in many other organisms, niche and neutral processes both contribute significantly to turnover in community composition in fungi, but environmental filtering plays the dominant role in structuring both free-living and symbiotic fungal communities at fine spatial scales. In our study system, we found pH and organic matter primarily drive environmental filtering in total soil fungal communities and that pH and cation exchange capacity-and, surprisingly, not host species-were the largest factors affecting EMF community composition. These findings support an emerging paradigm that pH may play a central role in the assembly of all soil-mediated systems.}, } @article {pmid30605507, year = {2017}, author = {Vera-Ponce de León, A and Ormeño-Orrillo, E and Ramírez-Puebla, ST and Rosenblueth, M and Degli Esposti, M and Martínez-Romero, J and Martínez-Romero, E}, title = {Candidatus Dactylopiibacterium carminicum, a Nitrogen-Fixing Symbiont of Dactylopius Cochineal Insects (Hemiptera: Coccoidea: Dactylopiidae).}, journal = {Genome biology and evolution}, volume = {9}, number = {9}, pages = {2237-2250}, doi = {10.1093/gbe/evx156}, pmid = {30605507}, issn = {1759-6653}, mesh = {Animals ; Female ; Genome, Bacterial ; Hemiptera/*microbiology ; *Nitrogen Fixation ; Ovary/microbiology ; Phylogeny ; Rhodocyclaceae/*classification/isolation & purification ; *Symbiosis ; }, abstract = {The domesticated carmine cochineal Dactylopius coccus (scale insect) has commercial value and has been used for more than 500 years for natural red pigment production. Besides the domesticated cochineal, other wild Dactylopius species such as Dactylopius opuntiae are found in the Americas, all feeding on nutrient poor sap from native cacti. To compensate nutritional deficiencies, many insects harbor symbiotic bacteria which provide essential amino acids or vitamins to their hosts. Here, we characterized a symbiont from the carmine cochineal insects, Candidatus Dactylopiibacterium carminicum (betaproteobacterium, Rhodocyclaceae family) and found it in D. coccus and in D. opuntiae ovaries by fluorescent in situ hybridization, suggesting maternal inheritance. Bacterial genomes recovered from metagenomic data derived from whole insects or tissues both from D. coccus and from D. opuntiae were around 3.6 Mb in size. Phylogenomics showed that dactylopiibacteria constituted a closely related clade neighbor to nitrogen fixing bacteria from soil or from various plants including rice and other grass endophytes. Metabolic capabilities were inferred from genomic analyses, showing a complete operon for nitrogen fixation, biosynthesis of amino acids and vitamins and putative traits of anaerobic or microoxic metabolism as well as genes for plant interaction. Dactylopiibacterium nif gene expression and acetylene reduction activity detecting nitrogen fixation were evidenced in D. coccus hemolymph and ovaries, in congruence with the endosymbiont fluorescent in situ hybridization location. Dactylopiibacterium symbionts may compensate for the nitrogen deficiency in the cochineal diet. In addition, this symbiont may provide essential amino acids, recycle uric acid, and increase the cochineal life span.}, } @article {pmid30683833, year = {2019}, author = {Wang, H and Wu, MA and Woo, YJ}, title = {Photosynthetic symbiotic therapy.}, journal = {Aging}, volume = {}, number = {}, pages = {}, doi = {10.18632/aging.101796}, pmid = {30683833}, issn = {1945-4589}, } @article {pmid30681912, year = {2019}, author = {Vostinar, AE and Ofria, C}, title = {Spatial Structure Can Decrease Symbiotic Cooperation.}, journal = {Artificial life}, volume = {}, number = {}, pages = {1-21}, doi = {10.1162/artl_a_00273}, pmid = {30681912}, issn = {1064-5462}, abstract = {Mutualisms occur when at least two species provide a net fitness benefit to each other. These types of interactions are ubiquitous in nature, with more being discovered regularly. Mutualisms are vital to humankind: Pollinators and soil microbes are critical in agriculture, bacterial microbiomes regulate our health, and domesticated animals provide us with food and companionship. Many hypotheses exist on how mutualisms evolve; however, they are difficult to evaluate without bias, due to the fragile and idiosyncratic systems most often investigated. Instead, we have created an artificial life simulation, Symbulation, which we use to examine mutualism evolution based on (1) the probability of vertical transmission (symbiont being passed to offspring) and (2) the spatial structure of the environment. We found that spatial structure can lead to less mutualism at intermediate vertical transmission rates. We provide evidence that this effect is due to the ability of quasi species to purge parasites, reducing the diversity of available symbionts. Our simulation is easily extended to test many additional hypotheses about the evolution of mutualism and serves as a general model to quantitatively compare how different environments affect the evolution of mutualism.}, } @article {pmid30680683, year = {2019}, author = {Garg, N and Kashyap, L}, title = {Joint effects of Si and mycorrhiza on the antioxidant metabolism of two pigeonpea genotypes under As (III) and (V) stress.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-019-04256-5}, pmid = {30680683}, issn = {1614-7499}, support = {UGC-No.f.25-1/2013-14(BSR)/7-151/2007(BSR)//University Grants Commission (IN)/ ; DBT- BT/PR9466/AGR/21/231/2007//Department of Biotechnology , Ministry of Science and Technology (IN)/ ; }, abstract = {Arsenic (As) is the most hazardous soil contaminant, which inactivates metabolic enzymes and restrains plant growth. To withstand As stress conditions, use of some alleviative tools, such as arbuscular mycorrhizal (AM) fungi and silicon (Si), has gained importance. Therefore, the present study evaluated comparative and interactive effects of Si and arbuscular mycorrhiza-Rhizophagus irregularis on phytotoxicity of arsenate (As V) and arsenite (As III) on plant growth, ROS generation, and antioxidant defense responses in pigeonpea genotypes (Tolerant-Pusa 2002; Sensitive-Pusa 991). Roots of As III treated plants accumulated significantly higher total As than As V supplemented plants, more in Pusa 991 than Pusa 2002, which corresponded to proportionately decreased plant growth, root to biomass ratio, and oxidative burst. Although Si nutrition and AM inoculations improved plant growth by significantly reducing As uptake and the resultant oxidative burst, AM was relatively more efficient in upregulating enzymatic and non-enzymatic antioxidant defense responses as well as ascorbate-glutathione pathway when compared with Si. Pusa 2002 was more receptive to Si nourishment due to its ability to establish more efficient mycorrhizal symbiosis, which led to higher Si uptake and lower As concentrations. Moreover, +Si+AM bestowed better metalloid resistance by further reducing ROS and strengthening antioxidants. Results demonstrated that the genotype with more efficient AM symbiosis in As-contaminated soils could accrue higher benefits of Si fertilization in terms of metalloid tolerance in pigeonpea.}, } @article {pmid30680121, year = {2019}, author = {Helmkampf, M and Bellinger, MR and Frazier, M and Takabayashi, M}, title = {Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata.}, journal = {Ecology and evolution}, volume = {9}, number = {1}, pages = {378-392}, doi = {10.1002/ece3.4756}, pmid = {30680121}, issn = {2045-7758}, abstract = {Reef-building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA-seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai'i Island with contrasting environmental conditions. We found that transcriptome-wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (FST = 0.046) and among corals harboring alternative symbiont clades (FST = 0.036), suggesting that site-related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.}, } @article {pmid30679075, year = {2019}, author = {Moraïs, S and Mizrahi, I}, title = {The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2018.12.011}, pmid = {30679075}, issn = {1878-4380}, abstract = {The rumen ecosystem represents a classic example of host-microbiome symbiosis. In this obligatory relationship, the host feeds on plant fibers that can only be degraded through a set of complex metabolic cascades, exclusively encoded in rumen-associated microbes. These various metabolic pathways are distributed across a multitude of microbial populations. Application of basic ecological principles to this ecosystem can contribute to profound understanding of the rules that shape it. Here, we discuss recent studies by examining the mapping between host attributes, rumen ecosystem composition, and functionality to propose simple, yet powerful concepts to guide the interpretation of microbiome data and enable a better understanding of how the system responds to perturbations.}, } @article {pmid30678653, year = {2019}, author = {Lin, HF and Xiong, J and Zhou, HM and Chen, CM and Lin, FZ and Xu, XM and Oelmüller, R and Xu, WF and Yeh, KW}, title = {Growth promotion and disease resistance induced in Anthurium colonized by the beneficial root endophyte Piriformospora indica.}, journal = {BMC plant biology}, volume = {19}, number = {1}, pages = {40}, doi = {10.1186/s12870-019-1649-6}, pmid = {30678653}, issn = {1471-2229}, support = {31761130073 and 31422047//National Natural Science Foundation of China/ ; KXGH17005//Ministry of Science and Technology, Taiwan/ ; }, abstract = {BACKGROUND: Anthurium andraeanum, an important ornamental flower, has to go through a growth-delaying period after transfer from tissue culture to soil, which requires time and extra costs. Furthermore, during this period, the plantlets are highly susceptible to bacterial infections, which results in impaired development and severe losses. Here, we aimed to address whether application of the endophytic fungus, Piriformospora indica protects the A. andraeanum root system during the critical propagation period, and whether P. indica reduce the mortality rate by stimulating the host's resistance against diseases.

RESULTS: We demonstrate that P. indica shortens the recovery period of Anthurium, promotes growth and confers disease resistance. The beneficial effect of P. indica results in faster elongation of Anthurium roots early in the interaction. P. indica-colonized plants absorb more phosphorus and exhibit higher photosynthesis rates than uncolonized control plants. Moreover, higher activities of stress-related enzymes, of jasmonic acid levels and mRNA levels of jasmonic acid-responsive genes suggest that the fungus prepares the plant to respond more efficiently to potentially upcoming threats, including bacterial wilt.

CONCLUSION: These results suggest that P. indica is a helpful symbiont for promoting Anthurium rooting and development. All our evidences are sufficient to support the disease resistance conferred by P. indica through the plant-fungal symbiosis. Furthermore, it implicates that P. indica has strong potential as bio-fertilizer for utilization in ornamental plant cultivation.}, } @article {pmid30356280, year = {2018}, author = {Winter, DJ and Ganley, ARD and Young, CA and Liachko, I and Schardl, CL and Dupont, PY and Berry, D and Ram, A and Scott, B and Cox, MP}, title = {Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae.}, journal = {PLoS genetics}, volume = {14}, number = {10}, pages = {e1007467}, pmid = {30356280}, issn = {1553-7404}, mesh = {AT Rich Sequence/genetics ; DNA, Fungal/chemistry/*genetics ; Epichloe/*genetics ; Fungal Proteins/genetics ; GC Rich Sequence/genetics ; Gene Expression Profiling/methods ; *Gene Expression Regulation, Fungal ; Genome, Fungal/*genetics ; Hyphae/genetics ; Repetitive Sequences, Nucleic Acid/*genetics ; Sequence Analysis, DNA/methods ; Symbiosis/genetics ; }, abstract = {Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C data to examine the three-dimensional organisation of the genome, and RNA-seq data to investigate how Epichloë genome structure contributes to the suite of transcriptional changes needed to maintain symbiotic relationships with the grass host. Our results reveal a genome in which very repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences that are almost repeat-free. In contrast to other species reported to date, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.}, } @article {pmid30676313, year = {2019}, author = {Cambronero-Heinrichs, JC and Matarrita-Carranza, B and Murillo-Cruz, C and Araya-Valverde, E and Chavarría, M and Pinto-Tomás, AA}, title = {Phylogenetic analyses of antibiotic-producing Streptomyces sp. isolates obtained from the stingless-bee Tetragonisca angustula (Apidae: Meliponini).}, journal = {Microbiology (Reading, England)}, volume = {}, number = {}, pages = {}, doi = {10.1099/mic.0.000754}, pmid = {30676313}, issn = {1465-2080}, abstract = {Many insects have been associated with actinobacteria in protective symbiosis where antimicrobial metabolites inhibit host pathogens. However, the microbiota of neotropical insects such as the stingless-bee Tetragonica angustula is poorly explored. T. angustula is a meliponid bee widely distributed in Latin America, its honey is traditionally exploited because of its ethno-pharmacological properties and its antimicrobial activity has been demonstrated. Also, the well-structured nest of this species allows exploration of the microbiota of its different components. Even though Streptomyces spp. have been cultured from stingless-bees, little is known about their role in this insect-microbe relationship. In this study, we examined the association between culturable actinobacteria and T. angustula, and evaluated the isolates' potential as antimicrobial producers. We isolated 51 actinobacteria from adult bees and different substrates of the hive of T. angustula (pollen and honey storage, garbage pellets and cerumen). We then performed a 16S rRNA phylogenetic analysis that clusters the bacteria to previously described lineages of host-associated Streptomyces. In addition, all the isolates were classified according to their antibacterial activity against human pathogens, measured by a growth inhibition test based on diffusion in agar. More than 50 % of our isolates exhibit antimicrobial activity, mainly to Gram-positive bacteria and fungi and only two against Gram-negative bacteria. Additionally, we obtained electron micrographs of adult bees with what appears to be patches of hyphae with Streptomyces-like cell morphology on their body surface. Our results suggest that T. angustula possibly uptakes and transfers actinobacteria from the environment, acting as vectors for these potentially beneficial organisms. This research provides new insights regarding the microbiota associated with T. angustula and justify future studies exploring the full diversity of the microbial community associated with the hive and the possible exchange of microbes with the crops they pollinate.}, } @article {pmid30106668, year = {2018}, author = {Wang, Y and Mao, L and Sun, Y and Wang, Z and Zhang, J and Zhang, J and Peng, Y and Xia, L}, title = {A Novel Francisella-Like Endosymbiont in Haemaphysalis longicornis and Hyalomma asiaticum, China.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {18}, number = {12}, pages = {669-676}, doi = {10.1089/vbz.2017.2252}, pmid = {30106668}, issn = {1557-7759}, mesh = {Animal Distribution ; Animals ; China ; Francisella/*genetics/*isolation & purification ; Ixodidae/*microbiology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Francisella tularensis causes a highly infectious zoonotic disease tularemia. Both Haemaphysalis longicornis and Hyalomma asiaticum are widely distributed in China, but the presence of Francisella and Francisella-like endosymbionts (FLEs) in the two tick species is poorly understood. Therefore, a total of 627 H. longicornis (471 adults and 156 nymphs) and 88 Hy. asiaticum ticks (adults) were collected, of which 88 were from Bole of Xinjiang, 236 from Liaoyang, and 176 from Shenyang of Liaoning, and 215 from Wuhan of Hubei. Notably, five H. longicornis pools from Liaoyang of Liaoning province might have harbored F. tularensis, showing a minimum prevalence of 2.12% (5/236). This study should alert the health department and veterinarians working within the region to prevent and control the emergence of tularemia. After the screening of 16S rRNA and tul4 genes, the results revealed that FLEs were detected in Hy. asiaticum ticks in Bole and in H. longicornis ticks in Liaoyang and Shenyang. Their infection rate was 100% (88/88), 3.39% (8/236 is a minimum), and 8.52% (15/176), respectively. Phylogenetic analyses indicated that the sequence named bole in Hy. Asiaticum from Bole, the sequence named liaoyang1 in H. longicornis from Liaoyang, and the sequence named shanyang1 in H. longicornis from Shenyang shared consistent 16S rRNA sequence, and the difference between Chinese FLEs and the known FLEs was obvious. These findings suggest that this FLE species might be a potentially novel FLE circulating in H. longicornis and Hy. asiaticum from China.}, } @article {pmid28620748, year = {2018}, author = {Guidolin, AS and Cônsoli, FL}, title = {Diversity of the Most Commonly Reported Facultative Symbionts in Two Closely-Related Aphids with Different Host Ranges.}, journal = {Neotropical entomology}, volume = {47}, number = {4}, pages = {440-446}, pmid = {28620748}, issn = {1678-8052}, support = {2011/50877-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2012/04287-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 490474/2011-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; Aphids/*microbiology ; Buchnera/isolation & purification ; DNA, Bacterial/genetics ; Plants ; Rickettsia/isolation & purification ; Species Specificity ; Spiroplasma/isolation & purification ; *Symbiosis ; }, abstract = {Richness and abundance of facultative symbionts vary strongly with aphid species and genotype, symbiont strain, host plant, biogeography, and a number of abiotic factors. Despite indications that aphids in the same ecological niche show similar levels of facultative symbiont richness, existing reports do not consider the potential role of host plants on aphid microbial community. Little is known about how oligophagy and polyphagy may be influenced by secondary symbiont distribution, mainly because studies on secondary symbiont diversity are biased towards polyphagous aphids from the Northern Hemisphere. Here, we demonstrate the richness and abundance of the most common aphid-associated facultative symbionts in two tropical aphid species, the oligophagous Aphis (Toxoptera) citricidus (Kirkaldy) (Hemiptera: Aphididae) and the polyphagous Aphis aurantii (Boyer de Fonscolombe) (Hemiptera: Aphididae). Aphis citricidus is restricted to Citrus sp. host plants and closely related genera, whereas A. aurantii successfully exploits a wide variety of host plants from different families. Both were collected in the same ecological niche and our data basically indicated the same richness of secondary symbionts, but the abundance at which secondary symbionts occurred was very distinct between the two species. Spiroplasma was the most abundant facultative symbiont associated with A. citricidus and A. aurantii in the ecological niche studied. Single and multiple secondary symbiont infections were observed, but diversity of multiple infections was particularly high in A. citricidus. We discuss our findings and suggest hypotheses to explain causes and consequences of the differences in secondary symbiont diversity observed between these two aphid species.}, } @article {pmid30671951, year = {2019}, author = {Clark, TJ and Friel, CA and Grman, E and Friesen, ML and Shachar-Hill, Y}, title = {Unfair trade underground revealed by integrating data with Nash bargaining models.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15703}, pmid = {30671951}, issn = {1469-8137}, abstract = {Mutually beneficial resource exchange is foundational to global biogeochemical cycles and plant and animal nutrition. However, there is inherent potential conflict in mutualisms, as each organism benefits more when the exchange ratio ('price') minimizes its own costs and maximizes its benefits. Understanding the bargaining power that each partner has in these interactions is key to our ability to predict the exchange ratio and thus the functionality of the cell, organism, community, and ecosystem. We tested whether partners have symmetric ('fair') or asymmetric ('unfair') bargaining power in a legume-rhizobia nitrogen fixing symbiosis using measurements of carbon and nitrogen dynamics in a mathematical modeling framework derived from economic theory. A model of symmetric bargaining power was not consistent with our data. Instead, our data indicate that the growth benefit to the plant (Medicago truncatula) has greater weight in determining trade dynamics than the benefit to the bacteria. Quantitative estimates of the relative power of the plant reveal that the plant's influence rises as soil nitrogen availability decreases and trade benefits to both partners increase. Our finding that M. truncatula legumes have more bargaining power than the rhizobial partner at lower nitrogen availabilities highlights the importance of context-dependence for the evolution of mutualism with increasing nutrient deposition. This article is protected by copyright. All rights reserved.}, } @article {pmid30671290, year = {2019}, author = {Vesala, R and Harjuntausta, A and Hakkarainen, A and Rönnholm, P and Pellikka, P and Rikkinen, J}, title = {Termite mound architecture regulates nest temperature and correlates with species identities of symbiotic fungi.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6237}, doi = {10.7717/peerj.6237}, pmid = {30671290}, issn = {2167-8359}, abstract = {Background: Large and complex mounds built by termites of the genus Macrotermes characterize many dry African landscapes, including the savannas, bushlands, and dry forests of the Tsavo Ecosystem in southern Kenya. The termites live in obligate symbiosis with filamentous fungi of the genus Termitomyces. The insects collect dead plant material from their environment and deposit it into their nests where indigestible cell wall compounds are effectively decomposed by the fungus. Above-ground mounds are built to enhance nest ventilation and to maintain nest interior microclimates favorable for fungal growth.

Objectives: In Tsavo Ecosystem two Macrotermes species associate with three different Termitomyces symbionts, always with a monoculture of one fungal species within each termite nest. As mound architecture differs considerably both between and within termite species we explored potential relationships between nest thermoregulatory strategies and species identity of fungal symbionts.

Methods: External dimensions were measured from 164 Macrotermes mounds and the cultivated Termitomyces species were identified by sequencing internal transcribed spacer (ITS) region of ribosomal DNA. We also recorded the annual temperature regimes of several termite mounds to determine relations between mound architecture and nest temperatures during different seasons.

Results: Mound architecture had a major effect on nest temperatures. Relatively cool temperatures were always recorded from large mounds with open ventilation systems, while the internal temperatures of mounds with closed ventilation systems and small mounds with open ventilation systems were consistently higher. The distribution of the three fungal symbionts in different mounds was not random, with one fungal species confined to "hot nests."

Conclusions: Our results indicate that different Termitomyces species have different temperature requirements, and that one of the cultivated species is relatively intolerant of low temperatures. The dominant Macrotermes species in our study area can clearly modify its mound architecture to meet the thermal requirements of several different symbionts. However, a treacherous balance seems to exist between symbiont identity and mound architecture, as the maintenance of the thermophilic fungal species obviously requires reduced mound architecture that, in turn, leads to inadequate gas exchange. Hence, our study concludes that while the limited ventilation capacity of small mounds sets strict limits to insect colony growth, in this case, improving nest ventilation would invariable lead to excessively low nest temperatures, with negative consequences to the symbiotic fungus.}, } @article {pmid30671068, year = {2018}, author = {Gauthier-Coles, C and White, RG and Mathesius, U}, title = {Nodulating Legumes Are Distinguished by a Sensitivity to Cytokinin in the Root Cortex Leading to Pseudonodule Development.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1901}, doi = {10.3389/fpls.2018.01901}, pmid = {30671068}, issn = {1664-462X}, abstract = {Root nodule symbiosis (RNS) is a feature confined to a single clade of plants, the Fabids. Among Fabids capable of RNS, legumes form root cortex-based nodules in symbioses with rhizobia, while actinorhizal species form lateral root-based nodules with actinomycetes. Cytokinin has previously been shown to be sufficient for "pseudonodule" initiation in model legumes. Here, we tested whether this response correlates with the ability to nodulate across a range of plant species. We analyzed the formation of pseudonodules in 17 nodulating and non-nodulating legume species, and 11 non-legumes, including nodulating actinorhizal species, using light and fluorescence microscopy. Cytokinin-induced pseudonodules arising from cortical cell divisions occurred in all nodulating legume species, but not in any of the other species, including non-nodulating legumes. Pseudonodule formation was dependent on the CRE1 cytokinin receptor in Medicago truncatula. Inhibition of root growth by cytokinin occurred across plant groups, indicating that pseudonodule development is the result of a specific cortical cytokinin response unique to nodulating legumes. Lack of a cortical cytokinin response from the Arabidopsis thaliana cytokinin reporter TCSn::GFP supported this hypothesis. Our results suggest that the ability to form cortical cell-derived nodules was gained in nodulating legumes, and likely lost in non-nodulating legumes, due to a specific root cortical response to cytokinin.}, } @article {pmid30670646, year = {2019}, author = {Aihara, Y and Maruyama, S and Baird, AH and Iguchi, A and Takahashi, S and Minagawa, J}, title = {Green fluorescence from cnidarian hosts attracts symbiotic algae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1812257116}, pmid = {30670646}, issn = {1091-6490}, abstract = {Reef-building corals thrive in nutrient-poor marine environments because of an obligate symbiosis with photosynthetic dinoflagellates of the genus Symbiodinium Symbiosis is established in most corals through the uptake of Symbiodinium from the environment. Corals are sessile for most of their life history, whereas free-living Symbiodinium are motile; hence, a mechanism to attract Symbiodinium would greatly increase the probability of encounter between host and symbiont. Here, we examined whether corals can attract free-living motile Symbiodinium by their green fluorescence, emitted by the excitation of endogenous GFP by purple-blue light. We found that Symbiodinium have positive and negative phototaxis toward weak green and strong purple-blue light, respectively. Under light conditions that cause corals to emit green fluorescence, (e.g., strong blue light), Symbiodinium were attracted toward live coral fragments. Symbiodinium were also attracted toward an artificial green fluorescence dye with similar excitation and emission spectra to coral-GFP. In the field, more Symbiodinium were found in traps painted with a green fluorescence dye than in controls. Our results revealed a biological signaling mechanism between the coral host and its potential symbionts.}, } @article {pmid30670545, year = {2019}, author = {Ogden, AJ and McAleer, JM and Kahn, ML}, title = {Characterization of the Sinorhizobium meliloti HslUV and ClpXP protease systems in free-living and symbiotic states.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00498-18}, pmid = {30670545}, issn = {1098-5530}, abstract = {Symbiotic nitrogen fixation (SNF) in the interaction between the soil bacteria Sinorhizobium meliloti and legume plant Medicago sativa is carried out in specialized root organs called nodules. During nodule development, each symbiont must drastically alter their proteins, transcripts and metabolites in order to support nitrogen fixation. Moreover, bacteria within the nodules are under stress, including challenges by plant antimicrobial peptides, low pH, limited oxygen availability, and strongly reducing conditions, all of which challenge proteome integrity. S. meliloti stress adaptation, proteome remodeling and quality control are controlled in part by the large oligomeric protease complexes HslUV and ClpXP1. To improve understanding of the roles of S. meliloti HslUV and ClpXP1 in free-living conditions and in symbiosis with M. sativa, we generated ΔhslU, ΔhslV, ΔhslUV, and ΔclpP1 knockout mutants. Shoot dry weight of M. sativa plants inoculated with each deletion mutant was significantly reduced, suggesting a role in symbiosis. Further, slower free-living growth of ΔhslUV and ΔclpP1 suggest HslUV and ClpP1 were involved in adapting to heat stress, while ΔhslU and ΔclpP1 mutants were sensitive to kanamycin. All deletion mutants produced less exopolysaccharide and succinoglycan, as shown by replicate spot plating and Calcofluor binding. We also generated endogenous C-terminal eGFP fusions to HslU, HslV, ClpX and ClpP1 in S. meliloti Using anti-eGFP antibodies, native coimmunoprecipitation experiments of proteins from free-living and nodule tissues were performed and analyzed by mass spectrometry. The results suggest HslUV and ClpXP were closely associated with ribosomal and proteome quality control proteins, and identified several novel putative protein-protein interactions.Importance Symbiotic nitrogen fixation (SNF) is the primary means by which biologically available nitrogen enters the biosphere, and is therefore a critical component of the global nitrogen cycle and modern agriculture. SNF is the result of highly coordinated interactions between legume plants and soil bacteria collectively referred to as rhizobia, e.g. Medicago sativa and S. meliloti, respectively. Accomplishing SNF requires significant proteome changes in both organisms to create a microaerobic environment suitable for high-level bacterial nitrogenase activity. Bacterial protease systems, HslUV and ClpXP are important in proteome quality control, metabolic remodeling, and in adapting to stress. This work shows that S. meliloti HslUV and ClpXP are involved in SNF, in exopolysaccharide production, and in free-living stress adaptation.}, } @article {pmid30669397, year = {2019}, author = {Chialva, M and Fangel, JU and Novero, M and Zouari, I and di Fossalunga, AS and Willats, WGT and Bonfante, P and Balestrini, R}, title = {Understanding Changes in Tomato Cell Walls in Roots and Fruits: The Contribution of Arbuscular Mycorrhizal Colonization.}, journal = {International journal of molecular sciences}, volume = {20}, number = {2}, pages = {}, doi = {10.3390/ijms20020415}, pmid = {30669397}, issn = {1422-0067}, abstract = {Modifications in cell wall composition, which can be accompanied by changes in its structure, were already reported during plant interactions with other organisms, such as the mycorrhizal fungi. Arbuscular mycorrhizal (AM) fungi are among the most widespread soil organisms that colonize the roots of land plants, where they facilitate mineral nutrient uptake from the soil in exchange for plant-assimilated carbon. In AM symbiosis, the host plasma membrane invaginates and proliferates around all the developing intracellular fungal structures, and cell wall material is laid down between this membrane and the fungal cell surface. In addition, to improve host nutrition and tolerance/resistance to environmental stresses, AM symbiosis was shown to modulate fruit features. In this study, Comprehensive Microarray Polymer Profiling (CoMMP) technique was used to verify the impact of the AM symbiosis on the tomato cell wall composition both at local (root) and systemic level (fruit). Multivariate data analyses were performed on the obtained datasets looking for the effects of fertilization, inoculation with AM fungi, and the fruit ripening stage. Results allowed for the discernment of cell wall component modifications that were correlated with mycorrhizal colonization, showing a different tomato response to AM colonization and high fertilization, both at the root and the systemic level.}, } @article {pmid30404910, year = {2018}, author = {Medeiros, LP and Garcia, G and Thompson, JN and Guimarães, PR}, title = {The geographic mosaic of coevolution in mutualistic networks.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {47}, pages = {12017-12022}, pmid = {30404910}, issn = {1091-6490}, mesh = {Adaptation, Physiological ; Biological Coevolution/*genetics ; Biological Evolution ; Ecosystem ; Gene Flow/genetics ; Geography ; Models, Genetic ; Pollination ; Symbiosis ; }, abstract = {Ecological interactions shape adaptations through coevolution not only between pairs of species but also through entire multispecies assemblages. Local coevolution can then be further altered through spatial processes that have been formally partitioned in the geographic mosaic theory of coevolution. A major current challenge is to understand the spatial patterns of coadaptation that emerge across ecosystems through the interplay between gene flow and selection in networks of interacting species. Here, we combine a coevolutionary model, network theory, and empirical information on species interactions to investigate how gene flow and geographical variation in selection affect trait patterns in mutualistic networks. We show that gene flow has the surprising effect of favoring trait matching, especially among generalist species in species-rich networks typical of pollination and seed dispersal interactions. Using an analytical approximation of our model, we demonstrate that gene flow promotes trait matching by making the adaptive landscapes of different species more similar to each other. We use this result to show that the progressive loss of gene flow associated with habitat fragmentation may undermine coadaptation in mutualisms. Our results therefore provide predictions of how spatial processes shape the evolution of species-rich interactions and how the widespread fragmentation of natural landscapes may modify the coevolutionary process.}, } @article {pmid30373839, year = {2018}, author = {Mehta, AP and Supekova, L and Chen, JH and Pestonjamasp, K and Webster, P and Ko, Y and Henderson, SC and McDermott, G and Supek, F and Schultz, PG}, title = {Engineering yeast endosymbionts as a step toward the evolution of mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {46}, pages = {11796-11801}, pmid = {30373839}, issn = {1091-6490}, support = {P41 GM103445/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Bioengineering/*methods ; Biological Evolution ; Escherichia coli/genetics/metabolism ; Mitochondria/*genetics/metabolism ; Models, Biological ; Saccharomyces cerevisiae/genetics/metabolism ; Symbiosis/*genetics ; Thiamine/metabolism ; }, abstract = {It has been hypothesized that mitochondria evolved from a bacterial ancestor that initially became established in an archaeal host cell as an endosymbiont. Here we model this first stage of mitochondrial evolution by engineering endosymbiosis between Escherichia coli and Saccharomyces cerevisiae An ADP/ATP translocase-expressing E. coli provided ATP to a respiration-deficient cox2 yeast mutant and enabled growth of a yeast-E. coli chimera on a nonfermentable carbon source. In a reciprocal fashion, yeast provided thiamin to an endosymbiotic E. coli thiamin auxotroph. Expression of several SNARE-like proteins in E. coli was also required, likely to block lysosomal degradation of intracellular bacteria. This chimeric system was stable for more than 40 doublings, and GFP-expressing E. coli endosymbionts could be observed in the yeast by fluorescence microscopy and X-ray tomography. This readily manipulated system should allow experimental delineation of host-endosymbiont adaptations that occurred during evolution of the current, highly reduced mitochondrial genome.}, } @article {pmid30348787, year = {2018}, author = {Harcombe, WR and Chacón, JM and Adamowicz, EM and Chubiz, LM and Marx, CJ}, title = {Evolution of bidirectional costly mutualism from byproduct consumption.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {47}, pages = {12000-12004}, pmid = {30348787}, issn = {1091-6490}, mesh = {Biological Evolution ; Carbon ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Galactose/biosynthesis/metabolism ; Methionine/biosynthesis/genetics ; Microbial Interactions/*physiology ; Salmonella enterica/genetics/metabolism ; Symbiosis/*physiology ; }, abstract = {Mutualisms are essential for life, yet it is unclear how they arise. A two-stage process has been proposed for the evolution of mutualisms that involve exchanges of two costly resources. First, costly provisioning by one species may be selected for if that species gains a benefit from costless byproducts generated by a second species, and cooperators get disproportionate access to byproducts. Selection could then drive the second species to provide costly resources in return. Previously, a synthetic consortium evolved the first stage of this scenario: Salmonella enterica evolved costly production of methionine in exchange for costless carbon byproducts generated by an auxotrophic Escherichia coli Growth on agar plates localized the benefits of cooperation around methionine-secreting S. enterica Here, we report that further evolution of these partners on plates led to hypercooperative E. coli that secrete the sugar galactose. Sugar secretion arose repeatedly across replicate communities and is costly to E. coli producers, but enhances the growth of S. enterica The tradeoff between individual costs and group benefits led to maintenance of both cooperative and efficient E. coli genotypes in this spatially structured environment. This study provides an experimental example of de novo, bidirectional costly mutualism evolving from byproduct consumption. The results validate the plausibility of costly cooperation emerging from initially costless exchange, a scenario widely used to explain the origin of the mutualistic species interactions that are central to life on Earth.}, } @article {pmid29935729, year = {2018}, author = {Kiran, GS and Sekar, S and Ramasamy, P and Thinesh, T and Hassan, S and Lipton, AN and Ninawe, AS and Selvin, J}, title = {Marine sponge microbial association: Towards disclosing unique symbiotic interactions.}, journal = {Marine environmental research}, volume = {140}, number = {}, pages = {169-179}, doi = {10.1016/j.marenvres.2018.04.017}, pmid = {29935729}, issn = {1879-0291}, mesh = {Animals ; Bacteria/genetics ; Biodiversity ; *Microbiota ; Phylogeny ; Porifera/microbiology/*physiology ; RNA, Ribosomal, 16S ; Seawater/microbiology ; *Symbiosis ; }, abstract = {Sponges are sessile benthic filter-feeding animals, which harbor numerous microorganisms. The enormous diversity and abundance of sponge associated bacteria envisages sponges as hot spots of microbial diversity and dynamics. Many theories were proposed on the ecological implications and mechanism of sponge-microbial association, among these, the biosynthesis of sponge derived bioactive molecules by the symbiotic bacteria is now well-indicated. This phenomenon however, is not exhibited by all marine sponges. Based on the available reports, it has been well established that the sponge associated microbial assemblages keep on changing continuously in response to environmental pressure and/or acquisition of microbes from surrounding seawater or associated macroorganisms. In this review, we have discussed nutritional association of sponges with its symbionts, interaction of sponges with other eukaryotic organisms, dynamics of sponge microbiome and sponge-specific microbial symbionts, sponge-coral association etc.}, } @article {pmid28717232, year = {2017}, author = {Tian, Z and Wang, R and Ambrose, KV and Clarke, BB and Belanger, FC}, title = {The Epichloë festucae antifungal protein has activity against the plant pathogen Sclerotinia homoeocarpa, the causal agent of dollar spot disease.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5643}, pmid = {28717232}, issn = {2045-2322}, mesh = {Ascomycota/*drug effects/pathogenicity ; Disease Resistance ; Epichloe/metabolism/*physiology ; Fungal Proteins/genetics/metabolism/*pharmacology ; Plant Diseases/microbiology ; Poaceae/microbiology ; Symbiosis ; }, abstract = {Epichloë spp. are naturally occurring fungal endophytic symbionts of many cool-season grasses. Infection by the fungal endophytes often confers biotic and abiotic stress tolerance to their hosts. Endophyte-mediated disease resistance is well-established in the fine fescue grass Festuca rubra subsp. rubra (strong creeping red fescue) infected with E. festucae. Resistance to fungal pathogens is not an established effect of endophyte infection of other grass species, and may therefore be unique to the fine fescues. The underlying mechanism of the disease resistance is unknown. E. festucae produces a secreted antifungal protein that is highly expressed in the infected plant tissues and may therefore be involved in the disease resistance. Most Epichloë spp. do not have a gene for a similar antifungal protein. Here we report the characterization of the E. festucae antifungal protein, designated Efe-AfpA. The antifungal protein partially purified from the apoplastic proteins of endophyte-infected plant tissue and the recombinant protein expressed in the yeast Pichia pastoris was found to have activity against the important plant pathogen Sclerotinia homoeocarpa. Efe-AfpA may therefore be a component of the disease resistance seen in endophyte-infected strong creeping red fescue.}, } @article {pmid28717170, year = {2017}, author = {Ruibal, MP and Triponez, Y and Smith, LM and Peakall, R and Linde, CC}, title = {Population structure of an orchid mycorrhizal fungus with genus-wide specificity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5613}, pmid = {28717170}, issn = {2045-2322}, mesh = {Agaricales/*classification/genetics/growth & development ; DNA, Fungal/genetics ; Evolution, Molecular ; Genotyping Techniques ; Inbreeding ; *Microsatellite Repeats ; Mycorrhizae/*classification/genetics/growth & development ; Orchidaceae/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; }, abstract = {Fundamental life history processes of mycorrhizal fungi with inconspicuous fruiting bodies can be difficult to elucidate. In this study we investigated the species identities and life history of the orchid mycorrhizal Tulasnella fungi, which associate with the south eastern Australia orchid genus Chiloglottis. Tulasnella prima was the primary partner and was found to be associated with all 17 Chiloglottis species across a range of >1000 km, and to occur in the two edaphic conditions investigated (soil and sphagnum hammocks). Another Tulasnella species (T. sphagneti) appears to be restricted to moist conditions of alpine sphagnum hammocks. The population genetic structure of the widespread species T. prima, was investigated at 10 simple sequence repeat (SSR) markers and at four cross-amplified SSR loci for T. sphagneti. For both taxa, no sharing of multilocus genotypes was found between sites, but clones were found within sites. Evidence for inbreeding within T. prima was found at 3 of 5 sites. Significant genetic differentiation was found within and between taxa. Significant local positive spatial genetic autocorrelation was detected among non-clonal isolates at the scale of two metres. Overall, the population genetic patterns indicated that in Tulasnella mating occurs by inbreeding and dispersal is typically restricted to short-distances.}, } @article {pmid28717159, year = {2017}, author = {Ruiz, L and Bottacini, F and Boinett, CJ and Cain, AK and O'Connell-Motherway, M and Lawley, TD and van Sinderen, D}, title = {The essential genomic landscape of the commensal Bifidobacterium breve UCC2003.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5648}, pmid = {28717159}, issn = {2045-2322}, support = {WT098051//Wellcome Trust/United Kingdom ; G1100100/1//Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/*genetics ; Bifidobacterium breve/genetics/*growth & development ; DNA Transposable Elements ; Evolution, Molecular ; Genes, Essential ; Genome, Plant ; Molecular Sequence Annotation ; *Mutagenesis, Insertional ; Phylogeny ; Sequence Homology, Nucleic Acid ; Symbiosis ; }, abstract = {Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the Bifidobacterium and B. breve core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.}, } @article {pmid30668787, year = {2019}, author = {Chebbi, MA and Becking, T and Moumen, B and Giraud, I and Gilbert, C and Peccoud, J and Cordaux, R}, title = {The genome of Armadillidium vulgare (Crustacea, Isopoda) provides insights into sex chromosome evolution in the context of cytoplasmic sex determination.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msz010}, pmid = {30668787}, issn = {1537-1719}, abstract = {The terrestrial isopod Armadillidium vulgare is an original model to study the evolution of sex determination and symbiosis in animals. Its sex can be determined by ZW sex chromosomes, or by feminizing Wolbachia bacterial endosymbionts. Here we report the sequence and analysis of the ZW female genome of A. vulgare. A distinguishing feature of the 1.72 gigabase assembly is the abundance of repeats (68% of genome). We show that the Z and W sex chromosomes are essentially undifferentiated at the molecular level and the W-specific region is extremely small (at most several hundreds of kilobases). Our results suggest that recombination suppression has not spread very far from the sex-determining locus, if at all. This is consistent with A. vulgare possessing evolutionarily young sex chromosomes. We characterized multiple Wolbachia nuclear inserts in the A. vulgare genome, none of which is associated with the W-specific region. We also identified several candidate genes that may be involved in the sex determination or sexual differentiation pathways. The A. vulgare genome serves as a resource for studying the biology and evolution of crustaceans, one of the most speciose and emblematic metazoan groups.}, } @article {pmid30668688, year = {2019}, author = {Fernández-Brime, S and Muggia, L and Maier, S and Grube, M and Wedin, M}, title = {Bacterial communities in an optional lichen symbiosis are determined by substrate, not algal photobionts.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz012}, pmid = {30668688}, issn = {1574-6941}, abstract = {Borderline lichens are simple mutualistic symbioses between fungi and algae, where the fungi form loose mycelia interweaving algal cells, instead of forming a lichen thallus. Schizoxylon albescens shows two nutritional modes: it can either live as a borderline lichen on Populus tremula bark or as a saprotroph on Populus wood. This enables us to investigate the microbiota diversity in simple fungal-algal associations and to study the impact of lichenization on the structure of bacterial communities. We sampled three areas in Sweden covering the distribution of Schizoxylon, and using high-throughput sequencing of the 16S rRNA gene and fluorescence in situ hybridization we characterized the associated microbiota. Bacterial communities in lichenized and saprotrophic Schizoxylon were clearly distinct, but when comparing the microbiota with the respective substrates, only the fruiting bodies show clear differences in composition and abundance from the communities in the substrates. The colonisation by either lichenized or saprotrophic mycelia of Schizoxylon did not significantly influence the microbiota in the substrate. This suggests that in a morphologically simple form of lichenization, as represented by the Schizoxylon-Coccomyxa system, algal-fungal interactions do not significantly influence bacterial communities, but a more complex structure of the lichen thallus is likely required for hosting specific microbiota.}, } @article {pmid30666424, year = {2019}, author = {Xie, S and Lan, Y and Sun, C and Shao, Y}, title = {Insect microbial symbionts as a novel source for biotechnology.}, journal = {World journal of microbiology & biotechnology}, volume = {35}, number = {2}, pages = {25}, doi = {10.1007/s11274-019-2599-8}, pmid = {30666424}, issn = {1573-0972}, support = {31601906//National Natural Science Foundation of China/ ; 2017QNA6024//The Fundamental Research Funds for the Central Universities/ ; CARS-18-ZJ0302//The Modern Agricultural Industry Technology System/ ; 2018C37060//Zhejiang province analysis and testing science and technology project/ ; }, abstract = {Insecta is the most diverse and largest class of animals on Earth, appearing together with the emergence of the first terrestrial ecosystem. Owing to this great diversity and long-term coexistence, an amazing variety of symbiotic microorganisms have adapted specifically to insects as hosts. Insect symbionts not only participate in many relationships with the hosts but also represent a novel resource for biotechnological applications. The exploitation of mutualistic symbiosis represents a promising area to search for bioactive compounds and new enzymes for potential clinical, industrial or environmental applications. Moreover, the manipulation of parasitic symbiosis has particular potential to solve practical problems for the control of agricultural pests and disease vectors. Although the study of microbial symbionts has been impaired by the unculturability of most symbionts, the rapidly growing catalogue of microbial genomes and the application of modern genetic techniques provide an alternative approach to using these microbes. This minireview presents examples of microbial symbionts isolated from insects for emerging biotechnological use and illuminates new ways for discovering microorganisms of applied value from a particularly promising source.}, } @article {pmid30476897, year = {2019}, author = {Qin, D and Shen, W and Wang, J and Han, M and Chai, F and Duan, X and Yan, X and Guo, J and Gao, T and Zuo, S and Dong, J}, title = {Enhanced production of unusual triterpenoids from Kadsura angustifolia fermented by a symbiont endophytic fungus, Penicillium sp. SWUKD4.1850.}, journal = {Phytochemistry}, volume = {158}, number = {}, pages = {56-66}, doi = {10.1016/j.phytochem.2018.11.005}, pmid = {30476897}, issn = {1873-3700}, mesh = {Antineoplastic Agents, Phytogenic/chemistry/pharmacology ; Drug Screening Assays, Antitumor ; Endophytes/physiology ; Fermentation ; Hep G2 Cells ; Humans ; Kadsura/chemistry/*metabolism/*microbiology ; Magnetic Resonance Spectroscopy ; Molecular Structure ; Penicillium/*physiology ; Spectrometry, Mass, Electrospray Ionization ; Symbiosis ; Triterpenes/*chemistry/*metabolism/pharmacology ; }, abstract = {Highly oxygenated schitriterpenoids are interesting for study of their structures, bioactivities and synthesis. From Kadsura angustifolia fermented by an associated symbiotic endophytic fungus, Penicillium sp. SWUKD4.1850, nine undescribed triterpenoids, kadhenrischinins A-H, and 7β-schinalactone C together with four known triterpenoids, henrischinins A and B, schinalactone C and nigranoic acid were isolated and established by the extensive 1D-, 2D-NMR, HR-ESI-MS and ECD data analysis. Except nigranoic acid, all these metabolites have been first detected in non-fermented K. angustifolia. Structurally, kadhenrischinins A-D belong to the relatively rare class of highly oxygenated schitriterpenoids that contain a unique 3-one-2-oxabicyclo [3,2,1]-octane motif, while kadhenrischinins E-H feature a cyclopentane ring in a side chain rarely found in the family Schisandraceae. These results indicated that fermentation of K. angustifolia with SWUKD4.1850 induced the production of highly oxygenated schitriterpenoids from nigranoic acid, which provided a guidance to obtain desired compounds from those plants initially thought not to produce. This is the first report on the fermentation of K. angustifolia medical plant and the first discovery of highly oxygenated schitriterpenoids by microbial technology.}, } @article {pmid30235351, year = {2018}, author = {Skalski, JH and Limon, JJ and Sharma, P and Gargus, MD and Nguyen, C and Tang, J and Coelho, AL and Hogaboam, CM and Crother, TR and Underhill, DM}, title = {Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice.}, journal = {PLoS pathogens}, volume = {14}, number = {9}, pages = {e1007260}, pmid = {30235351}, issn = {1553-7374}, support = {R01 AI071116/AI/NIAID NIH HHS/United States ; R01 HL123899/HL/NHLBI NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; }, mesh = {Allergens/administration & dosage ; Animals ; Anti-Bacterial Agents/adverse effects ; Antigens, Dermatophagoides/administration & dosage ; Basidiomycota/growth & development/*immunology/*pathogenicity ; Disease Models, Animal ; Environmental Microbiology ; Female ; Gastrointestinal Microbiome/drug effects/genetics/*immunology ; Germ-Free Life/immunology ; Humans ; Mice ; Mice, Inbred C57BL ; Mycobiome/genetics/*immunology ; Respiratory Hypersensitivity/*etiology/immunology/microbiology ; Symbiosis/immunology ; }, abstract = {The gastrointestinal microbiota influences immune function throughout the body. The gut-lung axis refers to the concept that alterations of gut commensal microorganisms can have a distant effect on immune function in the lung. Overgrowth of intestinal Candida albicans has been previously observed to exacerbate allergic airways disease in mice, but whether subtler changes in intestinal fungal microbiota can affect allergic airways disease is less clear. In this study we have investigated the effects of the population expansion of commensal fungus Wallemia mellicola without overgrowth of the total fungal community. Wallemia spp. are commonly found as a minor component of the commensal gastrointestinal mycobiota in both humans and mice. Mice with an unaltered gut microbiota community resist population expansion when gavaged with W. mellicola; however, transient antibiotic depletion of gut microbiota creates a window of opportunity for expansion of W. mellicola following delivery of live spores to the gastrointestinal tract. This phenomenon is not universal as other commensal fungi (Aspergillus amstelodami, Epicoccum nigrum) do not expand when delivered to mice with antibiotic-depleted microbiota. Mice with Wallemia-expanded gut mycobiota experienced altered pulmonary immune responses to inhaled aeroallergens. Specifically, after induction of allergic airways disease with intratracheal house dust mite (HDM) antigen, mice demonstrated enhanced eosinophilic airway infiltration, airway hyperresponsiveness (AHR) to methacholine challenge, goblet cell hyperplasia, elevated bronchoalveolar lavage IL-5, and enhanced serum HDM IgG1. This phenomenon occurred with no detectable Wallemia in the lung. Targeted amplicon sequencing analysis of the gastrointestinal mycobiota revealed that expansion of W. mellicola in the gut was associated with additional alterations of bacterial and fungal commensal communities. We therefore colonized fungus-free Altered Schaedler Flora (ASF) mice with W. mellicola. ASF mice colonized with W. mellicola experienced enhanced severity of allergic airways disease compared to fungus-free control ASF mice without changes in bacterial community composition.}, } @article {pmid30103809, year = {2018}, author = {Budachetri, K and Kumar, D and Crispell, G and Beck, C and Dasch, G and Karim, S}, title = {The tick endosymbiont Candidatus Midichloria mitochondrii and selenoproteins are essential for the growth of Rickettsia parkeri in the Gulf Coast tick vector.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {141}, pmid = {30103809}, issn = {2049-2618}, support = {P20 RR016476/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Arachnid Vectors/genetics/metabolism/microbiology ; Arthropod Proteins/genetics/metabolism ; Female ; Gene Expression Regulation, Bacterial ; Gene Silencing ; Gulf of Mexico ; Male ; Oxidative Stress ; Rickettsia/*growth & development ; Rickettsiaceae/*physiology ; Selenoproteins/*genetics/metabolism ; Symbiosis ; Ticks/genetics/metabolism/*microbiology ; Up-Regulation ; }, abstract = {BACKGROUND: Pathogen colonization inside tick tissues is a significant aspect of the overall competence of a vector. Amblyomma maculatum is a competent vector of the spotted fever group rickettsiae, Rickettsia parkeri. When R. parkeri colonizes its tick host, it has the opportunity to dynamically interact with not just its host but with the endosymbionts living within it, and this enables it to modulate the tick's defenses by regulating tick gene expression. The microbiome in A. maculatum is dominated by two endosymbiont microbes: a Francisella-like endosymbiont (FLE) and Candidatus Midichloria mitochondrii (CMM). A range of selenium-containing proteins (selenoproteins) in A. maculatum ticks protects them from oxidative stress during blood feeding and pathogen infections. Here, we investigated rickettsial multiplication in the presence of tick endosymbionts and characterized the functional significance of selenoproteins during R. parkeri replication in the tick.

RESULTS: FLE and CMM were quantified throughout the tick life stages by quantitative PCR in R. parkeri-infected and uninfected ticks. R. parkeri infection was found to decrease the FLE numbers but CMM thrived across the tick life cycle. Our qRT-PCR analysis indicated that the transcripts of genes with functions related to redox (selenogenes) were upregulated in ticks infected with R. parkeri. Three differentially expressed proteins, selenoprotein M, selenoprotein O, and selenoprotein S were silenced to examine their functional significance during rickettsial replication within the tick tissues. Gene silencing of the target genes was found to impair R. parkeri colonization in the tick vector. Knockdown of the selenogenes triggered a compensatory response from other selenogenes, as observed by changes in gene expression, but oxidative stress levels and endoplasmic reticulum stress inside the ticks were also found to have heightened.

CONCLUSIONS: This study illustrates the potential of this new research model for augmenting our understanding of the pathogen interactions occurring within tick hosts and the important roles that symbionts and various tick factors play in regulating pathogen growth.}, } @article {pmid29931623, year = {2019}, author = {Arai, H and Hirano, T and Akizuki, N and Abe, A and Nakai, M and Kunimi, Y and Inoue, MN}, title = {Multiple Infection and Reproductive Manipulations of Wolbachia in Homona magnanima (Lepidoptera: Tortricidae).}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {257-266}, doi = {10.1007/s00248-018-1210-4}, pmid = {29931623}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacterial Physiological Phenomena ; Cytoplasm ; DNA, Bacterial/analysis ; Female ; Larva/microbiology ; Male ; Moths/drug effects/*genetics/*microbiology ; Phenotype ; Pupa/microbiology ; Reproduction/*physiology ; Sex Ratio ; Symbiosis ; *Wolbachia/classification/genetics/physiology ; }, abstract = {Endosymbiotic bacterium Wolbachia interacts with host in either a mutualistic or parasitic manner. Wolbachia is frequently identified in various arthropod species, and to date, Wolbachia infections have been detected in different insects. Here, we found a triple Wolbachia infection in Homona magnanima, a serious tea pest, and investigated the effects of three infecting Wolbachia strains (wHm-a, -b, and -c) on the host. Starting with the triple-infected host line (Wabc), which was collected in western Tokyo in 1999 and maintained in laboratory, we established an uninfected line (W-) and three singly infected lines (Wa, Wb, and Wc) using antibiotics. Mating experiments with the host lines revealed that only wHm-b induced cytoplasmic incompatibility (CI) in H. magnanima, with the intensities of CI different between the Wb and Wabc lines. Regarding mutualistic effects, wHm-c shortened larval development time and increased pupal weight in both the Wc and Wabc lines to the same extent, whereas no distinct phenotype was observed in lines singly infected with wHm-a. Based on quantitative PCR analysis, Wolbachia density in the Wa line was higher than in the other host lines (p < 0.01, n = 10). Wolbachia density in the Wb line was also higher than in the Wc and Wabc lines, while no difference was observed between the Wc and Wabc lines. These results indicate that the difference in the CI intensity between a single or multiple infection may be attributed to the difference in wHm-b density. However, no correlation was observed between mutualistic effects and Wolbachia density.}, } @article {pmid29766224, year = {2019}, author = {García-Bonilla, E and Brandão, PFB and Pérez, T and Junca, H}, title = {Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida).}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {25-36}, doi = {10.1007/s00248-018-1201-5}, pmid = {29766224}, issn = {1432-184X}, support = {Doctoral Grant (Convocatoria 528-2011)//Colciencias-Colfuturo/ ; Projects (2012-2014 and 2015-2017//EcosNord-Colciencias/ ; }, mesh = {Animals ; Archaea/*classification/genetics/isolation & purification/physiology ; Bacteria ; Betaproteobacteria/*classification/genetics/isolation & purification/physiology ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; France ; Haliclona/*microbiology ; Mediterranean Sea ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Water Microbiology ; }, abstract = {Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.}, } @article {pmid29559567, year = {2018}, author = {Masson, F and Calderon Copete, S and Schüpfer, F and Garcia-Arraez, G and Lemaitre, B}, title = {In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29559567}, issn = {2150-7511}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism/physiology ; Drosophila/*microbiology ; Spiroplasma/genetics/*metabolism/*physiology ; Symbiosis/genetics/physiology ; }, abstract = {Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. Spiroplasma poulsonii is a maternally transmitted bacterial endosymbiont that is naturally associated with several Drosophila species. S. poulsonii strongly affects its host's physiology, for example by causing male killing or by protecting it against various parasites. Despite intense work on this model since the 1950s, attempts to cultivate endosymbiotic Spiroplasma in vitro have failed so far. Here, we developed a method to sustain the in vitro culture of S. poulsonii by optimizing a commercially accessible medium. We also provide a complete genome assembly, including the first sequence of a natural plasmid of an endosymbiotic Spiroplasma species. Last, by comparing the transcriptome of the in vitro culture to the transcriptome of bacteria extracted from the host, we identified genes putatively involved in host-symbiont interactions. This work provides new opportunities to study the physiology of endosymbiotic Spiroplasma and paves the way to dissect insect-endosymbiont interactions with two genetically tractable partners.IMPORTANCE The discovery of insect bacterial endosymbionts (maternally transmitted bacteria) has revolutionized the study of insects, suggesting novel strategies for their control. Most endosymbionts are strongly dependent on their host to survive, making them uncultivable in artificial systems and genetically intractable. Spiroplasma poulsonii is an endosymbiont of Drosophila that affects host metabolism, reproduction, and defense against parasites. By providing the first reliable culture medium that allows a long-lasting in vitro culture of Spiroplasma and by elucidating its complete genome, this work lays the foundation for the development of genetic engineering tools to dissect endosymbiosis with two partners amenable to molecular study. Furthermore, the optimization method that we describe can be used on other yet uncultivable symbionts, opening new technical opportunities in the field of host-microbes interactions.}, } @article {pmid29511084, year = {2018}, author = {Tashyreva, D and Prokopchuk, G and Votýpka, J and Yabuki, A and Horák, A and Lukeš, J}, title = {Life Cycle, Ultrastructure, and Phylogeny of New Diplonemids and Their Endosymbiotic Bacteria.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29511084}, issn = {2150-7511}, mesh = {Bacteria/genetics ; Life Cycle Stages/physiology ; Meiotic Prophase I/*physiology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Symbiosis/*physiology ; }, abstract = {Diplonemids represent a hyperdiverse and abundant yet poorly studied group of marine protists. Here we describe two new members of the genus Diplonema (Diplonemea, Euglenozoa), Diplonema japonicum sp. nov. and Diplonema aggregatum sp. nov., based on life cycle, morphology, and 18S rRNA gene sequences. Along with euglenozoan apomorphies, they contain several unique features. Their life cycle is complex, consisting of a trophic stage that is, following the depletion of nutrients, transformed into a sessile stage and subsequently into a swimming stage. The latter two stages are characterized by the presence of tubular extrusomes and the emergence of a paraflagellar rod, the supportive structure of the flagellum, which is prominently lacking in the trophic stage. These two stages also differ dramatically in motility and flagellar size. Both diplonemid species host endosymbiotic bacteria that are closely related to each other and constitute a novel branch within Holosporales, for which a new genus, "Candidatus Cytomitobacter" gen. nov., has been established. Remarkably, the number of endosymbionts in the cytoplasm varies significantly, as does their localization within the cell, where they seem to penetrate the mitochondrion, a rare occurrence.IMPORTANCE We describe the morphology, behavior, and life cycle of two new Diplonema species that established a relationship with two Holospora-like bacteria in the first report of an endosymbiosis in diplonemids. Both endosymbionts reside in the cytoplasm and the mitochondrion, which establishes an extremely rare case. Within their life cycle, the diplonemids undergo transformation from a trophic to a sessile and eventually a highly motile swimming stage. These stages differ in several features, such as the presence or absence of tubular extrusomes and a paraflagellar rod, along with the length of the flagella. These morphological and behavioral interstage differences possibly reflect distinct functions in dispersion and invasion of the host and/or prey and may provide novel insight into the virtually unknown function of diplonemids in the oceanic ecosystem.}, } @article {pmid29230812, year = {2018}, author = {Ascher, S and Reinhardt, C}, title = {The gut microbiota: An emerging risk factor for cardiovascular and cerebrovascular disease.}, journal = {European journal of immunology}, volume = {48}, number = {4}, pages = {564-575}, doi = {10.1002/eji.201646879}, pmid = {29230812}, issn = {1521-4141}, mesh = {Animals ; Atherosclerosis/immunology/*pathology ; Blood Platelets/metabolism ; Cardiovascular Diseases/*etiology ; Cerebrovascular Disorders/*etiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Immunity, Innate/immunology ; Infant ; Infant, Newborn ; Integrins/immunology ; Methylamines/metabolism ; Mice ; Plaque, Atherosclerotic/microbiology/*pathology ; Risk Factors ; Symbiosis ; Thrombosis/microbiology/*pathology ; Toll-Like Receptor 2/metabolism ; von Willebrand Factor/immunology ; }, abstract = {Commensal gut microbiota have recently been implicated in cardiovascular disease (CVD) and cerebrovascular disease. Atherosclerotic plaque formation depends on the colonization status of the host. In addition to host nutrition and the related microbiota-dependent metabolic changes, activation of innate immune pathways triggers the development of atherosclerosis and supports arterial thrombosis. Gnotobiotic mouse models have uncovered that activation of Toll-like receptor-2 by gut microbial ligands supports von Willebrand factor-integrin mediated platelet deposition to the site of vascular injury. Depending on nutritional factors, the microbiota-derived choline-metabolite trimethylamine N-oxide (TMAO) increases atherosclerotic plaque size, triggers prothrombotic platelet function and promotes arterial thrombus growth. Hence, the composition of the commensal microbiota is an emerging risk factor for CVD. Here, we provide an overview on microbiota-dependent pathomechanisms that drive the development of CVD and arterial thrombosis.}, } @article {pmid30664238, year = {2019}, author = {Sato, H and Toju, H}, title = {Timing of evolutionary innovation: scenarios of evolutionary diversification in a species-rich fungal clade, Boletales.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15698}, pmid = {30664238}, issn = {1469-8137}, abstract = {Acquisition of mutualistic symbiosis could provide hosts and/or symbionts with novel ecological opportunities for evolutionary diversification. Such a mechanism is one of the major components of coevolutionary diversification. However, whether the origin of mycorrhizal symbiosis promotes diversification in fungi still requires clarification. Here, we aimed to reveal evolutionary diversification in a clade comprising ectomycorrhizal (ECM) fungi. Based on a phylogenic tree inferred from the sequences of 87 single-copy genes, we reconstructed the origins of ECM symbiosis in a species-rich basidiomycetous order, Boletales. High-resolution phylogeny of Boletales revealed that ECM symbiosis independently evolved from non-ECM states at least four times in the group. Among them, only the second most recent event, occurring in the clade of Boletaceae, was inferred to involve an almost synchronous rapid diversification and rapid transition from non-ECM to ECM symbiosis. Our results contradict the hypothesis of evolutionary priority effect, which postulates the greatest ecological opportunities in the oldest lineages. Therefore, the novel resources that had not been preempted by the old ECM fungal lineages, supposedly the coevolving angiosperm hosts, could be available for the young ECM fungal lineages, which resulted in the evolutionary diversification occurring only in the young ECM fungal lineages. This article is protected by copyright. All rights reserved.}, } @article {pmid30662731, year = {2018}, author = {Muller, KE and Denison, RF}, title = {Resource acquisition and allocation traits in symbiotic rhizobia with implications for life-history outside of legume hosts.}, journal = {Royal Society open science}, volume = {5}, number = {12}, pages = {181124}, doi = {10.1098/rsos.181124}, pmid = {30662731}, issn = {2054-5703}, abstract = {Resources that microbial symbionts obtain from hosts may enhance fitness during free-living stages when resources are comparatively scarce. For rhizobia in legume root nodules, diverting resources from nitrogen fixation to polyhydroxybutyrate (PHB) has been discussed as a source of host-symbiont conflict. Yet, little is known about natural variation in PHB storage and its implications for rhizobial evolution. We therefore measured phenotypic variation in natural rhizobia populations and investigated how PHB might contribute to fitness in the free-living stage. We found that natural populations of rhizobia from Glycine max and Chamaecrista fasciculata had substantial, heritable variation in PHB acquisition during symbiosis. A model simulating temperature-dependent metabolic activity showed that the observed range of stored PHB per cell could support survival for a few days, for active cells, or over a century for sufficiently dormant cells. Experiments with field-isolated Bradyrhizobium in starvation culture suggest PHB is partitioned asymmetrically in dividing cells, consistent with individual-level bet-hedging previously demonstrated in E. meliloti. High-PHB isolates used more PHB over the first month, yet still retained more PHB for potential long-term survival in a dormant state. These results suggest that stored resources like PHB may support both short-term and long-term functions that contribute to fitness in the free-living stage.}, } @article {pmid30661799, year = {2019}, author = {Tuovinen, V and Ekman, S and Thor, G and Vanderpool, D and Spribille, T and Johannesson, H}, title = {Two Basidiomycete Fungi in the Cortex of Wolf Lichens.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2018.12.022}, pmid = {30661799}, issn = {1879-0445}, abstract = {Since the late 1800s, mycologists have been detecting fungi above and beyond the assumed single fungus in lichen thalli [1-6]. Over the last century, these fungi have been accorded roles ranging from commensalists to pathogens. Recently, Cyphobasidiales yeasts were shown to be ubiquitous in the cortex layer of many macrolichens [7], but for most species, little is known of their cellular distribution and constancy beyond visible fruiting structures. Here, we demonstrate the occurrence of an additional and distantly related basidiomycete, Tremella, in 95% of studied thalli in a global sample of one of the most intensively studied groups of lichens, the wolf lichens (genus Letharia). Tremella species are reported from a wide range of lichen genera [8], but until now, their biology was deduced from fruiting bodies (basidiomata) formed on lichen thalli. Based on this, they have been thought to be uncommon to rare, to occur exclusively in a hyphal form, and to be parasitic on the dominant fungal partner [9, 10]. We show that, in wolf lichens, Tremella occurs as yeast cells also in thalli that lack basidiomata and infer that this is its dominant stage in nature. We further show that the hyphal stage, when present in Letharia, is in close contact with algal cells, challenging the assumption that lichen-associated Tremella species are uniformly mycoparasites. Our results suggest that extent of occurrence and cellular interactions of known fungi within lichens have historically been underestimated and raise new questions about their function in specific lichen symbioses.}, } @article {pmid30661111, year = {2019}, author = {Plotnikov, AO and Balkin, AS and Gogoleva, NE and Lanzoni, O and Khlopko, YA and Cherkasov, SV and Potekhin, AA}, title = {High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01321-x}, pmid = {30661111}, issn = {1432-184X}, support = {16-14-10157//Russian Science Foundation/ ; 14-04-01796//Russian Foundation for Basic Research/ ; }, abstract = {Ciliates are the largest group of ubiquitous aquatic bacterivorous protists, and many species are easily cultivated. However, only few studies reported prokaryotic communities naturally associated with ciliate cells. Herein, we analyzed the microbiome composition of several strains of Paramecium (Ciliophora) originating from different locations and belonging to two morpho-species by high-throughput sequencing (HTS) of the 16S rRNA gene. Possible reasons of HTS results bias were addressed comparing DNA libraries obtained using different primers and different number of ciliate cells. Microbiomes associated with ciliates and their environments were always significantly different by prokaryotic taxonomic composition and bacterial richness. There were also pronounced differences between Paramecium strains. Interestingly, potentially pathogenic bacteria were revealed in Paramecium microbiomes.}, } @article {pmid30658977, year = {2019}, author = {Li, Y and Pinto-Tomás, AA and Rong, X and Cheng, K and Liu, M and Huang, Y}, title = {Population genomics insights into adaptive evolution and ecological differentiation in streptomycetes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02555-18}, pmid = {30658977}, issn = {1098-5336}, abstract = {Deciphering the genomic variation that represents microevolutionary processes towards species divergence is key to understanding microbial speciation, which has long been under debate. Streptomycetes are filamentous bacteria that are ubiquitous in nature and the richest source of antibiotics; however, their speciation processes remain unknown. To tackle this issue, here, we performed a comprehensive population genomics analysis on Streptomyces albidoflavus residing in different habitats and with a worldwide distribution, and identified and characterized the foundational changes within the species. We detected three well-defined phylogenomic clades, of which clades I and III mainly contained free-living (soil/marine) and insect-associated strains, respectively, and clade II had a mixed origin. By performing genome-wide association studies (GWAS), we identified a number of genetic variants associated with free-living or entomic (denoting or relating to insects) habitats in both the accessory and core genomes. These variants contributed collectively to the population structure and had annotated or confirmed functions that likely facilitate differential adaptation of the species. In addition, we detected higher levels of homologous recombination within each clade and in the free-living group than within the whole species and in the entomic group. A subset of the insect-associated strains (clade III) showed a relatively independent evolutionary trajectory with more symbiosis-favorable genes but little genetic interchange with the other lineages. Our results demonstrate that ecological adaptation promotes genetic differentiation in S. albidoflavus, suggesting a model of ecological speciation with gene flow in streptomycetes.IMPORTANCESpecies are the fundamental units of ecology and evolution, and speciation leads to the astounding diversity of life on Earth. Studying speciation is thus of great significance to understand, protect, and exploit biodiversity, but is a challenge in the microbial world. Here, using population genomics, we placed Streptomyces albidoflavus strains in a spectrum of speciation and showed that the genetic differences between phylogenomic clusters evolved mainly by environmental selection and gene-specific sweeps. These findings highlight the role of ecology in structuring recombining bacterial species, making a step towards a deeper understanding of microbial speciation. Our results also raise concerns of an underrated microbial diversity at the intraspecies level, which can be utilized for mining of ecologically relevant natural products.}, } @article {pmid30658579, year = {2019}, author = {Zhu, D and He, J and Yang, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Liu, Y and Zhang, L and Yu, Y and You, Y and Chen, X and Cheng, A}, title = {Comparative analysis reveals the Genomic Islands in Pasteurella multocida population genetics: on Symbiosis and adaptability.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {63}, doi = {10.1186/s12864-018-5366-6}, pmid = {30658579}, issn = {1471-2164}, support = {No. 2017YFD050080//the National Key Research and Development Program of China/ ; No. CARS-42-17//China Agricultural Research System/ ; No. 2016JPT0004//Special Fund for Key Laboratory of Animal Disease and Human Health of Sichuan Province/ ; CARS-SVDIP//Sichuan Veterinary Medicine and Drug Innovation Group of China Agricultural Research System/ ; }, abstract = {BACKGROUND: Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria acquire large fragments of foreign genes. However, the effects of GIs on P. multocida are unknown in the evolution of bacterial populations.

RESULTS: Ten avian-sourced P. multocida obtained through high-throughput sequencing together with 104 publicly available P. multocida genomes were used to analyse their population genetics, thus constructed a pan-genome containing 3948 protein-coding genes. Through the pan-genome, the open evolutionary pattern of P. multocida was revealed, and the functional components of 944 core genes, 2439 accessory genes and 565 unique genes were analysed. In addition, a total of 280 GIs were predicted in all strains. Combined with the pan-genome of P. multocida, the GIs accounted for 5.8% of the core genes in the pan-genome, mainly related to functional metabolic activities; the accessory genes accounted for 42.3%, mainly for the enrichment of adaptive genes; and the unique genes accounted for 35.4%, containing some defence mechanism-related genes.

CONCLUSIONS: The effects of GIs on the population genetics of P. multocida evolution and adaptation to the environment are reflected by the proportion and function of the pan-genome acquired from GIs, and the large quantities of GI data will aid in additional population genetics studies.}, } @article {pmid30658517, year = {2019}, author = {Quezada, EH and García, GX and Arthikala, MK and Melappa, G and Lara, M and Nanjareddy, K}, title = {Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis.}, journal = {Genes}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/genes10010059}, pmid = {30658517}, issn = {2073-4425}, support = {IA205117//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; IN211218//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; }, abstract = {Receptor-like kinases (RLKs) are conserved upstream signaling molecules that regulate several biological processes, including plant development and stress adaptation. Cysteine (C)-rich receptor-like kinases (CRKs) are an important class of RLK that play vital roles in disease resistance and cell death in plants. Genome-wide analyses of CRK genes have been carried out in Arabidopsis and rice, while functional characterization of some CRKs has been carried out in wheat and tomato in addition to Arabidopsis. A comprehensive analysis of the CRK gene family in leguminous crops has not yet been conducted, and our understanding of their roles in symbiosis is rather limited. Here, we report the comprehensive analysis of the PhaseolusCRK gene family, including identification, sequence similarity, phylogeny, chromosomal localization, gene structures, transcript expression profiles, and in silico promoter analysis. Forty-six CRK homologs were identified and phylogenetically clustered into five groups. Expression analysis suggests that PvCRK genes are differentially expressed in both vegetative and reproductive tissues. Further, transcriptomic analysis revealed that shared and unique CRK genes were upregulated during arbuscular mycorrhizal and rhizobial symbiosis. Overall, the systematic analysis of the PvCRK gene family provides valuable information for further studies on the biological roles of CRKs in various Phaseolus tissues during diverse biological processes, including Phaseolus-mycorrhiza/rhizobia symbiosis.}, } @article {pmid30657885, year = {2019}, author = {Jiang, G and Yang, J and Li, X and Cao, Y and Liu, X and Ling, J and Wang, H and Zhong, Z and Zhu, J}, title = {Alkyl hydroperoxide reductase (AhpCD) is important for oxidative stress resistance and symbiosis in Azorhizobium caulinodans.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz014}, pmid = {30657885}, issn = {1574-6968}, abstract = {Reactive oxygen species (ROS) are not only toxic products of oxygen from aerobic metabolism or stress but also signalling molecules involved in the development of the legume-Rhizobium symbiosis. To assess the importance of alkyl hydroperoxide reductase (AhpCD) in the nitrogen-fixating bacterium Azorhizobium caulinodans, we investigated the phenotypes of the ∆ahpCD strain with regards to ROS resistance and symbiotic interactions with Sesbania rostrata. The ∆ahpCD strain was notably more sensitive than its parent strain to hydrogen peroxide (H2O2) but not to two organic peroxides, in the early log phase. The expression of ahpCD was not controlled by a LysR-type transcriptional activator either in vitro or in vivo. The catalase activity of the ∆ahpCD strain was affected at a relatively low level of H2O2 stress. Furthermore, the ∆ahpCD strain induced a reduced the number of stem nodules in S. rostrata with lowering of nitrogenase activity. These data suggest that A. caulinodans AhpCD is not only important for H2O2 detoxification in vitro but also critical for symbiosis with S. rostrata. Functional analysis of AhpCD is worth investigating in other rhizobia to gain a comprehensive view of its contributions to ROS defence and symbiotic association with legumes.}, } @article {pmid30657593, year = {2019}, author = {Rillig, MC and Aguilar-Trigueros, CA and Camenzind, T and Cavagnaro, TR and Degrune, F and Hohmann, P and Lammel, DR and Mansour, I and Roy, J and van der Heijden, MGA and Yang, G}, title = {Why farmers should manage the arbuscular mycorrhizal symbiosis: A response to Ryan & Graham () 'Little evidence that farmers should consider abundance or diversity of arbuscular mycorrhizal fungi when managing crops'.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15602}, pmid = {30657593}, issn = {1469-8137}, support = {//German Federal Ministry for Education/ ; //European Union/ ; //World Food System Center and Mercator Foundation Switzerland/ ; 727230//Horizon 2020 Societal Challenges/ ; 166079//Swiss National Science Foundation/ ; //Gebert Rüf Foundation/ ; SERI//Swiss State Secretariat for Education, Research and Innovation/ ; 17.00090//Swiss State Secretariat for Education, Research and Innovation/ ; //Swiss Federal Office of Agriculture (FOAG)/ ; //Alexander von Humboldt-CAPES/ ; }, } @article {pmid30657177, year = {2019}, author = {Ryan, MH and Graham, JH and Morton, JB and Kirkegaard, JA}, title = {Research must use a systems agronomy approach if management of the arbuscular mycorrhizal symbiosis is to contribute to sustainable intensification: A response to Rillig et al. (2018) 'Why farmers should manage the arbuscular mycorrhizal symbiosis'.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15600}, pmid = {30657177}, issn = {1469-8137}, support = {FT140100103//ARC Future Fellowship/ ; }, } @article {pmid30653883, year = {2016}, author = {Kyrychenko, OV}, title = {[THE COMPLEX ESTIMATE OF THE RHIZOBIUM NODULATION ABILITY AND THE FEATURES OF SOYBEAN SYMBIOTIC SYSTEMS FORMATION AT THE MICROBIAL COMPOSITIONS SEED INOCULATION].}, journal = {Mikrobiolohichnyi zhurnal (Kiev, Ukraine : 1993)}, volume = {78}, number = {4}, pages = {90-101}, pmid = {30653883}, issn = {1028-0987}, abstract = {The features of the soybean symbiotic systems formation and carry out the complex es- timate of the rhizobium nodulation ability at the seed inoculation of the microbial composi- tions on the bases of nodule bacteria, azotobacter and phytolectins (soybean seeds lectin, wheat germ agglutinin) were studied in the green-house experiments with a soil cultures. It was shown, that complex inoculants accelerate the process of becoming infected of plants by rhizobia in the early stages of soybean development; contribute to the expansion of the spectrum of genetically determined ability of nodule bacteria in the formation of a certain number of nodules on the host plant during the growing season as well as the formation of more root nodules with more of their weight during the second half of the growing season of soybean and significant increase mass of the one nodule and also slow the root nodules aging process at the end of the growing season compared with a rhizobial monoinoculant. It was proposed to use a complex of criteria in the estimating of the rhizobia nodulation ability in the microbial compositions: "nodulation activity", "nodulation range", "the num- ber of nodules on the plant", "mass of nodules per plant", "mass of one nodule", which are indicative for different stages of the symbiosis formation.}, } @article {pmid30653880, year = {2016}, author = {Vozniuk, SV and Tytova, LV and Ratushinska, OV and Iutynska, GO}, title = {[FORMATION AND FUNCTIONING OF SYMBIOTIC SYSTEMS AND RHIZOSPHERE MICROBIOCENISIS OF SOYBEAN UNDER VARIOUS FUNGICIDES APPLICATION].}, journal = {Mikrobiolohichnyi zhurnal (Kiev, Ukraine : 1993)}, volume = {78}, number = {4}, pages = {59-70}, pmid = {30653880}, issn = {1028-0987}, abstract = {The Relevance. At the recent years in soybean crops the quantity of plant pathogenic fungi has increased. The fungicides of systemic and contact action have been applicated intensively against of them. After introducing into the soil fungicides and/or their deg- radation products can to disrupt the activities of non-target objects - beneficial soil mi- croorganisms, inhibit nodulation process and the nitrogen-fixing activity of diazotrophs. The purpose of the work was to investigate the impact of combined application of fungi- cides with inoculation on the soybean symbiotic system and rhizosphere microorganisms. The Methods. The microbiological and statistical methods, gas chromatography method. The Results. Inoculation of seeds by the highly active Bradyrhizobiumjaponicum UCM B-6035, UCM B-6018 and UCM B-6023 strains the activity of nitrogen-fixing symbiotic systems increased by 1.4-3.4 times in comparison with the variant without of fungicides application and bacterization. Seed treatment by Vitavaks 200 FF fungicide caused a de- crease of'nitrogen-fixing activity of rhizobia industrial strains in symbiosis with soybean by 3-5 times. The seeds inoculation by B. japonicum UCM B-6035 strain promoted to reduce the negative impact of the Maxim Star 025 FS fungicide on the nitrogenase activity of nodulation apparatus. The positive effect of seeds bacterization was observed in the in- crease of the quantity of rhizosphere microorganisms of main ecological trophic groups. In the variant with seed treatment by Maxim Star 025 FS and Kinto duo fungicides was found a decrease in the number of microorganisms of studied groups in comparison with the control variant; the Vitavaks 200 FF fungicide application promoted to improve of these microorganisms development compared with the variant without the fungicides application and bacterization. At the inoculation of rhizobia industrial strains the negative effect of the Maxim Star 025 FS and Kinto duo fungicides to oligoazotrophic and prototrophic micro- organisms was not observed. The Conclusion. The symbiotic system of variant with the combined application of the Kinto duo fungicide with B. japonicum UCM B-6023 strain characterized by the highest nodulation and nitrogen-fixing activity.}, } @article {pmid30007918, year = {2019}, author = {Wu, TR and Lin, CS and Chang, CJ and Lin, TL and Martel, J and Ko, YF and Ojcius, DM and Lu, CC and Young, JD and Lai, HC}, title = {Gut commensal Parabacteroides goldsteinii plays a predominant role in the anti-obesity effects of polysaccharides isolated from Hirsutella sinensis.}, journal = {Gut}, volume = {68}, number = {2}, pages = {248-262}, doi = {10.1136/gutjnl-2017-315458}, pmid = {30007918}, issn = {1468-3288}, mesh = {Animals ; *Ascomycota ; Bacteroidetes/*drug effects/*physiology ; Diabetes Mellitus, Type 2/*prevention & control ; Diet, High-Fat ; Fecal Microbiota Transplantation ; Fungal Polysaccharides/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Insulin Resistance ; Male ; Mice ; Mice, Inbred C57BL ; Molecular Weight ; Obesity/*prevention & control ; Prebiotics ; Symbiosis ; }, abstract = {OBJECTIVE: The medicinal fungus Ophiocordyceps sinensis and its anamorph Hirsutella sinensis have a long history of use in traditional Chinese medicine for their immunomodulatory properties. Alterations of the gut microbiota have been described in obesity and type 2 diabetes. We examined the possibility that H. sinensis mycelium (HSM) and isolated fractions containing polysaccharides may prevent diet-induced obesity and type 2 diabetes by modulating the composition of the gut microbiota.

DESIGN: High-fat diet (HFD)-fed mice were treated with HSM or fractions containing polysaccharides of different molecular weights. The effects of HSM and polysaccharides on the gut microbiota were assessed by horizontal faecal microbiota transplantation (FMT), antibiotic treatment and 16S rDNA-based microbiota analysis.

RESULTS: Fraction H1 containing high-molecular weight polysaccharides (>300 kDa) considerably reduced body weight gain (∼50% reduction) and metabolic disorders in HFD-fed mice. These effects were associated with increased expression of thermogenesis protein markers in adipose tissues, enhanced gut integrity, reduced intestinal and systemic inflammation and improved insulin sensitivity and lipid metabolism. Gut microbiota analysis revealed that H1 polysaccharides selectively promoted the growth of Parabacteroides goldsteinii, a commensal bacterium whose level was reduced in HFD-fed mice. FMT combined with antibiotic treatment showed that neomycin-sensitive gut bacteria negatively correlated with obesity traits and were required for H1's anti-obesogenic effects. Notably, oral treatment of HFD-fed mice with live P. goldsteinii reduced obesity and was associated with increased adipose tissue thermogenesis, enhanced intestinal integrity and reduced levels of inflammation and insulin resistance.

CONCLUSIONS: HSM polysaccharides and the gut bacterium P. goldsteinii represent novel prebiotics and probiotics that may be used to treat obesity and type 2 diabetes.}, } @article {pmid30651068, year = {2019}, author = {Huang, C and Leng, D and Sun, S and Zhang, XD}, title = {Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {48}, doi = {10.1186/s12864-019-5429-3}, pmid = {30651068}, issn = {1471-2164}, support = {SRG2016-00083-FHS//Start-up Research Grant at University of Macau/ ; }, abstract = {BACKGROUND: Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and accelerating devastation due to bleaching. The fact that the breakdown of symbiosis between coral and the dinoflagellate, zooxanthellae, has been well elucidated as the main cause of bleaching, implying the establishment of symbiosis with zooxanthellae plays a crucial role in maintaining coral survival. However, the relevant molecular and cellular mechanisms have not been well studied yet. In this study, based on the deep RNA-sequencing data derived from Mohamed, A. R. et al., an integrated transcriptome analysis was performed to deeply investigate global transcriptome changes of the coral Acropora digitifera in response to infection by dinoflagellate of the genus Symbiodinium.

RESULTS: The results revealed that compared to RefTranscriptome_v1.0 (A. digitifera transcriptome assembly v1.0), numerous novel transcripts and isoforms were identified, the Symbiodinium-infected coral larvae at 4 h generated the highest proportion of specific isoforms. Alternative splicing analysis showed that intron retention predominated in all alternative transcripts among six statuses. Additionally, 8117 lncRNAs were predicted via a stringent stepwise filtering pipeline. A complex lncRNAs-mRNAs network including 815 lncRNAs and 6395 mRNAs were established, in which 21 lncRNAs were differentially expressed at 4 h post infection. Functional clustering analysis for those differentially lncRNAs-coexpressed mRNAs demonstrated that several biological processes and pathways related to protein kinase activity, metabolic pathways, mitochondrion, ribosome, etc. were enriched.

CONCLUSIONS: Our study not only refined A. digitifera transcriptome via identification of novel transcripts and isoforms, but also predicted a high-confidence dataset of lncRNAs. Functional study based on the construction of lncRNAs-mRNAs co-expression network has disclosed a complex lncRNA-mediated regulation in response to Symbiodinium infection exhibited in A. digitifera. Once validated, these lncRNAs could be good potential targets for treatment and prevention of bleaching in coral.}, } @article {pmid29642523, year = {2018}, author = {Zhang, H and Zhao, Z and Chen, J and Bai, X and Wang, H}, title = {Tricycloalternarene Analogs from a Symbiotic Fungus Aspergillus sp. D and Their Antimicrobial and Cytotoxic Effects.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {4}, pages = {}, pmid = {29642523}, issn = {1420-3049}, mesh = {A549 Cells ; Anti-Bacterial Agents/*chemistry/pharmacology ; Antineoplastic Agents/*chemistry/pharmacology ; Aspergillus/*chemistry/physiology ; Candida albicans/drug effects ; Cell Survival/drug effects ; Humans ; Magnetic Resonance Spectroscopy/methods ; Malvales/physiology ; Mass Spectrometry/methods ; Molecular Structure ; Symbiosis ; Terpenes/*chemistry/pharmacology ; }, abstract = {Bioassay-guided fractionation of the crude extract of fermentation broth of one symbiotic strain Aspergillus sp. D from the coastal plant Edgeworthia chrysantha Lindl. led to isolation of one new meroterpenoid, tricycloalternarene 14b (1), together with four known analogs (2-5), tricycloalternarenes 2b (2), 3a (3), 3b (4), and ACTG-toxin F (5). Their chemical structures were unambiguously established on the basis of NMR, mass spectrometry, and optical rotation data analysis, as well as by comparison with literature data. Biological assays indicated that compound 2 exhibited potent in vitro cytotoxicity against human lung adenocarcinoma A549 cell line with an IC50 value of 2.91 μM, and compound 5 had a moderate inhibitory effect on Candida albicans, with an MIC value of 15.63 μM. The results indicated that this symbiotic strain D is an important producer of tricycloalternarene derivatives, with potential therapeutic application in treatment of cancer and pathogen infection.}, } @article {pmid30649463, year = {2019}, author = {Sun, Y and Wu, Z and Wang, Y and Yang, J and Wei, G and Chou, M}, title = {Identification of Phytocyanin Gene Family in Legume Plants and Their Involvement in Nodulation of Medicago truncatula.}, journal = {Plant & cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcz007}, pmid = {30649463}, issn = {1471-9053}, abstract = {The establishment of symbiosis between legume and rhizobium results in the formation of nodule. Phytocyanins (PCs) are a class of plant specific blue copper proteins, playing critical roles in plant development including nodule formation. Although a few PC genes have been isolated from nodules, their functions are still unclear. Here, we performed a genome-wide identification of PC family in seven sequenced legume species (Medicago truncatula, Glycine max, Cicer arietinum, Cajanus cajan, Lotus japonicus, Vigna angularis and Phaseolus vulgaris) and found PCs experienced a remarkable expansion in M. truncatula and G. max. Further, we conducted an in-depth analysis of PC family in the model legume M. truncatula. Briefly, 82 MtPCs were divided into four subfamilies and clustered into seven clades, with a large proportion of tandem duplications and various cross-tissues expression patterns. Importantly, some PCs, such as MtPLC1, MtENODL27 and MtENODL28 were preferentially expressed in nodules. Further, RNA interference (RNAi) experiment revealed the knockdown of MtENDOL27 and MtENDOL28 impaired rhizobia infection, nodule numbers and nitrogenase activity. Moreover, in the MtENODL27-RNAi nodules, the infected cells were reduced and the symbiosomes did not reach the elongated stage, indicating MtENDOL27 is required for rhizobia infection and nodule development. In addition, co-expression analysis showed MtPLC1, MtENODL27 and MtENODL28 were grouped into two different functional modules and co-expressed with the known symbiotic nitrogen fixation (SNF)-related genes, suggesting they might participate in nodulation via different ways. In summary, this study provides a useful resource for future researches on the structure and function of PCs in nodulation.}, } @article {pmid30649338, year = {2019}, author = {Russell, SL}, title = {Transmission mode is associated with environment type and taxa across bacteria-eukaryote symbioses: a systematic review and meta-analysis.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz013}, pmid = {30649338}, issn = {1574-6968}, abstract = {Symbiotic associations between bacteria and eukaryotes exhibit a range of transmission strategies. The rates and distributions of transmission modes have not been thoroughly investigated across associations, despite their consequences on symbiont and host evolution. To address this empirically, I compiled data from the literature on bacteria-multicellular eukaryote associations for which transmission mode data was available. Of the total 528 analyzed symbioses, 21.2% were strictly horizontally transmitted, 36.0% exhibited some form of mixed mode transmission, and 42.8% were strictly vertically transmitted. Controlling for phylogenetically independent symbiosis events revealed modes were approximately equally distributed among the 113 independent associations, at 32.1 + /-0.57% horizontal, 37.8 + /-1.4% mixed mode, and 31.1 + /-1.3% vertical transmission. Binning symbioses by environment revealed an abundance of vertical transmission on land and a lack of it in aquatic environments. The naturally-occurring uneven distribution of taxa among environments prevented controlling for host/symbiont phylogeny. However, the results were robust over a large number of independently evolved associations, suggesting that many vertically transmitted bacteria are capable of horizontal transmission and barriers exist that reduce the rate of these events. Thus, both the environment type and host/symbiont taxa influence symbiont transmission mode evolution.}, } @article {pmid30647460, year = {2019}, author = {Rubin-Blum, M and Antony, CP and Sayavedra, L and Martínez-Pérez, C and Birgel, D and Peckmann, J and Wu, YC and Cardenas, P and MacDonald, I and Marcon, Y and Sahling, H and Hentschel, U and Dubilier, N}, title = {Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0346-7}, pmid = {30647460}, issn = {1751-7370}, support = {N/A//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; 679849//EC | Horizon 2020 (Horizon 2020 - Research and Innovation Framework Programme)/ ; 679849//EC | European Research Council (ERC)/ ; GBMF3811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.}, } @article {pmid30647457, year = {2019}, author = {Mateus, ID and Masclaux, FG and Aletti, C and Rojas, EC and Savary, R and Dupuis, C and Sanders, IR}, title = {Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0342-3}, pmid = {30647457}, issn = {1751-7370}, support = {31003A_162549//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, most of the plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organization during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation has a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype × genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.}, } @article {pmid29514969, year = {2018}, author = {Binning, SA and Roche, DG and Grutter, AS and Colosio, S and Sun, D and Miest, J and Bshary, R}, title = {Cleaner wrasse indirectly affect the cognitive performance of a damselfish through ectoparasite removal.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1874}, pages = {}, pmid = {29514969}, issn = {1471-2954}, mesh = {Animals ; *Cognition ; *Feeding Behavior ; Host-Parasite Interactions ; Perciformes/*physiology ; *Symbiosis ; }, abstract = {Cleaning organisms play a fundamental ecological role by removing ectoparasites and infected tissue from client surfaces. We used the well-studied cleaning mutualisms involving the cleaner wrasse, Labroides dimidiatus, to test how client cognition is affected by ectoparasites and whether these effects are mitigated by cleaners. Ambon damselfish (Pomacentrus amboinensis) collected from experimental reef patches without cleaner wrasse performed worse in a visual discrimination test than conspecifics from patches with cleaners. Endoparasite abundance also negatively influenced success in this test. Visual discrimination performance was also impaired in damselfish experimentally infected with gnathiid (Crustacea: Isopoda) ectoparasites. Neither cleaner absence nor gnathiid infection affected performance in spatial recognition or reversal learning tests. Injection with immune-stimulating lipopolysaccharide did not affect visual discrimination performance relative to saline-injected controls, suggesting that cognitive impairments are not due to an innate immune response. Our results highlight the complex, indirect role of cleaning organisms in promoting the health of their clients via ectoparasite removal and emphasize the negative impact of parasites on host's cognitive abilities.}, } @article {pmid29146383, year = {2018}, author = {Papanicolas, LE and Gordon, DL and Wesselingh, SL and Rogers, GB}, title = {Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance?.}, journal = {Trends in microbiology}, volume = {26}, number = {5}, pages = {393-400}, doi = {10.1016/j.tim.2017.10.009}, pmid = {29146383}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/*pharmacology ; Antineoplastic Agents/*pharmacology ; Bacteria/drug effects/genetics ; DNA Damage ; Drug Combinations ; Drug Resistance, Bacterial/*drug effects/genetics ; Dysbiosis/microbiology ; Gastrointestinal Microbiome/drug effects ; Gene Transfer, Horizontal ; Humans ; Mutagenesis ; Neoplasms/complications/drug therapy ; Sepsis/microbiology ; Symbiosis/drug effects ; }, abstract = {The global spread of antibiotic-resistant pathogens threatens to increase the mortality of cancer patients significantly. We propose that chemotherapy contributes to the emergence of antibiotic-resistant bacteria within the gut and, in combination with antibiotics, drives pathogen overgrowth and translocation into the bloodstream. In our model, these processes are mediated by the effects of chemotherapy on bacterial mutagenesis and horizontal gene transfer, the disruption of commensal gut microbiology, and alterations to host physiology. Clinically, this model manifests as a cycle of recurrent sepsis, with each episode involving ever more resistant organisms and requiring increasingly broad-spectrum antimicrobial therapy. Therapies that restore the gut microbiota following chemotherapy or antibiotics could provide a means to break this cycle of infection and treatment failure.}, } @article {pmid28702707, year = {2018}, author = {Dastogeer, KMG and Li, H and Sivasithamparam, K and Jones, MGK and Wylie, SJ}, title = {Host Specificity of Endophytic Mycobiota of Wild Nicotiana Plants from Arid Regions of Northern Australia.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {74-87}, pmid = {28702707}, issn = {1432-184X}, support = {the Research Training Scholarship//Australian Government and Murdoch University/ ; }, mesh = {Australia ; Desert Climate ; Endophytes/classification/genetics/isolation & purification/*physiology ; Fungi/classification/genetics/isolation & purification/*physiology ; *Host Specificity ; *Mycobiome ; Phylogeny ; Soil/chemistry ; Symbiosis ; Tobacco/*microbiology ; }, abstract = {In arid regions of northern Australia, plants survive under water deficit, high temperatures, intense solar radiation and nutrient-impoverished soils. They employ various morpho-physiological and biochemical adaptations including interaction with microbial symbionts. We evaluated identity, host and tissue association with geographical distribution of fungal endophytes isolated from above- and below-ground tissues of plants of three indigenous Australian Nicotiana species. Isolation frequency and α-diversity were significantly higher for root endophyte assemblages than those of stem and leaf tissues. We recorded no differences in endophyte species richness or diversity as a function of sampling location, but did detect differences among different host genotypes and plant tissues. There was a significant pattern of community similarity associated with host genotypes but no consistent pattern of fungal community structuring associated with sampling location and tissue type, regardless of the community similarity measurements used.}, } @article {pmid28646410, year = {2018}, author = {Hajek, AE and Harris, DC and Bittner, TD}, title = {Symbiont Spillover from Invasive to Native Woodwasps.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {7-9}, pmid = {28646410}, issn = {1432-184X}, support = {12-CA-11420004-043//USDA Forest Service/ ; 2009-02182//USDA NIFA AFRI/ ; }, mesh = {Animals ; Basidiomycota/classification/genetics/isolation & purification/*physiology ; Female ; Host-Pathogen Interactions ; Male ; North America ; Phylogeny ; Pinus/parasitology ; *Symbiosis ; Trees/parasitology ; Wasps/*microbiology/physiology ; }, abstract = {Hosts and their associated microbes are being increasingly introduced around the world, which can lead to novel host/microbe associations via new sympatries. Woodwasps (Hymenoptera: Siricidae) are able to utilize wood for its nutrients due to obligate mutualistic associations with white rot fungi in the genus Amylostereum and when invasive woodwasps are introduced to new areas, their symbionts accompany them. There is increasing evidence that woodwasp-fungus associations previously believed to be highly specific are actually flexible. We show that in North America, both Urocerus albicornis and Urocerus cressoni, which develop in trees in the Pinaceae, usually use Amylostereum chailletii but sometimes carry an Amylostereum areolatum strain putatively introduced to North America by the invasive woodwasp Sirex noctilio. Symbiont spillover from invasive to native hosts is a source of new host/introduced symbiont associations that could result in changes in microbes and host fitness with the potential to impact communities.}, } @article {pmid30643907, year = {2019}, author = {Baturina, OA and Muntyan, VS and Afonin, AM and Cherkasova, ME and Simarov, BV and Kabilov, MR and Roumiantseva, ML}, title = {Draft Genome Sequence of Sinorhizobium meliloti Strain CXM1-105.}, journal = {Microbiology resource announcements}, volume = {8}, number = {2}, pages = {}, doi = {10.1128/MRA.01621-18}, pmid = {30643907}, issn = {2576-098X}, abstract = {Sinorhizobium meliloti is a Gram-negative bacterium which fixes atmospheric nitrogen in symbiosis with Medicago spp. We report the draft genome sequence of S. meliloti strain CXM1-105, associated with nodules of Medicago sativa subsp. varia (Martyn) Arcang.}, } @article {pmid30643201, year = {2019}, author = {Faure, E and Not, F and Benoiston, AS and Labadie, K and Bittner, L and Ayata, SD}, title = {Mixotrophic protists display contrasted biogeographies in the global ocean.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0340-5}, pmid = {30643201}, issn = {1751-7370}, abstract = {Mixotrophy, or the ability to acquire carbon from both auto- and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes represented by 89,951,866 sequences and belonging to 133 taxonomic lineages were identified and classified into four mixotrophic functional types: constitutive mixotrophs (CM), generalist non-constitutive mixotrophs (GNCM), endo-symbiotic specialist non-constitutive mixotrophs (eSNCM), and plastidic specialist non-constitutive mixotrophs (pSNCM). Mixotrophy appeared ubiquitous, and the distributions of the four mixotypes were analyzed to identify the abiotic factors shaping their biogeographies. Kleptoplastidic mixotrophs (GNCM and pSNCM) were detected in new zones compared to previous morphological studies. Constitutive and non-constitutive mixotrophs had similar ranges of distributions. Most lineages were evenly found in the samples, yet some of them displayed strongly contrasted distributions, both across and within mixotypes. Particularly divergent biogeographies were found within endo-symbiotic mixotrophs, depending on the ability to form colonies or the mode of symbiosis. We showed how metabarcoding can be used in a complementary way with previous morphological observations to study the biogeography of mixotrophic protists and to identify key drivers of their biogeography.}, } @article {pmid30641698, year = {2019}, author = {Banerjee, J and Mishra, N and Damle, G and Dhas, Y}, title = {Beyond LDL-c: The importance of serum oxidized LDL in predicting risk for type 2 diabetes in the middle-aged Asian Indians.}, journal = {Diabetes & metabolic syndrome}, volume = {13}, number = {1}, pages = {206-213}, doi = {10.1016/j.dsx.2018.08.036}, pmid = {30641698}, issn = {1878-0334}, abstract = {AIMS: Oxidized low-density lipoprotein (OxLDL) as the residual lipid plays a crucial role in cardiovascular complications and type 2 diabetes. This study aimed to evaluate the relationship of OxLDL with the conventional risk markers and to find the association of OxLDL with the risk of development of type 2 diabetes in middle-aged (30-50 years) Asian Indians.

MATERIALS AND METHODS: A total of 78 type 2 diabetes patients and 78 age-matched controls were recruited. The serum OxLDL concentration was assessed by enzyme-linked immunosorbent assay (ELISA). Other anthropometric and biochemical measures were also carried out. Multiple logistic regression was used to determine the association of OxLDL and OxLDL to non-oxidized lipoproteins with the occurrence of type 2 diabetes.

RESULTS: OxLDL was significantly higher in type 2 diabetes cases than controls (p < 0.001) even though there was no significant difference in LDL cholesterol (LDL-c) between type 2 diabetes patients and controls. OxLDL correlated significantly with fasting plasma glucose (FPG) and insulin resistance (HOMA-IR). OxLDL did not show any significant correlation with LDL-c. Multiple logistic regression showed a significant association of OxLDL, OxLDL/LDL-c and OxLDL/HDL-c with type 2 diabetes (p < 0.001). LDL-c showed no association with type 2 diabetes. ROC-AUC curve analyses showed OxLDL/HDL-c to have highest discriminatory power for type 2 diabetes (AUC: 0.710 with 95% CI: 0.629-0.791, p < 0.001).

CONCLUSION: Our findings highlight the possibly more attention has to be given to OxLDL for managing lipids and diabetes progression as well as reducing cardiac risk in middle-aged type 2 diabetes patients.}, } @article {pmid30463523, year = {2018}, author = {Sui, X and Wu, Q and Chang, W and Fan, X and Song, F}, title = {Proteomic analysis of the response of Funnelifor mismosseae/Medicago sativa to atrazine stress.}, journal = {BMC plant biology}, volume = {18}, number = {1}, pages = {289}, pmid = {30463523}, issn = {1471-2229}, support = {31570635//National Natural Science Foundation of China/ ; 31500431//National Natural Science Foundation of China/ ; 31270535//National Natural Science Foundation of China/ ; JC201306//Outstanding Youth Science Foundation of Heilongjiang Province/ ; }, mesh = {Atrazine/metabolism/*toxicity ; Biodegradation, Environmental ; Glomeromycota/drug effects/*metabolism ; Herbicides/metabolism/*toxicity ; Medicago sativa/drug effects/*metabolism/microbiology ; Mycorrhizae/drug effects/*metabolism ; Plant Proteins/metabolism ; Proteome/*drug effects ; Soil Pollutants/metabolism/*toxicity ; Symbiosis ; }, abstract = {BACKGROUND: Arbuscular mycorrhizal (AM) fungi form symbiotic associations with host plants can protect host plants against diverse biotic and abiotic stresses, and promote biodegradation of various contaminants. However, the molecular mechanisms of how the arbuscular mycorrhizal fungi and host plant association on atrazine stress were still poorly understood. To better characterize how arbuscular mycorrhizal fungi and host plant interactions increase atrazine stress, we performed physiological and proteomic analysis of Funneliformis mosseae (mycorrhizal fungi) and Medicago sativa (alfalfa) association under atrazine stress.

RESULTS: The results showed that in the Arbuscular mycorrhizal, protective enzymes were up regulated and the malondialdehyde content increased relative to those of non-mycorrhizal M.sativa. We also examined the atrazine degradation rates within the nutrient solution, and a 44.43% reduction was observed with the mycorrhizal M.sativa, with 30.83% of the reduction attributed to F. mosseae. The accumulation content in root and stem of mycorrhizal M.sativa were obviously increased 11.89% and 16.33% than those of non- mycorrhizal M.sativa. The activity of PPO, POD, CAT and SOD in mycorrhizal M.sativa were obviously higher than non mycorrhizal M.sativa under atrazine stess. We identified differential root proteins using isobaric tags for relative and absolute quantization coupled with liquid chromatography-mass spectrometry, with 533 proteins identified (276 unregulated and 257 downregulated). The differentially expressed proteins were further examined using GO, BLAST comparisons, and a literature inquiry and were classified into the categories of atrazine degradation (37.1%); atrazine stress response (28.6%); plant immune responses (14.3%); translation, synthesis, and processing (10%); and signal transduction and biological processes (10%). Furthermore, we identified glycosyl transferase, glutathione S-transferase, laccase, cytochrome P450 monooxygenase, peroxidase, and other proteins closely related to the degradation process.

CONCLUSIONS: Mycorrhizal Medicago showed improved atrazine degradation within the culturing medium and increased atrazine enrichment in the roots and stems. Additionally, AMF increased the plant root response to atrazine, with relevant enzymes up regulated and toxic effects alleviated. Overall, the findings of this study show that AMF played an important role in easing atrazine stress in plants and contributed to atrazine remediation and further contributed to the understanding of the molecular mechanism associated with atrazine stresses and potential mycorrhizal contributions in M.sativa.}, } @article {pmid30308966, year = {2018}, author = {Kaczanowski, S and Klim, J and Zielenkiewicz, U}, title = {An Apoptotic and Endosymbiotic Explanation of the Warburg and the Inverse Warburg Hypotheses.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, pmid = {30308966}, issn = {1422-0067}, support = {2017/27/B/NZ8/02502//Narodowe Centrum Nauki/ ; }, mesh = {Aging/metabolism ; Animals ; *Apoptosis ; *Cell Respiration ; Cell Transformation, Neoplastic/genetics/metabolism ; Energy Metabolism ; Eukaryota/metabolism ; Humans ; Mitochondria/metabolism ; Neoplasms/genetics/metabolism ; Neurodegenerative Diseases/genetics/metabolism ; Oxygen/metabolism ; *Symbiosis ; }, abstract = {Otto Warburg, a Nobel prize winner, observed that cancer cells typically "switch" from aerobic to anaerobic respiration. He hypothesized that mitochondrial damage induces neoplastic transformation. In contrast, pathological aging is observed mainly in neuron cells in neurodegenerative diseases. Oxidative respiration is particularly active in neurons. There is inverse comorbidity between cancer and neurodegenerative diseases. This led to the creation of the "inverse Warburg hypothesis", according to which excessive mitochondrial activity induces pathological aging. The findings of our studies suggest that both the Warburg effect and the "inverse Warburg hypothesis" can be elucidated by the activation or suppression of apoptosis through oxidative respiration. The key outcome of our phylogenetic studies was the discovery that apoptosis and apoptosis-like cell death evolved due to an evolutionary "arms race" conducted between "prey" protomitochondrion and "predator" primitive eukaryotes. The ancestral protomitochondrial machinery produces and releases toxic mitochondrial proteins. Extant apoptotic factors evolved from these toxins. Our experiments indicate that the mitochondrial machinery is directly involved in adaptation to aerobic conditions. Additionally, our hypothesis is supported by the fact that different apoptotic factors are directly involved in respiration.}, } @article {pmid30070049, year = {2019}, author = {Wang, LX and Ren, LL and Liu, XB and Shi, J and Wang, JZ and Luo, YQ}, title = {Effects of endophytic fungi in Mongolian pine on the selection behavior of woodwasp (Sirex noctilio) and the growth of its fungal symbiont.}, journal = {Pest management science}, volume = {75}, number = {2}, pages = {492-505}, doi = {10.1002/ps.5146}, pmid = {30070049}, issn = {1526-4998}, support = {201504304//The Special Fund for Forest Scientific Research in the Public Welfare of China/ ; 31500529//Chinese National Natural Science Foundation/ ; }, mesh = {Animals ; Basidiomycota/growth & development/*physiology ; Endophytes/growth & development/*physiology ; Female ; Hymenoptera/*physiology ; *Oviposition ; Pinus/*microbiology/*physiology ; Symbiosis ; }, abstract = {BACKGROUND: The European woodwasp, Sirex noctilio, is a global invasive pest, attacking a wide variety of pine species by inoculating spores of a symbiotic fungus (Amylostereum areolatum) at oviposition. The woodwasp larvae depend on the growth of the symbiotic fungus to feed. The relationship among host endophytic fungi, symbiotic fungus and woodwasp remain elusive. Here, the effects of endophytes in Mongolian pine on the growth of Amylostereum areolatum and the selection behavior of female woodwasp were investigated by quantifying the mycelium growth rates and olfactometry assays.

RESULTS: The endophytic plant fungi, Trichoderma harzianum, Phlebiopsis gigantea, T. viride and T. atroviride, completely killed the mycelia of Amylostereum areolatum. Mycelium fermentation broth of Chaetomium globosum inhibited the growth of the symbiont. Moreover, we observed that volatiles of Ophiostoma minus and Aspergillus niger (acetophenone, acetylacetone, hexadecane, phenylethyl alcohol, and isopropyl myristate) had repellent effects on adult female woodwasp. While volatiles of Amylostereum areolatum ((-)-globulol, 2-hexene, cycloprop[e]indene-1a,2(1H)-dicarboxaldehyde, terpene and cyclopentanone) had a significant attractiveness to adult female woodwasp.

CONCLUSIONS: Some species of the host endophytic fungi had a significant negative effect on the growth and development of woodwasps, which could be useful in the monitoring and effective management of woodwasps. © 2018 Society of Chemical Industry.}, } @article {pmid28710832, year = {2018}, author = {Gile, GH and James, ER and Tai, V and Harper, JT and Merrell, TL and Boscaro, V and Husník, F and Scheffrahn, RH and Keeling, PJ}, title = {New Species of Spirotrichonympha from Reticulitermes and the Relationships Among Genera in Spirotrichonymphea (Parabasalia).}, journal = {The Journal of eukaryotic microbiology}, volume = {65}, number = {2}, pages = {159-169}, doi = {10.1111/jeu.12447}, pmid = {28710832}, issn = {1550-7408}, mesh = {Animals ; Digestive System/microbiology ; Isoptera/*microbiology ; Parabasalidea/*classification/*cytology/*ultrastructure ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; }, abstract = {Spirotrichonymphea is a class of hypermastigote parabasalids defined by their spiral rows of many flagella. They are obligate hindgut symbionts of lower termites. Despite more than 100 yr of morphological and ultrastructural study, the group remains poorly characterised by molecular data and the phylogenetic positions and taxonomic validity of most genera remain in question. The genus Spirotrichonympha has been reported to inhabit several termite genera, including Reticulitermes, Coptotermes, and Hodotermopsis. The type species for this genus, Spirotrichonympha flagellata, was described from Reticulitermes lucifugus but no molecular data are yet available for this species. In this study, three new Spirotrichonympha species are described from three species of Reticulitermes. Their molecular phylogenetic position indicates that the genus is not monophyletic, as Spirotrichonympha species from Coptotermes, Paraneotermes, and Hodotermopsis branch separately. In contrast, the genus Holomastigotoides is monophyletic, as demonstrated using new sequences from Holomastigotoides species. The presence of Holomastigotoides in Prorhinotermes and the distinct phylogenetic positions of Spirotrichonympha from Reticulitermes and Coptotermes are consistent with a previously proposed symbiont fauna replacement in the ancestor of Reticulitermes.}, } @article {pmid30641263, year = {2019}, author = {Ingavle, GC and Gionet-Gonzales, M and Vorwald, CE and Bohannon, LK and Clark, K and Galuppo, LD and Leach, JK}, title = {Injectable mineralized microsphere-loaded composite hydrogels for bone repair in a sheep bone defect model.}, journal = {Biomaterials}, volume = {197}, number = {}, pages = {119-128}, doi = {10.1016/j.biomaterials.2019.01.005}, pmid = {30641263}, issn = {1878-5905}, abstract = {The efficacy of cell-based therapies as an alternative to autologous bone grafts requires biomaterials to localize cells at the defect and drive osteogenic differentiation. Hydrogels are ideal cell delivery vehicles that can provide instructional cues via their composition or mechanical properties but commonly lack osteoconductive components that nucleate mineral. To address this challenge, we entrapped mesenchymal stromal cells (MSCs) in a composite hydrogel based on two naturally-derived polymers (alginate and hyaluronate) containing biomineralized polymeric microspheres. Mechanical properties of the hydrogels were dependent upon composition. The presentation of the adhesive tripeptide Arginine-Glycine-Aspartic Acid (RGD) from both polymers induced greater osteogenic differentiation of ovine MSCs in vitro compared to gels formed of RGD-alginate or RGD-alginate/hyaluronate alone. We then evaluated the capacity of this construct to stimulate bone healing when transplanting autologous, culture-expanded MSCs into a surgical induced, critical-sized ovine iliac crest bone defect. At 12 weeks post-implantation, defects treated with MSCs transplanted in composite gels exhibited significant increases in blood vessel density, osteoid formation, and bone formation compared to acellular gels or untreated defects. These findings demonstrate the capacity of osteoconductive hydrogels to promote bone formation with autologous MSCs in a large animal bone defect model and provide a promising vehicle for cell-based therapies of bone healing.}, } @article {pmid30640903, year = {2019}, author = {Rabillé, H and Billoud, B and Tesson, B and Le Panse, S and Rolland, É and Charrier, B}, title = {The brown algal mode of tip growth: Keeping stress under control.}, journal = {PLoS biology}, volume = {17}, number = {1}, pages = {e2005258}, doi = {10.1371/journal.pbio.2005258}, pmid = {30640903}, issn = {1545-7885}, abstract = {Tip growth has been studied in pollen tubes, root hairs, and fungal and oomycete hyphae and is the most widely distributed unidirectional growth process on the planet. It ensures spatial colonization, nutrient predation, fertilization, and symbiosis with growth speeds of up to 800 μm h-1. Although turgor-driven growth is intuitively conceivable, a closer examination of the physical processes at work in tip growth raises a paradox: growth occurs where biophysical forces are low, because of the increase in curvature in the tip. All tip-growing cells studied so far rely on the modulation of cell wall extensibility via the polarized excretion of cell wall-loosening compounds at the tip. Here, we used a series of quantitative measurements at the cellular level and a biophysical simulation approach to show that the brown alga Ectocarpus has an original tip-growth mechanism. In this alga, the establishment of a steep gradient in cell wall thickness can compensate for the variation in tip curvature, thereby modulating wall stress within the tip cell. Bootstrap analyses support the robustness of the process, and experiments with fluorescence recovery after photobleaching (FRAP) confirmed the active vesicle trafficking in the shanks of the apical cell, as inferred from the model. In response to auxin, biophysical measurements change in agreement with the model. Although we cannot strictly exclude the involvement of a gradient in mechanical properties in Ectocarpus morphogenesis, the viscoplastic model of cell wall mechanics strongly suggests that brown algae have evolved an alternative strategy of tip growth. This strategy is largely based on the control of cell wall thickness rather than fluctuations in cell wall mechanical properties.}, } @article {pmid30637337, year = {2018}, author = {Bayer, K and Jahn, MT and Slaby, BM and Moitinho-Silva, L and Hentschel, U}, title = {Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00150-18}, pmid = {30637337}, issn = {2379-5077}, abstract = {Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for "Candidatus Poribacteria" and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCEChloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.}, } @article {pmid30529448, year = {2018}, author = {Suesdek, L}, title = {Microevolution of medically important mosquitoes - A review.}, journal = {Acta tropica}, volume = {191}, number = {}, pages = {162-171}, doi = {10.1016/j.actatropica.2018.12.013}, pmid = {30529448}, issn = {1873-6254}, abstract = {This review intends to discuss central issues regarding the microevolution of mosquito (Culicidae) vectors of several pathogens and how this process impacts vector biology, disease transmission, and vector control attempts. On the microevolutionary context, it comparatively discusses the current knowledge on the population genetics of representatives of the genera Aedes, Anopheles and Culex, and comments on insecticide resistance of culicids. It also discusses other biological aspects of culicids that are not usually addressed in microevolutionary studies, such as vectorial competence, endosymbiosis, and wing morphology. One conclusion is that mosquitoes are highly genetically variable, adaptable, fast evolving, and have versatile vectorial competence. Unveiling microevolutionary patterns is fundamental for the design and maintenance of all control programs. Sampling methods for assessing microevolution must be standardized and must follow meaningful guidelines, such as those of "landscape genetics". A good understanding of microevolution requires more than a collection of case studies on population genetics and resistance. Future research could deal not only with the microevolution sensu stricto, but also with evolutionarily meaningful issues, such as inheritable characters, epigenetics, physiological cost-free plasticity, vector immunity, symbiosis, pathogen-mosquito co-evolution and environmental variables. A genotyping panel for seeking adaptive phenotypes as part of the standardization of population genetics methods is proposed. The investigative paradigm should not only be retrospective but also prospective, despite the unpredictability of evolution. If we integrate all suggestions to tackle mosquito evolution, a global revolution to counter vector-borne diseases can be provoked.}, } @article {pmid30267766, year = {2018}, author = {Frynta, D and Kaftanová-Eliášová, B and Žampachová, B and Voráčková, P and Sádlová, J and Landová, E}, title = {Behavioural strategies of three wild-derived populations of the house mouse (Mus m. musculus and M. m. domesticus) in five standard tests of exploration and boldness: Searching for differences attributable to subspecies and commensalism.}, journal = {Behavioural processes}, volume = {157}, number = {}, pages = {133-141}, doi = {10.1016/j.beproc.2018.09.008}, pmid = {30267766}, issn = {1872-8308}, mesh = {Animals ; *Animals, Wild/classification/physiology/psychology ; Czech Republic ; *Exploratory Behavior ; Female ; Male ; Maze Learning ; *Mice/classification/physiology/psychology ; Motor Activity ; Species Specificity ; *Symbiosis ; }, abstract = {Animal populations adopting a commensal way of life, e. g. house mice in buildings and stores, are subject to different selection pressures than those living in a non-commensal environment. This may radically influence their behaviour. This study investigated the effects of a commensal way of life on exploratory behaviour in mice. The focal population was non-commensal Mus musculus musculus from Northern Iran. To assess the effect of commensal way of life on exploratory behaviour, it was compared with commensal M. m. musculus from the Czech Republic and to assess the effect of subspecies, it was compared to non-commensal M. m. domesticus from Eastern Syria. We compared their behaviour in five tests of exploratory behaviour and boldness: an open field test with 1) free exploration and 2) forced exploration, 3) hole-board test, 4) test of vertical activity and 5) elevated plus maze. We detected a significant effect of population on behaviour in all five tests. M. m. domesticus was generally bolder and more active than M. m. musculus. Commensal mice were characterized by a higher level of vertical activity (climbing, rearing, jumping). These results suggest that the specific selection pressures of the commensal lifestyle select mice for higher affinity towards elevated places.}, } @article {pmid30052670, year = {2018}, author = {Rossitto De Marchi, B and Kinene, T and Mbora Wainaina, J and Krause-Sakate, R and Boykin, L}, title = {Comparative transcriptome analysis reveals genetic diversity in the endosymbiont Hamiltonella between native and exotic populations of Bemisia tabaci from Brazil.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0201411}, pmid = {30052670}, issn = {1932-6203}, mesh = {Animals ; *Enterobacteriaceae/classification/genetics/metabolism ; *Gene Expression Profiling ; *Genetic Variation ; Hemiptera/*microbiology ; *Phylogeny ; Symbiosis/*physiology ; }, abstract = {The whitefly, Bemisia tabaci, is a species complex of more than 40 cryptic species and a major agricultural pest. It causes extensive damage to plants mainly by transmitting plant viruses. There is still a lack of genomic data available for the different whitefly species found in Brazil and their bacterial endosymbionts. Understanding the genetic and transcriptomic composition of these insect pests, the viruses they transmit and the microbiota is crucial to sustainable solutions for farmers to control whiteflies. Illumina RNA-Seq was used to obtain the transcriptome of individual whiteflies from 10 different populations from Brazil including Middle East-Asia Minor 1 (MEAM1), Mediterranean (MED) and New World 2 (NW2). Raw reads were assembled using CLC Genomics Workbench and subsequently mapped to reference genomes. We obtained whitefly complete mitochondrial genomes and draft genomes from the facultative bacterial endosymbiont Hamiltonella for further phylogenetic analyses. In addition, nucleotide sequences of the GroEL chaperonin gene from Hamiltonella from different populations were obtained and analysed. There was concordance in the species clustering using the whitefly complete mitogenome and the mtCOI gene tree. On the other hand, the phylogenetic analysis using the 12 ORF's of Hamiltonella clustered the native species NW2 apart from the exotics MEAM1 and MED. In addition, the amino acid analysis of GroEL chaperonin revealed a deletion only in Hamiltonella infecting NW2 among whiteflies populations analysed which was further confirmed by PCR and Sanger sequencing. The genomic data obtained in this study will aid understanding the functions that Hamiltonella may have in whitefly biology and serve as a reference for further studies regarding whiteflies in Brazil.}, } @article {pmid30024971, year = {2018}, author = {Matsuo, M and Katahata, A and Satoh, S and Matsuzaki, M and Nomura, M and Ishida, KI and Inagaki, Y and Obokata, J}, title = {Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200961}, pmid = {30024971}, issn = {1932-6203}, mesh = {Biodiversity ; Cercozoa/classification/*genetics/growth & development ; Chromatophores/metabolism ; DNA, Protozoan/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Protozoan ; *Photosynthesis ; Phylogeny ; RNA, Spliced Leader/*genetics ; Symbiosis ; *Trans-Splicing ; }, abstract = {Paulinella micropora is a rhizarian thecate amoeba, belonging to a photosynthetic Paulinella species group that has a unique organelle termed chromatophore, whose cyanobacterial origin is distinct from that of plant and algal chloroplasts. Because acquisition of the chromatophore was quite a recent event compared with that of the chloroplast ancestor, the Paulinella species are thought to be model organisms for studying the early process of primary endosymbiosis. To obtain insight into how endosymbiotically transferred genes acquire expression competence in the host nucleus, here we analyzed the 5' end sequences of the mRNAs of P. micropora MYN1 strain with the aid of a cap-trapper cDNA library. As a result, we found that mRNAs of 27 genes, including endosymbiotically transferred genes, possessed the common 5' end sequence of 28-33 bases that were posttranscriptionally added by spliced leader (SL) trans-splicing. We also found two subtypes of SL RNA genes encoded by the P. micropora MYN1 genome. Differing from the other SL trans-splicing organisms that usually possess poly(A)-less SL RNAs, this amoeba has polyadenylated SL RNAs. In this study, we characterize the SL trans-splicing of this unique organism and discuss the putative merits of SL trans-splicing in functional gene transfer and genome evolution.}, } @article {pmid29562933, year = {2018}, author = {Ravanbakhsh, M and Sasidharan, R and Voesenek, LACJ and Kowalchuk, GA and Jousset, A}, title = {Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {52}, pmid = {29562933}, issn = {2049-2618}, mesh = {Bacteria/*metabolism ; Environment ; Ethylenes/*metabolism ; Gene Expression Regulation, Plant/*genetics ; Microbiota/physiology ; Plants/*microbiology ; Signal Transduction ; Stress, Physiological/physiology ; Symbiosis/*physiology ; }, abstract = {The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants upregulate ethylene production in response to stress, and this hormone triggers defense mechanisms. Due to the pleiotropic effects of ethylene, adjusting stress responses to maximize resistance, while minimizing costs, is a central determinant of plant fitness. Ethylene signaling is influenced by the plant-associated microbiome. We therefore argue that the regulation, physiology, and evolution of the ethylene signaling can best be viewed as the interactive result of plant genotype and associated microbiota. In this article, we summarize the current knowledge on ethylene signaling and recapitulate the multiple ways microorganisms interfere with it. We present ethylene signaling as a model system for holobiont-level evolution of plant phenotype: this cascade is tractable, extremely well studied from both a plant and a microbial perspective, and regulates fundamental components of plant life history. We finally discuss the potential impacts of ethylene modulation microorganisms on plant ecology and evolution. We assert that ethylene signaling cannot be fully appreciated without considering microbiota as integral regulatory actors, and we more generally suggest that plant ecophysiology and evolution can only be fully understood in the light of plant-microbiome interactions.}, } @article {pmid29543554, year = {2018}, author = {Weis, AM and Soto, R and Round, JL}, title = {Commensal regulation of T cell survival through Erdr1.}, journal = {Gut microbes}, volume = {9}, number = {5}, pages = {458-464}, pmid = {29543554}, issn = {1949-0984}, support = {T32 GM007464/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Survival ; Encephalomyelitis, Autoimmune, Experimental/genetics/*immunology/microbiology ; *Gastrointestinal Microbiome ; Humans ; Membrane Proteins/genetics/*immunology ; Mice ; Symbiosis ; T-Lymphocytes/*cytology/immunology ; Tumor Suppressor Proteins/genetics/*immunology ; }, abstract = {The commensal microbiota influences many aspects of immune system regulation, including T cells, but molecular details of how this occurs are largely unknown. Here we review our findings that the microbiota regulates Erdr1, a secreted apoptotic factor, to control T cell survival. Erdr1 is highly upregulated in CD4+ T cells from germfree mice and antibiotic treated animals, and our study shows that Erdr1 is suppressed by the microbiota via Toll-like receptor signaling and MyD88 dependent pathways. Erdr1 functions in an autocrine fashion and promotes apoptosis through the FAS/FASL pathway. Suppression of Erdr1 leads to survival of autoreactive T cells and exacerbated autoimmune disease in the EAE model, and overexpression of Erdr1 results in lessened disease. This novel T cell apoptotic factor has implications for autoimmunity, cancer biology, and invasive pathogens and thus represents a novel therapeutic target in disease.}, } @article {pmid29517960, year = {2018}, author = {Cieplak, T and Soffer, N and Sulakvelidze, A and Nielsen, DS}, title = {A bacteriophage cocktail targeting Escherichia coli reduces E. coli in simulated gut conditions, while preserving a non-targeted representative commensal normal microbiota.}, journal = {Gut microbes}, volume = {9}, number = {5}, pages = {391-399}, pmid = {29517960}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/isolation & purification ; Bacteriophages/*physiology ; Biological Therapy ; Escherichia coli/drug effects/physiology/*virology ; Escherichia coli Infections/drug therapy/microbiology/*therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Intestines/*microbiology ; Symbiosis/drug effects ; }, abstract = {Antibiotics offer an efficient means for managing diseases caused by bacterial pathogens. However, antibiotics are typically broad spectrum and they can indiscriminately kill beneficial microbes in body habitats such as the gut, deleteriously affecting the commensal gut microbiota. In addition, many bacteria have developed or are developing resistance to antibiotics, which complicates treatment and creates significant challenges in clinical medicine. Therefore, there is a real and urgent medical need to develop alternative antimicrobial approaches that will kill specific problem-causing bacteria without disturbing a normal, and often beneficial, gut microbiota. One such potential alternative approach is the use of lytic bacteriophages for managing bacterial infections, including those caused by multidrug-resistant pathogens. In the present study, we comparatively analysed the efficacy of a bacteriophage cocktail targeting Escherichia coli with that of a broad-spectrum antibiotic (ciprofloxacin) using an in vitro model of the small intestine. The parameters examined included (i) the impact on a specific, pre-chosen targeted E. coli strain, and (ii) the impact on a selected non-targeted bacterial population, which was chosen to represent a defined microbial consortium typical of a healthy small intestine. During these studies, we also examined stability of bacteriophages against various pH and bile concentrations commonly found in the intestinal tract of humans. The bacteriophage cocktail was slightly more stable in the simulated duodenum conditions compared to the simulated ileum (0.12 vs. 0.58 log decrease in phage titers, respectively). It was equally effective as ciprofloxacin in reducing E. coli in the simulated gut conditions (2-3 log reduction), but had much milder (none) impact on the commensal, non-targeted bacteria compared to the antibiotic.}, } @article {pmid29463295, year = {2018}, author = {Brener-Raffalli, K and Clerissi, C and Vidal-Dupiol, J and Adjeroud, M and Bonhomme, F and Pratlong, M and Aurelle, D and Mitta, G and Toulza, E}, title = {Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {39}, pmid = {29463295}, issn = {2049-2618}, support = {ANR-12-ADAP-0016//Agence Nationale de la Recherche/International ; }, mesh = {Acinetobacter/genetics/*isolation & purification ; Animals ; Anthozoa/*microbiology/*parasitology ; Arcobacter/genetics/*isolation & purification ; DNA, Intergenic/genetics ; Dinoflagellida/genetics/*isolation & purification ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Oceanospirillaceae/genetics/*isolation & purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis/physiology ; }, abstract = {BACKGROUND: Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues.

RESULTS: We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions < 1%) of A1, C3, C15, and G Symbiodinum sub-clades. Using redundancy analyses, we found that the effect of geography was very low for both communities and that host genotypes and temperatures differently influenced Symbiodinium and bacterial microbiota. Indeed, while the constraint of host haplotype was higher than temperatures on bacterial composition, we showed for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures.

CONCLUSION: Because Symbiodinium assemblages are more constrained by the thermal regime than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature changes might be higher than the influence of bacterial microbiota. Moreover, the link between Symbiodinium community composition and minimal temperatures suggests low relative fitness of clade D at lower temperatures. This observation is particularly relevant in the context of climate change, since corals will face increasing temperatures as well as much frequent abnormal cold episodes in some areas of the world.}, } @article {pmid28992342, year = {2017}, author = {Bellucci, M and De Marchis, F and Pompa, A}, title = {The endoplasmic reticulum is a hub to sort proteins toward unconventional traffic pathways and endosymbiotic organelles.}, journal = {Journal of experimental botany}, volume = {69}, number = {1}, pages = {7-20}, doi = {10.1093/jxb/erx286}, pmid = {28992342}, issn = {1460-2431}, mesh = {Endoplasmic Reticulum/*metabolism ; Eukaryotic Cells/*metabolism ; Organelles/*metabolism ; Plants/*metabolism ; Protein Transport ; *Symbiosis ; }, abstract = {The discovery that much of the extracellular proteome in eukaryotic cells consists of proteins lacking a signal peptide, which cannot therefore enter the secretory pathway, has led to the identification of alternative protein secretion routes bypassing the Golgi apparatus. However, proteins harboring a signal peptide for translocation into the endoplasmic reticulum can also be transported along these alternative routes, which are still far from being well elucidated in terms of the molecular machineries and subcellular/intermediate compartments involved. In this review, we first try to provide a definition of all the unconventional protein secretion pathways in eukaryotic cells, as those pathways followed by proteins directed to an 'external space' bypassing the Golgi, where 'external space' refers to the extracellular space plus the lumen of the secretory route compartments and the inner space of mitochondria and plastids. Then, we discuss the role of the endoplasmic reticulum in sorting proteins toward unconventional traffic pathways in plants. In this regard, various unconventional pathways exporting proteins from the endoplasmic reticulum to the vacuole, plasma membrane, apoplast, mitochondria, and plastids are described, including the short routes followed by the proteins resident in the endoplasmic reticulum.}, } @article {pmid30636349, year = {2019}, author = {Morin, E and Miyauchi, S and San Clemente, H and Chen, EC and Pelin, A and de la Providencia, I and Ndikumana, S and Beaudet, D and Hainaut, M and Drula, E and Kuo, A and Tang, N and Roy, S and Viala, J and Henrissat, B and Grigoriev, IV and Corradi, N and Roux, C and Martin, FM}, title = {Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15687}, pmid = {30636349}, issn = {1469-8137}, abstract = {• Glomeromycotina is a lineage of early diverging Fungi establishing arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, genetic bases of their obligate mutualism are largely unknown, hindering our understanding of their evolution and biology. • We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. • Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organization. • The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi. This article is protected by copyright. All rights reserved.}, } @article {pmid30636324, year = {2019}, author = {Miri, M and Janakirama, P and Huebert, T and Ross, L and McDowell, T and Orosz, K and Markmann, K and Szczyglowski, K}, title = {Inside out: root cortex-localized LHK1 cytokinin receptor limits epidermal infection of Lotus japonicus roots by Mesorhizobium loti.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15683}, pmid = {30636324}, issn = {1469-8137}, abstract = {•During Lotus japonicas-Mesorhizobium loti symbiosis, the LOTUS HISTIDINE KINASE1 (LHK1) cytokinin receptor regulates both the initiation of nodule formation and the scope of root infection. However, the exact spatio-temporal mechanism by which this receptor exerts its symbiotic functions has remained elusive. •In this study, we performed cell type-specific complementation experiments in the hyperinfected lhk1-1 mutant background, targeting LHK1 to either the root epidermis or the root cortex. We also utilized various genetic backgrounds to characterize expression of several genes regulating symbiotic infection. •We show here that expression of LHK1 in the root cortex is required and sufficient to regulate both nodule formation and epidermal infections. The LHK1-dependent signalling that restricts subsequent infection events is triggered before initial cell divisions for nodule primordium formation. We demonstrate also that AHK4, the Arabidopsis orthologue of LHK1, is able to regulate M. loti infection in L. japonicus, suggesting that an endogenous cytokinin receptor could be sufficient for engineering nitrogen-fixing root nodule symbiosis in nonlegumes. •Our data provide experimental evidence for the existence of an LHK1-dependent root cortex-to-epidermis feedback mechanism regulating rhizobial infection. This root-localized regulatory module functionally links with the systemic autoregulation of nodulation (AON) to maintain the homeostasis of symbiotic infection. This article is protected by copyright. All rights reserved.}, } @article {pmid30635418, year = {2019}, author = {Belcaid, M and Casaburi, G and McAnulty, SJ and Schmidbaur, H and Suria, AM and Moriano-Gutierrez, S and Pankey, MS and Oakley, TH and Kremer, N and Koch, EJ and Collins, AJ and Nguyen, H and Lek, S and Goncharenko-Foster, I and Minx, P and Sodergren, E and Weinstock, G and Rokhsar, DS and McFall-Ngai, M and Simakov, O and Foster, JS and Nyholm, SV}, title = {Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1817322116}, pmid = {30635418}, issn = {1091-6490}, abstract = {Microbes have been critical drivers of evolutionary innovation in animals. To understand the processes that influence the origin of specialized symbiotic organs, we report the sequencing and analysis of the genome of Euprymna scolopes, a model cephalopod with richly characterized host-microbe interactions. We identified large-scale genomic reorganization shared between E. scolopes and Octopus bimaculoides and posit that this reorganization has contributed to the evolution of cephalopod complexity. To reveal genomic signatures of host-symbiont interactions, we focused on two specialized organs of E. scolopes: the light organ, which harbors a monoculture of Vibrio fischeri, and the accessory nidamental gland (ANG), a reproductive organ containing a bacterial consortium. Our findings suggest that the two symbiotic organs within E. scolopes originated by different evolutionary mechanisms. Transcripts expressed in these microbe-associated tissues displayed their own unique signatures in both coding sequences and the surrounding regulatory regions. Compared with other tissues, the light organ showed an abundance of genes associated with immunity and mediating light, whereas the ANG was enriched in orphan genes known only from E. scolopes Together, these analyses provide evidence for different patterns of genomic evolution of symbiotic organs within a single host.}, } @article {pmid30635058, year = {2019}, author = {Simon, JC and Marchesi, JR and Mougel, C and Selosse, MA}, title = {Host-microbiota interactions: from holobiont theory to analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {5}, doi = {10.1186/s40168-019-0619-4}, pmid = {30635058}, issn = {2049-2618}, abstract = {In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.}, } @article {pmid30631330, year = {2018}, author = {Wang, J and Andersen, SU and Ratet, P}, title = {Editorial: Molecular and Cellular Mechanisms of the Legume-Rhizobia Symbiosis.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1839}, doi = {10.3389/fpls.2018.01839}, pmid = {30631330}, issn = {1664-462X}, } @article {pmid30454662, year = {2019}, author = {Gupta, R and Singh, A and Srivastava, M and Shanker, K and Pandey, R}, title = {Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress.}, journal = {Microbiological research}, volume = {218}, number = {}, pages = {87-96}, doi = {10.1016/j.micres.2018.10.006}, pmid = {30454662}, issn = {1618-0623}, mesh = {Animals ; *Bacopa/growth & development/microbiology/parasitology ; Betaproteobacteria/*metabolism ; Denaturing Gradient Gel Electrophoresis ; Microbiota ; Nitrogen/metabolism ; Plant Diseases/*parasitology ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Saponins/metabolism ; Soil Microbiology ; Streptomyces/*metabolism ; Stress, Physiological/physiology ; Symbiosis/physiology ; Triterpenes/metabolism ; Tylenchoidea/*growth & development ; }, abstract = {The modification of rhizosphere microbial diversity and ecological processes are of rising interest as shifting in microbial community structure impacts the mutual role of host-microbe interactions. Nevertheless, the connection between host-microbial community diversity, their function under biotic stress in addition to their impact on plant performances is poorly understood. The study was designed with the aim to analyze the tripartite interactions among Chitiniphilus sp., Streptomyces sp. and their combination with indigenous rhizospheric microbial population of Bacopa monnieri for enhancing the plant growth and bacoside A content under Meloidogyne incognita stress. Overall, plants treated with the microbial combination recorded enhanced growth as illustrated by significantly higher biomass (2.0 fold), nitrogen uptake (1.8 fold) and bacoside A content (1.3 fold) along with biocontrol efficacy (58.5%) under nematode infected field. The denaturing gradient gel electrophoresis (DGGE) fingerprints of 16S-rDNA revealed that microbial inoculations are major initiators of bacterial community structure in the plant rhizosphere. Additionally, the plants treated with microbial combination showed maximum diversity viz., Shannon's (3.29), Margalef's (4.21), and Simpson's (0.96) indices. Likewise the metabolic profiling data also showed a significant variation among the diversity and evenness indices upon microbial application on the native microflora. We surmise that the application of beneficial microbes in combinational mode not only helped in improving the microbial community structure but also successfully enhanced plant and soil health under biotic stress.}, } @article {pmid30454659, year = {2019}, author = {Yu, F and Jing, X and Li, X and Wang, H and Chen, H and Zhong, L and Yin, J and Pan, D and Yin, Y and Fu, J and Xia, L and Bian, X and Tu, Q and Zhang, Y}, title = {Recombineering Pseudomonas protegens CHA0: An innovative approach that improves nitrogen fixation with impressive bactericidal potency.}, journal = {Microbiological research}, volume = {218}, number = {}, pages = {58-65}, doi = {10.1016/j.micres.2018.09.009}, pmid = {30454659}, issn = {1618-0623}, mesh = {Arabidopsis/*growth & development/microbiology ; Bacterial Proteins/genetics ; Biological Control Agents/*metabolism ; Crop Production/methods ; Gene Deletion ; Nitrogen Fixation/*genetics/physiology ; Nitrogenase/metabolism ; Phloroglucinol/analogs & derivatives/metabolism ; Plant Diseases/microbiology/*prevention & control ; Plant Roots/microbiology ; Pseudomonas/*genetics/*metabolism ; Symbiosis/genetics ; Virulence Factors/genetics ; }, abstract = {Pseudomonas protegens CHA0 is a well-characterized, root-colonizing bacterium with broad-spectrum biocontrol ability. Therefore, it has a great potential to curb plant diseases and to partly replace synthetic chemical pesticides that are harmful to humans. Here, we obtained the multifunctional mutant CHA0-ΔretS-Nif via Red/ET recombineering technology. After deletion of the retS gene and integration of the nitrogen-fixing gene island (Nif) into the CHA0 genome, the resulting mutant, CHA0-ΔretS-Nif, manifested improved both bactericidal activity and biological nitrogen-fixation function. A pot experiment of Arabidopsis thaliana indicated that the strain CHA0-ΔretS-Nif promoted plant growth via expressing several secondary factors, such as the antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG) and nitrogenase. In order to grow this biocontrol strain at an industrial level, the growth conditions in a 1 L continuous-flow fermenter were optimized to 28 °C, pH of 7.0, and 600 rpm. Moreover, growth experiments in a 5 L fermenter with these optimal growth conditions yielded the maximum cell density, providing vital insights for the industrialization and large-scale fermentation of P. protegens CHA0 for further applications. CHA0-ΔretS-Nif possesses both bactericidal and nitrogen-fixation activities and thus could be used as a biological agent to enhance crop production.}, } @article {pmid30454657, year = {2019}, author = {Chen, L and Shi, H and Heng, J and Wang, D and Bian, K}, title = {Antimicrobial, plant growth-promoting and genomic properties of the peanut endophyte Bacillus velezensis LDO2.}, journal = {Microbiological research}, volume = {218}, number = {}, pages = {41-48}, doi = {10.1016/j.micres.2018.10.002}, pmid = {30454657}, issn = {1618-0623}, mesh = {Anti-Bacterial Agents/*metabolism ; Antifungal Agents/*metabolism ; Arachis/*microbiology ; Aspergillus flavus/growth & development ; Bacillus/classification/genetics/*metabolism ; Biological Control Agents/*metabolism ; Endophytes/*metabolism ; Genome, Bacterial/genetics ; Mycelium/growth & development ; Plant Diseases/microbiology/*prevention & control ; Symbiosis/genetics ; }, abstract = {Peanut suffer from a number of fungal and bacterial pathogens, while plant endophytes were considered excellent candidates as biocontrol agents. In this study, the peanut endophytic bacterium LDO2 was evaluated for the potential of peanut pathogens inhibition and growth-promotion, and the genetic mechanisms were explored by genome mining. Strain LDO2 significantly inhibited the growth of peanut pathogenic fungi and pathogenic bacteria, and specifically, it showed pronounced inhibition on mycelia growth of Aspergillus flavus mycelia and caused mycelial deformity. Gene clusters responsible for antifungal metabolites (fengycin, surfactin, bacilysin) and antibacterial metabolites (butirosin, bacillaene, difficidin, macrolactin, surfactin, bacilysin) were identified. Strain LDO2 also exhibited several growth-promoting related features including phosphate solubilization, siderophore production and growth promotion of peanut root. Genes associated with plant growth promotion were also identified and analyzed, as well as genes related to secreted proteins. These findings suggested that this peanut endophyte could be a potential biocontrol agent in peanut production and a source of antimicrobial compounds for further exploitation.}, } @article {pmid29885666, year = {2018}, author = {Meng, A and Marchet, C and Corre, E and Peterlongo, P and Alberti, A and Da Silva, C and Wincker, P and Pelletier, E and Probert, I and Decelle, J and Le Crom, S and Not, F and Bittner, L}, title = {A de novo approach to disentangle partner identity and function in holobiont systems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {105}, pmid = {29885666}, issn = {2049-2618}, support = {ANR-15-CE02-0011//Agence Nationale de la Recherche (FR)/International ; }, mesh = {Animals ; Cnidaria/*parasitology ; Computational Biology ; *Coral Reefs ; Microalgae/metabolism ; Plankton/parasitology ; Porifera/*microbiology ; Rhizaria/*parasitology ; Symbiosis/*physiology ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept.

RESULTS: We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner's transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited.

CONCLUSIONS: In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.}, } @article {pmid29747692, year = {2018}, author = {Benjamino, J and Lincoln, S and Srivastava, R and Graf, J}, title = {Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {86}, pmid = {29747692}, issn = {2049-2618}, support = {1137249//National Science Foundation/International ; }, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Base Sequence ; DNA, Bacterial/genetics ; Diet ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Isoptera/*microbiology ; Lignin/metabolism ; Sequence Analysis, DNA ; Symbiosis/physiology ; }, abstract = {BACKGROUND: As the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions.

RESULTS: Shifts in the termite gut microbiota after diet change in each colony were observed using 16S rRNA gene sequencing and beta diversity analyses. The artificial neural network accurately predicted the relative abundances of taxa at random points in the temporal study and showed that low-abundant taxa maintain community driving correlations in the hindgut.

CONCLUSIONS: This combinatorial approach utilizing 16S rRNA gene sequencing and deep learning revealed that low-abundant bacteria that often do not belong to the core community are drivers of the termite hindgut bacterial community composition.}, } @article {pmid29739445, year = {2018}, author = {Sorek, M and Schnytzer, Y and Ben-Asher, HW and Caspi, VC and Chen, CS and Miller, DJ and Levy, O}, title = {Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {83}, pmid = {29739445}, issn = {2049-2618}, support = {1294//Taiwan-Israel cooperative program/International ; }, mesh = {Animals ; Biological Clocks/*physiology ; Circadian Rhythm/genetics/*physiology ; Dinoflagellida/*metabolism ; Gene Expression Regulation/*genetics ; Oxygen/metabolism ; Sea Anemones/*genetics/parasitology ; Symbiosis/physiology ; }, abstract = {BACKGROUND: All organisms employ biological clocks to anticipate physical changes in the environment; however, the integration of biological clocks in symbiotic systems has received limited attention. In corals, the interpretation of rhythmic behaviours is complicated by the daily oscillations in tissue oxygen tension resulting from the photosynthetic and respiratory activities of the associated algal endosymbiont Symbiodinium. In order to better understand the integration of biological clocks in cnidarian hosts of Symbiodinium, daily rhythms of behaviour and gene expression were studied in symbiotic and aposymbiotic morphs of the sea-anemone Aiptasia diaphana.

RESULTS: The results showed that whereas circatidal (approx. 12-h) cycles of activity and gene expression predominated in aposymbiotic morphs, circadian (approx. 24-h) patterns were the more common in symbiotic morphs, where the expression of a significant number of genes shifted from a 12- to 24-h rhythm. The behavioural experiments on symbiotic A. diaphana displayed diel (24-h) rhythmicity in body and tentacle contraction under the light/dark cycles, whereas aposymbiotic morphs showed approximately 12-h (circatidal) rhythmicity. Reinfection experiments represent an important step in understanding the hierarchy of endogenous clocks in symbiotic associations, where the aposymbiotic Aiptasia morphs returned to a 24-h behavioural rhythm after repopulation with algae.

CONCLUSION: Whilst some modification of host metabolism is to be expected, the extent to which the presence of the algae modified host endogenous behavioural and transcriptional rhythms implies that it is the symbionts that influence the pace. Our results clearly demonstrate the importance of the endosymbiotic algae in determining the timing and the duration of the extension and contraction of the body and tentacles and temporal gene expression.}, } @article {pmid29729663, year = {2018}, author = {Deutscher, AT and Burke, CM and Darling, AE and Riegler, M and Reynolds, OL and Chapman, TA}, title = {Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {85}, pmid = {29729663}, issn = {2049-2618}, support = {Olivia L Reynolds//Horticulture Australia/International ; }, mesh = {*Acetobacteraceae/classification/genetics/isolation & purification ; Animals ; Gastrointestinal Microbiome/*genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing ; Larva/microbiology ; RNA, Ribosomal, 16S/*genetics ; Symbiosis/physiology ; Tephritidae/*microbiology ; }, abstract = {BACKGROUND: Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome. Read lengths of previous fruit fly next-generation sequencing (NGS) studies have limited the resolution of microbiome studies, and the diversity within populations is often overlooked. In this study, we used a new near full-length (> 1300 nt) 16S rRNA gene amplicon NGS approach to characterize gut bacterial communities of individual B. tryoni larvae from two field populations (developing in peaches) and three domesticated populations (mass- or laboratory-reared on artificial diets).

RESULTS: Near full-length 16S rRNA gene sequences were obtained for 56 B. tryoni larvae. OTU clustering at 99% similarity revealed that gut bacterial diversity was low and significantly lower in domesticated larvae. Bacteria commonly associated with fruit (Acetobacteraceae, Enterobacteriaceae, and Leuconostocaceae) were detected in wild larvae, but were largely absent from domesticated larvae. However, Asaia, an acetic acid bacterium not frequently detected within adult tephritid species, was detected in larvae of both wild and domesticated populations (55 out of 56 larval gut samples). Larvae from the same single peach shared a similar gut bacterial profile, whereas larvae from different peaches collected from the same tree had different gut bacterial profiles. Clustering of the Asaia near full-length sequences at 100% similarity showed that the wild flies from different locations had different Asaia strains.

CONCLUSIONS: Variation in the gut bacterial communities of B. tryoni larvae depends on diet, domestication, and horizontal acquisition. Bacterial variation in wild larvae suggests that more than one bacterial species can perform the same functional role; however, Asaia could be an important gut bacterium in larvae and warrants further study. A greater understanding of the functions of the bacteria detected in larvae could lead to increased fly quality and performance as part of the SIT.}, } @article {pmid29716650, year = {2018}, author = {van de Guchte, M and Blottière, HM and Doré, J}, title = {Humans as holobionts: implications for prevention and therapy.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {81}, pmid = {29716650}, issn = {2049-2618}, mesh = {Bacteria/classification/*immunology ; Bacterial Physiological Phenomena/*immunology ; Dysbiosis/microbiology ; Gastrointestinal Microbiome/*immunology ; Host Microbial Interactions/*immunology/physiology ; Humans ; Inflammation/microbiology ; Inflammatory Bowel Diseases/microbiology ; Obesity/microbiology ; Symbiosis/*physiology ; }, abstract = {The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota-host association imposes itself. Ideally, a stable state of equilibrium, homeostasis, is maintained and serves health, but signs are that perturbation of this equilibrium beyond the limits of resilience can propel the system into an alternative stable state, a pre-disease state, more susceptible to the development of chronic diseases. The microbiota-host equilibrium of a large and growing proportion of individuals in Western society may represent such a pre-disease state and explain the explosive development of chronic diseases such as inflammatory bowel disease, obesity, and other inflammatory diseases. These diseases themselves represent other alternative stable states again and are therefore hard to cure. The holistic view of the microbiota-host association where feedback loops between microbiota and host are thought to maintain the system in a stable state-be it a healthy, pre-disease, or disease state-implies that integrated approaches, addressing host processes and microbiota, should be used to treat or prevent (pre-)disease.}, } @article {pmid29695294, year = {2018}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The hologenome concept of evolution after 10 years.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {78}, pmid = {29695294}, issn = {2049-2618}, mesh = {Animals ; *Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome/genetics ; Humans ; Microbiota/*genetics ; Plants ; Symbiosis/*physiology ; }, abstract = {The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selection operates. The holobiont can function as a whole: anatomically, metabolically, immunologically, developmentally, and during evolution. Consideration of the holobiont with its hologenome as an independent level of selection in evolution has led to a better understanding of underappreciated modes of genetic variation and evolution. The hologenome is comprised of two complimentary parts: host and microbiome genomes. Changes in either genome can result in variations that can be selected for or against. The host genome is highly conserved, and genetic changes within it occur slowly, whereas the microbiome genome is dynamic and can change rapidly in response to the environment by increasing or reducing particular microbes, by acquisition of novel microbes, by horizontal gene transfer, and by mutation. Recent experiments showing that microbiota can play an initial role in speciation have been suggested as an additional mode of enhancing evolution. Some of the genetic variations can be transferred to offspring by a variety of mechanisms. Strain-specific DNA analysis has shown that at least some of the microbiota can be maintained across hundreds of thousands of host generations, implying the existence of a microbial core. We argue that rapid changes in the microbiome genome could allow holobionts to adapt and survive under changing environmental conditions thus providing the time necessary for the host genome to adapt and evolve. As Darwin wrote, "It is not the strongest of the species that survives but the most adaptable".}, } @article {pmid29695286, year = {2018}, author = {Vannier, N and Mony, C and Bittebiere, AK and Michon-Coudouel, S and Biget, M and Vandenkoornhuyse, P}, title = {A microorganisms' journey between plant generations.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {79}, pmid = {29695286}, issn = {2049-2618}, support = {EC2CO program (MIME project)//Centre National de la Recherche Scientifique/International ; PEPS program (MYCOLAND project)//Centre National de la Recherche Scientifique/International ; }, mesh = {Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; Fungi/*classification/genetics/isolation & purification ; Lamiaceae/*microbiology ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Soil Microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer local environmental changes, with a positive influence on plant fitness. In this context, the transmission of the microbiota to the progeny represent a way to ensure the presence of beneficial symbionts within the habitat. Examples of such transmission have been mainly described for seed transmission and concern a few pathogenic microorganisms. We investigated the transmission of symbiotic partners to plant progeny within clonal plant network.

METHODS: We used the clonal plant Glechoma hederacea as plant model and forced newly emitted clonal progeny to root in separated pots while controlling the presence of microorganisms. We used an amplicon sequencing approach of 16S and 18S rRNA targeting bacteria/archaea and fungi respectively to describe the root microbiota of mother and clonal-plant offspring.

RESULTS: We demonstrated the vertical transmission of a significant proportion of the mother plants' symbiotic bacteria and fungi to the daughters. Interestingly, archaea were not transmitted to the daughter plants. Transmitted communities had lower richness, suggesting a filtration during transmission. We found that the transmitted pool of microorganisms was similar among daughters, constituting the heritability of a specific cohort of microorganisms, opening a new understanding of the plant holobiont. We also found significant effects of distance to the mother plant and of growth time on the richness of the microbiota transmitted.

CONCLUSIONS: In this clonal plant, microorganisms are transmitted between individuals through connections, thereby ensuring the availability of microbe partners for the newborn plants as well as the dispersion between hosts for the microorganisms. This previously undescribed ecological process allows the dispersal of microorganisms in space and across plant generations. As the vast majority of plants are clonal, this process might be therefore a strong driver of ecosystem functioning and assembly of plant and microorganism communities in a wide range of ecosystems.}, } @article {pmid28600542, year = {2017}, author = {Ye, Z and Vollhardt, IMG and Girtler, S and Wallinger, C and Tomanovic, Z and Traugott, M}, title = {An effective molecular approach for assessing cereal aphid-parasitoid-endosymbiont networks.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3138}, pmid = {28600542}, issn = {2045-2322}, mesh = {Animals ; Aphids/classification/genetics/*parasitology ; Edible Grain/*parasitology ; Europe ; Host-Parasite Interactions ; Multiplex Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Symbiosis ; }, abstract = {Molecular approaches are increasingly being used to analyse host-parasitoid food webs as they overcome several hurdles inherent to conventional approaches. However, such studies have focused primarily on the detection and identification of aphids and their aphidiid primary parasitoids, largely ignoring primary parasitoid-hyperparasitoid interactions or limiting these to a few common species within a small geographical area. Furthermore, the detection of bacterial secondary endosymbionts has not been considered in such assays despite the fact that endosymbionts may alter aphid-parasitoid interactions, as they can confer protection against parasitoids. Here we present a novel two-step multiplex PCR (MP-PCR) protocol to assess cereal aphid-primary parasitoid-hyperparasitoid-endosymbiont interactions. The first step of the assay allows detection of parasitoid DNA at a general level (24 primary and 16 hyperparasitoid species) as well as the species-specific detection of endosymbionts (3 species) and cereal aphids (3 species). The second step of the MP-PCR assay targets seven primary and six hyperparasitoid species that commonly occur in Central Europe. Additional parasitoid species not covered by the second-step of the assay can be identified via sequencing 16S rRNA amplicons generated in the first step of the assay. The approach presented here provides an efficient, highly sensitive, and cost-effective (~consumable costs of 1.3 € per sample) tool for assessing cereal aphid-parasitoid-endosymbiont interactions.}, } @article {pmid30629747, year = {2019}, author = {Reyes, ML and Laughton, AM and Parker, BJ and Wichmann, H and Fan, M and Sok, D and Hrček, J and Acevedo, T and Gerardo, NM}, title = {The influence of symbiotic bacteria on reproductive strategies and wing polyphenism in pea aphids responding to stress.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.12942}, pmid = {30629747}, issn = {1365-2656}, abstract = {1.Environmental stressors can be key drivers of phenotypes, including reproductive strategies and morphological traits. The response to stress may be altered by the presence of microbial associates. For example, in aphids, facultative (secondary) bacterial symbionts can provide protection against natural enemies and stress induced by elevated temperatures. Furthermore, aphids exhibit phenotypic plasticity, producing winged (rather than wingless) progeny that may be better able to escape danger, and the combination of these factors improve the response to stress. How symbionts and phenotypic plasticity, both of which shape aphids' stress response, influence one another, and together influence host fitness, remains unclear. 2.In this study, we investigate how environmental stressors drive shifts in fecundity and winged/wingless offspring production, and how secondary symbionts influence the process. We induced production of winged offspring through distinct environmental stressors, including exposure to aphid alarm pheromone and crowding, and, in one experiment we assessed whether the aphid response is influenced by host plant. 3.In the winged morph, energy needed for wing maintenance may lead to trade-offs with other traits, such as reproduction or symbiont maintenance. Potential trade-offs between symbiont maintenance and fitness have been proposed but have not been tested. Thus, beyond studying the production of offspring of alternative morphs, we also explore the influence of symbionts across wing/wingless polyphenism as well as symbiont interaction with cross-generational impacts of environmental stress on reproductive output. 4.All environmental stressors resulted in increased production of winged offspring and shifts in fecundity rates. Additionally, in some cases, aphid host-by-symbiont interactions influenced fecundity. Stress on first generation aphids had cross-generational impacts on second generation adults, and the impact on fecundity was further influenced by the presence of secondary symbionts and presence/absence of wings. 5.Our study suggests a complex interaction between beneficial symbionts and environmental stressors. Winged aphids have the advantage of being able to migrate out of danger with more ease, but energy needed for wing production and maintenance may come with reproductive costs for their mothers and for themselves, where in certain cases, these costs are altered by secondary symbionts. This article is protected by copyright. All rights reserved.}, } @article {pmid30629179, year = {2019}, author = {Dombrowski, N and Lee, JH and Williams, TA and Offre, P and Spang, A}, title = {Genomic diversity, lifestyles and evolutionary origins of DPANN archaea.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz008}, pmid = {30629179}, issn = {1574-6968}, abstract = {Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical nutrient cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.}, } @article {pmid30629176, year = {2019}, author = {Caputo, A and Nylander, JAA and Foster, RA}, title = {The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fny297}, pmid = {30629176}, issn = {1574-6968}, abstract = {Diatom diazotroph associations (DDAs) are a widespread marine planktonic symbiosis between several diatom genera and di-nitrogen-fixing bacteria. Combining single cell confocal microscopy observations and molecular genetic approaches on individual field collected cells, we determined the phylogenetic diversity, distribution, and evolution of the DDAs. Confocal analyses coupled with 3-D imaging re-evaluated the cellular location of DDA symbionts. DDA diversity was resolved by paired gene sequencing (18S rRNA and rbcL genes and 16S rRNA and nifH genes). A survey using the newly acquired sequences against public databases found sequences with high similarity (99-100%) to either host (18S rRNA) or symbiont (16S rRNA) in atypical regions for DDAs (high latitudes, anoxic basin, copepod gut). Concatenated phylogenies were congruent for the host and cyanobacteria sequences and implied co-evolution. Time-calibrated trees dated the appearance of N2 fixing planktonic symbiosis from 100-50Mya and were consistent with the symbiont cellular location: symbioses with internal partners are more ancient. An ancestral state reconstruction traced the evolution of traits in DDAs and highlight that the adaptive radiation to the marine environment was likely facilitated by the symbiosis. Our results present the evolutionary nature of DDAs and provide new genetic and phenotypic information for these biogeochemically relevant populations.}, } @article {pmid30628192, year = {2019}, author = {Piromyou, P and Songwattana, P and Teamtisong, K and Tittabutr, P and Boonkerd, N and Tantasawat, PA and Giraud, E and Göttfert, M and Teaumroong, N}, title = {Mutualistic co-evolution of T3SSs during the establishment of symbiotic relationships between Vigna radiata and Bradyrhizobia.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e781}, doi = {10.1002/mbo3.781}, pmid = {30628192}, issn = {2045-8827}, support = {//Suranaree University of Technology/ ; }, abstract = {This study supports the idea that the evolution of type III secretion system (T3SS) is one of the factors that controls Vigna radiata-bradyrhizobia symbiosis. Based on phylogenetic tree data and gene arrangements, it seems that the T3SSs of the Thai bradyrhizobial strains SUTN9-2, DOA1, and DOA9 and the Senegalese strain ORS3257 may share the same origin. Therefore, strains SUTN9-2, DOA1, DOA9, and ORS3257 may have evolved their T3SSs independently from other bradyrhizobia, depending on biological and/or geological events. For functional analyses, the rhcJ genes of ORS3257, SUTN9-2, DOA9, and USDA110 were disrupted. These mutations had cultivar-specific effects on nodulation properties. The T3SSs of ORS3257 and DOA9 showed negative effects on V. radiata nodulation, while the T3SS of SUTN9-2 showed no effect on V. radiata symbiosis. In the roots of V. radiata CN72, the expression levels of the PR1 gene after inoculation with ORS3257 and DOA9 were significantly higher than those after inoculation with ORS3257 ΩT3SS, DOA9 ΩT3SS, and SUTN9-2. The T3Es from ORS3257 and DOA9 could trigger PR1 expression, which ultimately leads to abort nodulation. In contrast, the T3E from SUTN9-2 reduced PR1 expression. It seems that the mutualistic relationship between SUTN9-2 and V. radiata may have led to the selection of the most well-adapted combination of T3SS and symbiotic bradyrhizobial genotype.}, } @article {pmid30627761, year = {2019}, author = {Fokin, SI and Serra, V and Ferrantini, F and Modeo, L and Petroni, G}, title = {"Candidatus Hafkinia simulans" gen. nov., sp. nov., a Novel Holospora-Like Bacterium from the Macronucleus of the Rare Brackish Water Ciliate Frontonia salmastra (Oligohymenophorea, Ciliophora): Multidisciplinary Characterization of the New Endosymbiont and Its Host.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1311-0}, pmid = {30627761}, issn = {1432-184X}, support = {PRA_2018_63//Università di Pisa/ ; }, abstract = {We characterized a novel Holospora-like bacterium (HLB) (Alphaproteobacteria, Holosporales) living in the macronucleus of the brackish water ciliate Frontonia salmastra. This bacterium was morphologically and ultrastructurally investigated, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and performed in situ hybridization experiments with a specifically-designed probe. A new taxon, "Candidatus Hafkinia simulans", was established for this HLB. The phylogeny of the family Holosporaceae based on 16S rRNA gene sequences was inferred, adding to the already available data both the sequence of the novel bacterium and those of other Holospora and HLB species recently characterized. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and placed the new endosymbiont as the sister genus of Holospora. Additionally, the host ciliate F. salmastra, recorded in Europe for the first time, was concurrently described through a multidisciplinary study. Frontonia salmastra's phylogenetic position in the subclass Peniculia and the genus Frontonia was assessed according to 18S rRNA gene sequencing. Comments on the biodiversity of this genus were added according to past and recent literature.}, } @article {pmid30626325, year = {2019}, author = {Hsu, CC and Lai, PH and Chen, TC and Tsai, WC and Hsu, JL and Hsiao, YY and Wu, WL and Tsai, CH and Chen, WH and Chen, HH}, title = {PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {25}, doi = {10.1186/s12864-018-5420-4}, pmid = {30626325}, issn = {1471-2164}, abstract = {BACKGROUND: Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus and multiplication of adventitious buds on inflorescence. However, somaclonal variations occur during micropropagation.

RESULTS: We isolated the two most expressed transposable elements belonging to P Instability Factor (PIF)-like transposons. Among them, a potential autonomous element was identified by similarity analysis against the whole-genome sequence of Phalaenopsis equestris and named PePIF1. It contains a 19-bp terminal inverted repeat flanked by a 3-bp target site duplication and two coding regions encoding ORF1- and transposase-like proteins. Phylogenetic analysis revealed that PePIF1 belongs to a new P-lineage of PIF. Furthermore, two distinct families, PePIF1a and PePIF1b, with 29 and 37 putative autonomous elements, respectively, were isolated, along with more than 3000 non-autonomous and miniature inverted-repeat transposable element (MITE)-like elements. Among them, 828 PePIF1-related elements were inserted in 771 predicted genes. Intriguingly, PePIF1 was transposed in the somaclonal variants of Phalaenopsis cultivars, as revealed by transposon display, and the newly inserted genes were identified and sequenced.

CONCLUSION: A PIF-like element, PePIF1, was identified in the Phalaenopsis genome and actively transposed during micropropagation. With the identification of PePIF1, we have more understanding of the Phalaenopsis genome structure and somaclonal variations during micropropagation for use in orchid breeding and production.}, } @article {pmid30625663, year = {2019}, author = {Chou, M and Sun, Y and Yang, J and Wang, Y and Li, Y and Yuan, G and Zhang, D and Wang, J and Wei, G}, title = {Comprehensive analysis of phenotype, microstructure and global transcriptional profiling to unravel the effect of excess copper on the symbiosis between nitrogen-fixing bacteria and Medicago lupulina.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {1346-1357}, doi = {10.1016/j.scitotenv.2018.12.005}, pmid = {30625663}, issn = {1879-1026}, abstract = {Legume-rhizobial symbiosis plays an important role in agriculture and ecological restoration. However, knowledge of the molecular mechanisms, especially the microstructure and global transcriptional profiling, of the symbiosis process under heavy metal contamination is limited. In this study, a heavy metal-tolerant legume, Medicago lupulina, was treated with different concentrations of copper (Cu). The results showed that the early infection process was inhibited and the nodule ultrastructure was changed under 200 mg kg-1 Cu stress. Most infection threads (ITs) were prevented from entering the nodule cells, and few rhizobia were released into the host cells, in which thickening of the plant cell wall and IT wall was observed, demonstrating that rhizobial invasion was inhibited under Cu stress. RNA-seq analysis indicated that a strong shift in gene expression occurred (3257 differentially expressed genes, DEGs). The most pronounced effect was the upregulation of a set of 71 of 73 DEGs for nodule-specific cysteine-rich peptides, which have been shown to control the terminal differentiation of rhizobia in the nodules and to have antimicrobial activity. Various genes for metal transport, chelation binding and antioxidant defence were regulated. In particular, the DEGs for Cu trafficking and detoxification were induced during nodule formation. The DEGs for ethylene (ET) biosynthesis and signalling were also differentially expressed during nodulation, suggesting that the inhibition of nodulation by Cu occurred partially through ET signalling. Furthermore, the genes related to the cell wall were mostly upregulated and most likely involved in cell wall thickening. These findings provide an integrated understanding of the effects of Cu on legume nodule symbiosis at the molecular and phenotypic levels.}, } @article {pmid28701713, year = {2017}, author = {Huang, J and Zhang, PJ and Zhang, J and Tang, YY}, title = {An ant-coccid mutualism affects the behavior of the parasitoid Aenasius bambawalei, but not that of the ghost ant Tetramorium bicarinatum.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5175}, pmid = {28701713}, issn = {2045-2322}, mesh = {Animals ; Ants/*physiology ; Ectoparasitic Infestations ; Feeding Behavior ; Host-Parasite Interactions ; Plants/metabolism/parasitology ; *Symbiosis ; Volatile Organic Compounds ; Wasps/*physiology ; }, abstract = {Mutualisms between honeydew-producing insects and ants change the emission of volatiles from plants, but whether such changes alter the behaviors of ants that tend honeydew-producing insects or wasps that parasitize honeydew-producing insects remain unknown. This study compared the behavioral responses of the ant Tetramorium bicarinatum and the parasitoid wasp Aenasius bambawalei to odors from cotton plants infested with the mealybug Phenacoccus solenopsis or infested with the mealybug and the ant, which tends the mealybug. The ant could not distinguish between the volatiles from plants infested with the mealybug alone and those from plants infested with the mealybug and the ant. Likewise, naïve wasps failed to distinguish between volatiles from the two treatments. In contrast, experienced wasps preferred volatiles from plants infested with the mealybug and the ant. Volatile analysis showed that the amounts of MeSA were increased and those of methyl nicotinate were decreased when plants were infested by the mealybug and the ant rather than when plants were uninfested or were infested by the mealybug alone. Thus, the mutualism between the mealybug and ant changed the volatiles emitted by cotton plants such that the attraction of A. bambawalei (but not that of the ant) to the plants was increased.}, } @article {pmid28652610, year = {2017}, author = {Xing, X and Men, J and Guo, S}, title = {Phylogenetic constrains on Polyporus umbellatus-Armillaria associations.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4226}, pmid = {28652610}, issn = {2045-2322}, mesh = {Armillaria/classification/genetics/*physiology ; China ; Genotype ; Geography ; Mycelium/*physiology ; Phylogeny ; Polyporus/classification/genetics/*physiology ; Species Specificity ; *Symbiosis ; }, abstract = {It has been well established that some Armillaria species are symbionts of Polyporus umbellatus, However, little is known about the evolutionary history of P. umbellatus-Armillaria associations. In this research, we used an analysis based on the strength of the phylogenetic signal to investigate P. umbellatus-Armillaria associations in 57 sclerotial samples across 11 provinces of China. We isolated Armillaria strains from the invasion cavity inside the sclerotia of P. umbellatus and then phylogenetically analyzed these Armillaria isolates. We also tested the effect of P. umbellatus and Armillaria phylogenies on the P. umbellatus-Armillaria associations. We isolated forty-seven Armillaria strains from 26 P. umbellatus sclerotial samples. All Armillaria isolates were classified into the 5 phylogenetic lineages found in China except for one singleton. Among the 5 phylogenetic lineages, one lineage (lineage 8) was recognized by delimitation of an uncertain phylogenetic lineage in previous study. Results of simple Mantel test implied that phylogenetically related P. umbellatus populations tend to interact with phylogenetically related Armillaria species. Phylogenetic network analyses revealed that the interaction between P. umbellatus and Armillaria is significantly influenced by the phylogenetic relationships between the Armillaria species.}, } @article {pmid30621489, year = {2019}, author = {Liu, L and Xu, L and Jia, Q and Pan, R and Oelmüller, R and Zhang, W and Wu, C}, title = {Arms race: diverse effector proteins with conserved motifs.}, journal = {Plant signaling & behavior}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/15592324.2018.1557008}, pmid = {30621489}, issn = {1559-2324}, abstract = {Effector proteins play important roles in the infection by pathogenic oomycetes and fungi or the colonization by endophytic and mycorrhizal fungi. They are either translocated into the host plant cells via specific translocation mechanisms and function in the host's cytoplasm or nucleus, or they reside in the apoplast of the plant cells and act at the extracellular host-microbe interface. Many effector proteins possess conserved motifs (such as the RXLR, CRN, LysM, RGD, DELD, EAR, RYWT, Y/F/WXC or CFEM motifs) localized in their N- or C-terminal regions. Analysis of the functions of effector proteins, especially so-called "core effectors", is crucial for the understanding of pathogenicity/symbiosis mechanisms and plant defense strategies, and helps to develop breeding strategies for pathogen-resistant cultivars, and to increase crop yield and quality as well as abiotic stress resistance. This review summarizes current knowledge about these effector proteins with the conversed motifs and their involvement in pathogenic or mutualistic plant/fungal interactions.}, } @article {pmid29569807, year = {2018}, author = {Ferrier-Pagès, C and Sauzéat, L and Balter, V}, title = {Coral bleaching is linked to the capacity of the animal host to supply essential metals to the symbionts.}, journal = {Global change biology}, volume = {24}, number = {7}, pages = {3145-3157}, doi = {10.1111/gcb.14141}, pmid = {29569807}, issn = {1365-2486}, mesh = {Animals ; Anthozoa/*physiology ; Global Warming ; *Heterotrophic Processes ; Metals/analysis/*metabolism ; Seawater/chemistry ; Stress, Physiological/*physiology ; Symbiosis/*physiology ; }, abstract = {Massive coral bleaching events result in extensive coral loss throughout the world. These events are mainly caused by seawater warming, but are exacerbated by the subsequent decrease in nutrient availability in surface waters. It has therefore been shown that nitrogen, phosphorus or iron limitation contribute to the underlying conditions by which thermal stress induces coral bleaching. Generally, information on the trophic ecology of trace elements (micronutrients) in corals, and on how they modulate the coral response to thermal stress is lacking. Here, we demonstrate for the first time that heterotrophic feeding (i.e. the capture of zooplankton prey by the coral host) and thermal stress induce significant changes in micro element concentrations and isotopic signatures of the scleractinian coral Stylophora pistillata. The results obtained first reveal that coral symbionts are the major sink for the heterotrophically acquired micronutrients and accumulate manganese, magnesium and iron from the food. These metals are involved in photosynthesis and antioxidant protection. In addition, we show that fed corals can maintain high micronutrient concentrations in the host tissue during thermal stress and do not bleach, whereas unfed corals experience a significant decrease in copper, zinc, boron, calcium and magnesium in the host tissue and bleach. In addition, the significant increase in δ65 Cu and δ66 Zn signature of symbionts and host tissue at high temperature suggests that these isotopic compositions are good proxy for stress in corals. Overall, present findings highlight a new way in which coral heterotrophy and micronutrient availability contribute to coral resistance to global warming and bleaching.}, } @article {pmid30619423, year = {2018}, author = {Liu, A and Contador, CA and Fan, K and Lam, HM}, title = {Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1860}, doi = {10.3389/fpls.2018.01860}, pmid = {30619423}, issn = {1664-462X}, abstract = {Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C4-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.}, } @article {pmid30619390, year = {2018}, author = {Bedini, A and Mercy, L and Schneider, C and Franken, P and Lucic-Mercy, E}, title = {Unraveling the Initial Plant Hormone Signaling, Metabolic Mechanisms and Plant Defense Triggering the Endomycorrhizal Symbiosis Behavior.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1800}, doi = {10.3389/fpls.2018.01800}, pmid = {30619390}, issn = {1664-462X}, abstract = {Arbuscular mycorrhizal (AM) fungi establish probably one of the oldest mutualistic relationships with the roots of most plants on earth. The wide distribution of these fungi in almost all soil ecotypes and the broad range of host plant species demonstrate their strong plasticity to cope with various environmental conditions. AM fungi elaborate fine-tuned molecular interactions with plants that determine their spread within root cortical tissues. Interactions with endomycorrhizal fungi can bring various benefits to plants, such as improved nutritional status, higher photosynthesis, protection against biotic and abiotic stresses based on regulation of many physiological processes which participate in promoting plant performances. In turn, host plants provide a specific habitat as physical support and a favorable metabolic frame, allowing uptake and assimilation of compounds required for the life cycle completion of these obligate biotrophic fungi. The search for formal and direct evidences of fungal energetic needs raised strong motivated projects since decades, but the impossibility to produce AM fungi under axenic conditions remains a deep enigma and still feeds numerous debates. Here, we review and discuss the initial favorable and non-favorable metabolic plant context that may fate the mycorrhizal behavior, with a focus on hormone interplays and their links with mitochondrial respiration, carbon partitioning and plant defense system, structured according to the action of phosphorus as a main limiting factor for mycorrhizal symbiosis. Then, we provide with models and discuss their significances to propose metabolic targets that could allow to develop innovations for the production and application of AM fungal inocula.}, } @article {pmid30619219, year = {2018}, author = {Nguyen, HP and Ratu, STN and Yasuda, M and Göttfert, M and Okazaki, S}, title = {InnB, a Novel Type III Effector of Bradyrhizobium elkanii USDA61, Controls Symbiosis With Vigna Species.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3155}, doi = {10.3389/fmicb.2018.03155}, pmid = {30619219}, issn = {1664-302X}, abstract = {Bradyrhizobium elkanii USDA61 is incompatible with mung bean (Vigna radiata cv. KPS1) and soybean (Glycine max cv. BARC2) and unable to nodulate either plant. This incompatibility is due to the presence of a functional type III secretion system (T3SS) that translocates effector protein into host cells. We previously identified five genes in B. elkanii that are responsible for its incompatibility with KPS1 plants. Among them, a novel gene designated as innB exhibited some characteristics associated with the T3SS and was found to be responsible for the restriction of nodulation on KPS1. In the present study, we further characterized innB by analysis of gene expression, protein secretion, and symbiotic phenotypes. The innB gene was found to encode a hypothetical protein that is highly conserved among T3SS-harboring rhizobia. Similar to other rhizobial T3SS-associated genes, the expression of innB was dependent on plant flavonoids and a transcriptional regulator TtsI. The InnB protein was secreted via the T3SS and was not essential for secretion of other nodulation outer proteins. In addition, T3SS-dependent translocation of InnB into nodule cells was confirmed by an adenylate cyclase assay. According to inoculation tests using several Vigna species, InnB promoted nodulation of at least one V. mungo cultivar. These results indicate that innB encodes a novel type III effector controlling symbiosis with Vigna species.}, } @article {pmid30618841, year = {2018}, author = {Huitzil, S and Sandoval-Motta, S and Frank, A and Aldana, M}, title = {Modeling the Role of the Microbiome in Evolution.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {1836}, doi = {10.3389/fphys.2018.01836}, pmid = {30618841}, issn = {1664-042X}, abstract = {There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.}, } @article {pmid30617861, year = {2019}, author = {Bogar, L and Peay, K and Kornfeld, A and Huggins, J and Hortal, S and Anderson, I and Kennedy, P}, title = {Plant-mediated partner discrimination in ectomycorrhizal mutualisms.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-018-00879-7}, pmid = {30617861}, issn = {1432-1890}, support = {1554375//National Science Foundation/ ; Graduate Research Fellowship//National Science Foundation/ ; Graduate Scholarship//Mycological Society of San Francisco/ ; Predoctoral Fellowship//Center for Computational, Evolutionary and Human Genomics, Stanford University/ ; }, abstract = {Although ectomycorrhizal fungi have well-recognized effects on ecological processes ranging from plant community dynamics to carbon cycling rates, it is unclear if plants are able to actively influence the structure of these fungal communities. To address this knowledge gap, we performed two complementary experiments to determine (1) whether ectomycorrhizal plants can discriminate among potential fungal partners, and (2) to what extent the plants might reward better mutualists. In experiment 1, split-root Larix occidentalis seedlings were inoculated with spores from three Suillus species (S. clintonianus, S. grisellus, and S. spectabilis). In experiment 2, we manipulated the symbiotic quality of Suillus brevipes isolates on split-root Pinus muricata seedlings by changing the nitrogen resources available, and used carbon-13 labeling to track host investment in fungi. In experiment 1, we found that hosts can discriminate in multi-species settings. The split-root seedlings inhibited colonization by S. spectabilis whenever another fungus was available, despite similar benefits from all three fungi. In experiment 2, we found that roots and fungi with greater nitrogen supplies received more plant carbon. Our results suggest that plants may be able to regulate this symbiosis at a relatively fine scale, and that this regulation can be integrated across spatially separated portions of a root system.}, } @article {pmid30616707, year = {2019}, author = {Dessì, D and Margarita, V and Cocco, AR and Marongiu, A and Fiori, PL and Rappelli, P}, title = {Trichomonas vaginalis and Mycoplasma hominis: new tales of two old friends.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-6}, doi = {10.1017/S0031182018002135}, pmid = {30616707}, issn = {1469-8161}, abstract = {Trichomonas vaginalis is an anaerobic protist, responsible for the most prevalent non-viral sexually transmitted infection in humans. One of the most intriguing aspects of T. vaginalis pathobiology is the complex relationship with intracellular microbial symbionts: a group of dsRNA viruses belonging to family of Totiviridae (T. vaginalis virus), and eubacteria belonging to the Mycoplasma genus, in particular Mycoplasma hominis. Both microorganisms seem to strongly influence the lifestyle of T. vaginalis, suggesting a role of the symbiosis in the high variability of clinical presentation and sequelae during trichomoniasis. In the last few years many aspects of this unique symbiotic relationship have been investigated: M. hominis resides and replicates in the protozoan cell, and T. vaginalis is able to pass the bacterial infection to both mycoplasma-free protozoan isolates and human epithelial cells; M. hominis synergistically upregulates the proinflammatory response of human monocytes to T. vaginalis. Furthermore, the influence of M. hominis over T. vaginalis metabolism and physiology has been characterized. The identification of a novel species belonging to the class of Mollicutes (Candidatus Mycoplasma girerdii) exclusively associated to T. vaginalis opens new perspectives in the research of the complex series of events taking place in the multifaceted world of the vaginal microbiota, both under normal and pathological conditions.}, } @article {pmid29945091, year = {2018}, author = {Zhang, B and Du, N and Li, Y and Shi, P and Wei, G}, title = {Distinct biogeographic patterns of rhizobia and non-rhizobial endophytes associated with soybean nodules across China.}, journal = {The Science of the total environment}, volume = {643}, number = {}, pages = {569-578}, doi = {10.1016/j.scitotenv.2018.06.240}, pmid = {29945091}, issn = {1879-1026}, mesh = {China ; Endophytes/*physiology ; Phylogeny ; RNA, Ribosomal, 16S ; Rhizobium/physiology ; Root Nodules, Plant ; Soybeans/*physiology ; *Symbiosis ; }, abstract = {Both rhizobia and non-rhizobial endophytes (NRE) are inhabitants of legume nodules. The biogeography of rhizobia has been well investigated, but little is known about the spatial distribution and community assemblage of NRE. By using high-throughput sequencing, we compared biogeographic patterns of rhizobial and non-rhizobial subcommunities and investigated their bacterial co-occurrence patterns in nodules collected from 50 soybean fields across China. Dispersal probability was lower in NRE than in rhizobia, as revealed by a significant distance-decay relationship found in NRE, but not in rhizobia, in addition to a significant occupancy-abundance relationship in the entire community. Rhizobial and NRE subcommunities were significantly influenced by different environmental and spatial variables. Moreover, the rhizobial subcommunities were grouped into Ensifer- and Bradyrhizobium-dominated clusters that were significantly related to soil pH. The non-rhizobial subcommunities were grouped into Proteobacteria- and Firmicutes-dominated clusters that were more influenced by climatic than by edaphic factors. These results demonstrated that rhizobial and non-rhizobial subcommunities are characterized by distinct biogeographic patterns. Network analysis showed rhizobia and NRE as separately grouped and uncorrelated with each other, suggesting they did not share niche space in soybean nodules. In sum, these results broaden our knowledge of how bacteria are distributed and assemble as a community in root nodules.}, } @article {pmid30616152, year = {2019}, author = {Zhang, XF and Hu, ZH and Yan, TX and Lu, RR and Peng, CL and Li, SS and Jing, YX}, title = {Arbuscular mycorrhizal fungi alleviate Cd phytotoxicity by altering Cd subcellular distribution and chemical forms in Zea mays.}, journal = {Ecotoxicology and environmental safety}, volume = {171}, number = {}, pages = {352-360}, doi = {10.1016/j.ecoenv.2018.12.097}, pmid = {30616152}, issn = {1090-2414}, abstract = {Arbuscular mycorrhizal fungus (AMF) can relieve Cd phytotoxicity and improve plant growth, but the mechanisms involved in this process have still been not completely known. In the present work, a pot experiment was conducted to examine productions of glutathione (GSH) and phytochelatins (PCs), and absorption, chemical forms and subcellular distribution of Cd in maize (Zea mays) inoculated with or without AMF (Rhizophagus intraradices (Ri) and Glomus versiforme (Gv)) in Cd-amended soils (0, 1 and 5 mg Cd kg-1 soil). In general, both Ri and Gv inoculation dramatically enhanced biomass production and reduced Cd concentrations in shoots and roots of maize when compared to the non-mycorrhizal treatment. Moreover, both Ri and Gv symbiosis obviously increased contents of GSH and PCs, both in shoots and roots. Subcellular distribution of Cd in maize indicated that most of Cd (more than 90%) was accumulated in cell wall and soluble fraction. In addition, Cd proportions in soluble fractions in shoots of maize inoculated with Gv or Ri were considerably increased, but reduced in cell wall fractions compared to non-mycorrhizal maize, indicating that mycorrhizal symbiosis promoted Cd transfer to vacuoles. Furthermore, proportions of Cd in inorganic and water-soluble forms were declined, but elevated in pectates and proteins-integrated forms in mycorrhizal maize, which suggested that Gv and Ri could convert Cd into inactive forms. These observations could provide a further understanding of potential Cd detoxification mechanism in maize inoculated with AMF.}, } @article {pmid30615203, year = {2019}, author = {Zhang, XW and Dunn, DW and Wen, XL and Sun, BF and Wang, RW}, title = {Differential deployment of sanctioning mechanisms by male and female host trees in a gynodioecious fig-wasp mutualism.}, journal = {Ecology}, volume = {}, number = {}, pages = {e02597}, doi = {10.1002/ecy.2597}, pmid = {30615203}, issn = {0012-9658}, abstract = {In some insect nursery pollination mutualisms, plant hosts impose net costs to uncooperative 'cheater' symbionts. These 'sanctions' promote mutualism stability but their precise adaptive nature remains unclear. In fig-wasp mutualisms host trees (Ficus spp.) are only pollinated by female agaonid wasps whose larvae only use galled fig flowers as food. In actively pollinated systems, if wasps fail to pollinate sanctions can result via fig abortion, killing all wasp offspring, or by increased offspring mortality within un-aborted figs. These sanctions result from selective investment to pollinated inflorescences, a mechanism present in almost all angiosperms. To more fully understand how selective investment functions as sanctions requires the measurement of variation in their costs and benefits to both hosts and symbionts. Gynodioecious fig tree-fig wasp mutualisms are particularly suitable for this because pollen and wasps are produced only in the figs of 'male' trees and seeds only in the figs of 'female' trees. Male and female trees thus incur different net costs of pollen absence, and costs of sanctions to pollen-free 'cheater' wasps only occur in male trees. We used the actively pollinated host tree F. hispida and introduced into male and female figs either 1,3,5,7 or 9 all pollen-laden 'cooperative' (P+) or all pollen-free 'cheater' (P-) wasps. Abortion in both male and female trees was highest in P- figs, with P- fig abortion higher in females (~90%) than in males (~40%). Fig abortion was negatively associated with foundress number mainly in P+ figs; in P- figs abortion was only weakly associated with the number of 'cheater' wasps, especially in female figs. In un-aborted male figs, wasp offspring mortality was higher in P- figs than in P+ figs, and in P- figs correlated positively with foundress (cheater) number. Increased offspring mortality was biased against female wasp offspring and likely resulted from reduced larval nutrition in un-pollinated flowers. Variation in selective investment to P- figs thus reflects costs and benefits of pollen absence/presence to hosts, variation that translates directly to net costs to cheater wasps. This article is protected by copyright. All rights reserved.}, } @article {pmid30613897, year = {2019}, author = {Shang, N and Ding, M and Dai, M and Si, H and Li, S and Zhao, G}, title = {Biodegradation of malachite green by an endophytic bacterium Klebsiella aerogenes S27 involving a novel oxidoreductase.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-09583-0}, pmid = {30613897}, issn = {1432-0614}, support = {31640002//National Natural Science Foundation of China/ ; ZR2015JL013//Natural Science Foundation of Shandong Province/ ; 2016M600551//Postdoctoral Research Foundation of China/ ; 20170058//International Postdoctoral Exchange Fellowship, China/ ; }, abstract = {Endophytic microorganisms can metabolize organic contaminants and assist in plant growth, thus facilitating the phytoremediation of polluted environments. An endophytic bacterium capable of decoloring malachite green (MG) was isolated from the leaves of the wetland plant Suaeda salsa and was identified as Klebsiella aerogenes S27. Complete decolorization of MG (100 mg/l) was achieved in 8 h at 30 °C and pH 7.0. Ultraviolet-visible spectroscopy and Fourier-transform infrared spectroscopy analyses indicated the degradation of MG by the isolate. The enzymic assays of the strain showed the triphenylmethane reductase (TMR) activity. A gene encoding putative TMR-like protein (named as KaTMR) was cloned and heterologously expressed in Escherichia coli. KaTMR showed only 42.6-43.3% identities in amino acids compared with well-studied TMRs, and it phylogenetically formed a new branch in the family of TMRs. The degraded metabolites by recombinant KaTMR were detected by liquid chromatography-mass spectrometry, showing differences from the products of reported TMRs. The biotransformation pathway of MG was proposed. Phytotoxicity studies revealed the less-toxic nature of the degraded metabolites compared to the dye. This study presented the first report of an endophyte on the degradation and detoxification of triphenylmethane dye via a novel oxidoreductase, thus facilitating the study of the plant-endophyte symbiosis in the bioremediation processes.}, } @article {pmid30612723, year = {2018}, author = {Ramírez-Puebla, ST and Hernández, MAR and Guerrero Ruiz, G and Ormeño-Orrillo, E and Martinez-Romero, JC and Servín-Garcidueñas, LE and Núñez-de la Mora, A and Amescua-Villela, G and Negrete-Yankelevich, S and Martínez-Romero, E}, title = {Nodule bacteria from the cultured legume Phaseolus dumosus (belonging to the Phaseolus vulgaris cross-inoculation group) with common tropici phenotypic characteristics and symbiovar but distinctive phylogenomic position and chromid.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2018.12.007}, pmid = {30612723}, issn = {1618-0984}, abstract = {Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI). CCGE531 and CCGE532 had common phenotypic characteristics with tropici type B rhizobial symbionts. Genome synteny analysis and ANI showed that P. dumosus isolates had different chromids and our analysis suggests that chromids have independently evolved in different lineages of the Rhizobium genus. Finally, we considered that P. dumosus and Phaseolus vulgaris plants belong to the same cross-inoculation group since they have conserved symbiotic affinites for rhizobia.}, } @article {pmid30474599, year = {2018}, author = {Ohtsuka, S and Nishikawa, J and Boxshall, GA}, title = {A new species of Peniculus (Copepoda: Siphonostomatoida) parasitizing mesopelagic myctophid fish: first discovery of colonization of the genus in deep water.}, journal = {Parasite (Paris, France)}, volume = {25}, number = {}, pages = {58}, pmid = {30474599}, issn = {1776-1042}, mesh = {Animal Fins/parasitology ; Animals ; Copepoda/anatomy & histology/genetics/*physiology ; Ectoparasitic Infestations/epidemiology/parasitology/*veterinary ; Female ; Fish Diseases/epidemiology/*parasitology ; Fishes ; Japan/epidemiology ; Seafood/parasitology ; Socioeconomic Factors ; Species Specificity ; Symbiosis ; }, abstract = {Peniculus hokutoae n. sp. is described on the basis of an ovigerous adult female parasitizing the caudal fin of the myctophid fish Symbolophorus evermanni (Gilbert, 1905), collected from Suruga Bay, Japan. This is the first record of parasitism by this genus on mesopelagic myctophid fish. The new species is easily distinguished from other congeners in: (1) the presence of a conical process anterior to the rostrum; (2) the secondary elongation of the first pedigerous somite; (3) the incorporation of the third and fourth pedigerous somites into the trunk; (4) the unilobate maxillule bearing two unequal apical setae; (5) the lack of any processes on the first segment of the maxilla. Four morphological patterns of the cephalothorax, neck and anterior parts of the trunk can be found in the genus. We infer that initial colonization of a mesopelagic myctophid fish as host is likely to have occurred when the diurnally-migrating myctophid host was feeding in near-surface waters at night and was exposed to infective stages of Peniculus.}, } @article {pmid30298666, year = {2018}, author = {Yang, CY and Tarng, DC}, title = {Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients.}, journal = {Nephrology (Carlton, Vic.)}, volume = {23 Suppl 4}, number = {}, pages = {16-20}, doi = {10.1111/nep.13452}, pmid = {30298666}, issn = {1440-1797}, support = {VGHUST107-G5-3-3//Taipei Veterans General Hospital/ ; V106D25-003-MY3//Taipei Veterans General Hospital/ ; MOST 107-2633-B-009-003//Ministry of Science and Technology, Taiwan/ ; MOST 105-2628-B-075-008-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 106-2314-B-010-039-MY3//Ministry of Science and Technology, Taiwan/ ; //Foundation for Poison Control/ ; }, mesh = {Animals ; Bacteria/*metabolism ; Dietary Fiber/administration & dosage/metabolism ; Dysbiosis ; Fruit ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; *Healthy Diet/adverse effects ; Host-Pathogen Interactions ; Humans ; Indican/*metabolism ; Prognosis ; Recommended Dietary Allowances ; Renal Insufficiency, Chronic/diagnosis/diet therapy/metabolism/microbiology ; Risk Factors ; Symbiosis ; Vegetables ; }, abstract = {Emerging evidence suggests that intestinal dysbiosis plays an important role in host inflammation locally and systemically. Such pathological condition is even more prevailing in patients with chronic kidney disease (CKD). Of note, indoxyl sulphate (IS), a gut-derived uremic toxin, is notorious for its pro-inflammatory feature in CKD patients. IS accumulates in the body as the urinary excretion of uremic toxins is impaired, and further worsens the kidney function in a vicious cycle to CKD. Dietary restriction in vegetables, fruits and yogurt leads to the predominance of indole-producing intestinal microbial flora and further exaggerates the accumulation of IS in CKD patients. Recently, interventional studies have shown that circulating IS can be reduced by dietary prebiotic and/or probiotic supplements. However, further randomized controlled trials are warranted to examine whether such beneficial effect of dietary prebiotic/probiotic supplements could be extrapolated to better hard outcomes in CKD population. In this review, we would also like to emphasize the importance of achieving sufficient intake of dietary fibre by proper vegetable pre-treatment and accurate fruit selection, instead of directly avoiding these potassium-rich yet fibre-rich and base-producing foods.}, } @article {pmid30297781, year = {2018}, author = {Shane, JL and Grogan, CL and Cwalina, C and Lampe, DJ}, title = {Blood meal-induced inhibition of vector-borne disease by transgenic microbiota.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4127}, pmid = {30297781}, issn = {2041-1723}, support = {R15 AI107735/AI/NIAID NIH HHS/United States ; R15 AI107735//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/International ; }, mesh = {Acetobacteraceae/physiology ; Animals ; Animals, Genetically Modified ; Anopheles/*genetics/microbiology/parasitology ; Antibiosis/*physiology ; Digestive System/microbiology/parasitology ; Disease Resistance/genetics ; Malaria/*blood/microbiology/parasitology ; Microbiota/physiology ; Mosquito Vectors/*genetics/microbiology/parasitology ; Plasmodium berghei/physiology ; Symbiosis ; }, abstract = {Vector-borne diseases are a substantial portion of the global disease burden; one of the deadliest of these is malaria. Vector control strategies have been hindered by mosquito and pathogen resistances, and population alteration approaches using transgenic mosquitos still have many hurdles to overcome before they can be implemented in the field. Here we report a paratransgenic control strategy in which the microbiota of Anopheles stephensi was engineered to produce an antiplasmodial effector causing the mosquito to become refractory to Plasmodium berghei. The midgut symbiont Asaia was used to conditionally express the antiplasmodial protein scorpine only when a blood meal was present. These blood meal inducible Asaia strains significantly inhibit pathogen infection, and display improved fitness compared to strains that constitutively express the antiplasmodial effector. This strategy may allow the antiplasmodial bacterial strains to survive and be transmitted through mosquito populations, creating an easily implemented and enduring vector control strategy.}, } @article {pmid30191497, year = {2018}, author = {Clanner-Engelshofen, BM and Ruzicka, T and Reinholz, M}, title = {Efficient isolation and observation of the most complex human commensal, Demodex spp.}, journal = {Experimental & applied acarology}, volume = {76}, number = {1}, pages = {71-80}, pmid = {30191497}, issn = {1572-9702}, mesh = {Animals ; Coloring Agents ; Host-Parasite Interactions ; Humans ; Mite Infestations/*diagnosis/parasitology ; Mites/*physiology ; Parasitology/*methods ; Propidium ; Staining and Labeling/*methods ; Symbiosis ; }, abstract = {Demodex spp. mites are an often neglected member of the human skin microbiome. Mostly they are commensals, although their pathophysiological role in rosacea, spinulosis folliculorum, and other skin diseases is recognized. Little is known about their life cycle, biology, and physiology. Demodex mites cannot be cultivated in vitro, thereby complicating research immensely. The manual extraction from human sebum is laborious and death can only be detected by surrogate markers like ceased movement or loss of fluorescence. Here we present a new approach for the extraction of larger mite numbers and the hitherto most precise way to detect death. The extraction of mites from sebum and debris by hand can be accelerated by a factor 10 using sucrose gradient centrifugation, which is well tolerated by the mites. Staining with propidium iodide allows for easy identification of dead mites, excluding frail mites that stopped moving, and has no negative effect on overall mite survival. We anticipate our methods to be a starting point for more sophisticated research and ultimately in vitro cultivation of Demodex spp. mites.}, } @article {pmid30117802, year = {2018}, author = {Kanté Tagueu, S and Farikou, O and Njiokou, F and Simo, G}, title = {Prevalence of Sodalis glossinidius and different trypanosome species in Glossina palpalis palpalis caught in the Fontem sleeping sickness focus of the southern Cameroon.}, journal = {Parasite (Paris, France)}, volume = {25}, number = {}, pages = {44}, pmid = {30117802}, issn = {1776-1042}, mesh = {Animals ; Cameroon/epidemiology ; DNA, Bacterial/genetics ; DNA, Protozoan/genetics ; Enterobacteriaceae/genetics/*isolation & purification ; Humans ; Insect Control ; Insect Vectors/*microbiology/*parasitology ; Polymerase Chain Reaction ; Prevalence ; Symbiosis ; Trypanosoma/genetics/*isolation & purification ; Trypanosoma congolense/genetics ; Trypanosoma vivax/genetics ; Trypanosomiasis, African/epidemiology/parasitology ; Tsetse Flies/*microbiology/*parasitology ; }, abstract = {Tsetse flies are the cyclical vector of human and animal African trypanosomiasis. To improve vector control in order to achieve the elimination of human African trypanosomiasis (HAT) and boost the control of animal diseases, investigations have been undertaken on the tripartite association between tsetse, trypanosome, and symbionts. It is in this light that Sodalis glossinidius and different trypanosomes were identified in Glossina palpalis palpalis caught in Fontem in southern Cameroon. For this study, DNA was extracted from whole flies, and S. glossinidius and different trypanosome species were identified by polymerase chain reaction (PCR). Statistical analyses were performed to compare the trypanosome and S. glossinidius infection rates and to look for an association between these microorganisms. Of the 274 G. p. palpalis caught, 3.3% (9/274) were teneral. About 35% (96/274) of these flies harbored S. glossinidius. Of the 265 non-teneral flies, 37.7% were infected by trypanosomes. The infection rates of Trypanosoma congolense "forest type" and Trypanosoma vivax were 26.04% and 18.11%, respectively. About 6.41% of tsetse harbored mixed infections of T. congolense and T. vivax. Of the 69 tsetse with T. congolense infections, 33.33% (23/69) harbored S. glossinidius while 71.86% (69/96) of flies harboring S. glossinidius were not infected by trypanosomes. No association was observed between S. glossinidius and trypanosome infections. Some wild tsetse harbor S. glossinidius and trypanosomes, while others have no infection or are infected by only one of these microorganisms. We conclude that the presence of S. glossinidius does not favor trypanosome infections in G. p. palpalis of the Fontem focus.}, } @article {pmid30093613, year = {2018}, author = {Albrecht, J and Classen, A and Vollstädt, MGR and Mayr, A and Mollel, NP and Schellenberger Costa, D and Dulle, HI and Fischer, M and Hemp, A and Howell, KM and Kleyer, M and Nauss, T and Peters, MK and Tschapka, M and Steffan-Dewenter, I and Böhning-Gaese, K and Schleuning, M}, title = {Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3177}, pmid = {30093613}, issn = {2041-1723}, support = {For1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; }, mesh = {Altitude ; Animals ; Bayes Theorem ; *Biodiversity ; Birds/*physiology ; Climate ; *Ecosystem ; Feeding Behavior ; Flowers/*physiology ; Fruit ; Insecta/*physiology ; Phylogeny ; Plants ; Research Design ; Species Specificity ; *Symbiosis ; Tanzania ; }, abstract = {Species' functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird-fruit, bird-flower and insect-flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant-animal interaction networks.}, } @article {pmid30001328, year = {2018}, author = {Medina, V and Sardoy, PM and Soria, M and Vay, CA and Gutkind, GO and Zavala, JA}, title = {Characterized non-transient microbiota from stinkbug (Nezara viridula) midgut deactivates soybean chemical defenses.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200161}, pmid = {30001328}, issn = {1932-6203}, mesh = {Animals ; Cysteine Proteinase Inhibitors/metabolism ; DNA, Bacterial/genetics ; Enterobacteriaceae/genetics/isolation & purification ; Enterococcus/genetics/isolation & purification ; Gastrointestinal Microbiome/genetics/*physiology ; Heteroptera/*microbiology/*pathogenicity ; Host-Pathogen Interactions/physiology ; Pantoea/genetics/isolation & purification ; Phylogeny ; Phytochemicals/metabolism ; Plant Diseases/microbiology/parasitology ; Soybeans/growth & development/*metabolism/*parasitology ; Symbiosis ; }, abstract = {The Southern green stinkbug (N. viridula) feeds on developing soybean seeds in spite of their strong defenses against herbivory, making this pest one of the most harmful to soybean crops. To test the hypothesis that midgut bacterial community allows stinkbugs to tolerate chemical defenses of soybean developing seeds, we identified and characterized midgut microbiota of stinkbugs collected from soybean crops, different secondary plant hosts or insects at diapause on Eucalyptus trees. Our study demonstrated that while more than 54% of N. viridula adults collected in the field had no detectable bacteria in the V1-V3 midgut ventricles, the guts of the rest of stinkbugs were colonized by non-transient microbiota (NTM) and transient microbiota not present in stinkbugs at diapause. While transient microbiota Bacillus sp., Micrococcus sp., Streptomyces sp., Staphylococcus sp. and others had low abundance, NTM microbiota was represented by Yokenella sp., Pantoea sp. and Enterococcus sp. isolates. We found some isolates that showed in vitro β-glucosidase and raffinase activities plus the ability to degrade isoflavonoids and deactivate soybean protease inhibitors. Our results suggest that the stinkbugs´ NTM microbiota may impact on nutrition, detoxification and deactivation of chemical defenses, and Enterococcus sp., Yokenella sp. and Pantoea sp. strains might help stinkbugs to feed on soybean developing seeds in spite of its chemical defenses.}, } @article {pmid29978435, year = {2018}, author = {Tetz, G and Tetz, V}, title = {Tetz's theory and law of longevity.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {137}, number = {2}, pages = {145-154}, pmid = {29978435}, issn = {1611-7530}, mesh = {Aging/*genetics ; Animals ; DNA/analysis ; Humans ; Longevity/*physiology ; Microbiota ; Models, Theoretical ; Mutation ; Symbiosis/*physiology ; Time Factors ; }, abstract = {Here, we present new theory and law of longevity intended to evaluate fundamental factors that control lifespan. This theory is based on the fact that genes affecting host organism longevity are represented by subpopulations: genes of host eukaryotic cells, commensal microbiota, and non-living genetic elements. Based on Tetz's theory of longevity, we propose that lifespan and aging are defined by the accumulation of alterations over all genes of macroorganism and microbiome and the non-living genetic elements associated with them. Tetz's law of longevity states that longevity is limited by the accumulation of alterations to the limiting value that is not compatible with life. Based on theory and law, we also propose a novel model to calculate several parameters, including the rate of aging and the remaining lifespan of individuals. We suggest that this theory and model have explanatory and predictive potential to eukaryotic organisms, allowing the influence of diseases, medication, and medical procedures to be re-examined in relation to longevity. Such estimates also provide a framework to evaluate new fundamental aspects that control aging and lifespan.}, } @article {pmid29897662, year = {2018}, author = {Redanz, S and Cheng, X and Giacaman, RA and Pfeifer, CS and Merritt, J and Kreth, J}, title = {Live and let die: Hydrogen peroxide production by the commensal flora and its role in maintaining a symbiotic microbiome.}, journal = {Molecular oral microbiology}, volume = {33}, number = {5}, pages = {337-352}, pmid = {29897662}, issn = {2041-1014}, support = {R21 DE023850/DE/NIDCR NIH HHS/United States ; R01 DE022083/DE/NIDCR NIH HHS/United States ; R56 DE021726/DE/NIDCR NIH HHS/United States ; R01 DE018893/DE/NIDCR NIH HHS/United States ; R01 DE021726/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms/growth & development ; Humans ; Hydrogen Peroxide/*metabolism ; *Microbiota ; Oral Health ; Pyruvate Oxidase/metabolism ; Streptococcus/*metabolism ; *Symbiosis ; }, abstract = {The majority of commensal oral streptococci are able to generate hydrogen peroxide (H2 O2) during aerobic growth, which can diffuse through the cell membrane and inhibit competing species in close proximity. Competing H2 O2 production is mainly dependent upon the pyruvate oxidase SpxB, and to a lesser extent the lactate oxidase LctO, both of which are important for energy generation in aerobic environments. Several studies point to a broad impact of H2 O2 production in the oral environment, including a potential role in biofilm homeostasis, signaling, and interspecies interactions. Here, we summarize the current research regarding oral streptococcal H2 O2 generation, resistance mechanisms, and the ecological impact of H2 O2 production. We also discuss the potential therapeutic utility of H2 O2 for the prevention/treatment of dysbiotic diseases as well as its potential role as a biomarker of oral health.}, } @article {pmid30612363, year = {2019}, author = {Jelassi, R and Khemaissia, H and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K}, title = {Ecotoxicological effects of trace element contamination in talitrid amphipod Orchestia montagui Audouin, 1826.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-018-3974-y}, pmid = {30612363}, issn = {1614-7499}, abstract = {This study deals with the evaluation of trace element bioaccumulation and histological alterations in the hepatopancreas of the supralittoral amphipod Orchestia montagui Audouin, 1826 due to the exposure to cadmium, copper, and zinc. Orchestia montagui individuals were maintained during 14 days in soils contaminated with different trace elements namely cadmium, copper, and zinc; a control was also prepared. Our results show that the mortality and the body mass vary according to the metal and the nominal concentration used. In general, the mortality increases from the seventh day. However, the body mass shows a decrease with cadmium exposure and an increase with copper and zinc exposures. Furthermore, the concentration factor highlights that this species is considered a macroconcentrator for copper and zinc. The hepatopancreas of unexposed and exposed animals were compared to detect histological changes. Our results show significant alterations in the hepatopancreas of the exposed animals after the experiment. The degree of these alterations was found to be dose-dependent. Among the histological changes in the hepatopancreas in O. montagui, a loss of cell structure was noted, especially cell remoteness and border lyses, the reduction of nuclear volume, an increase in the cytoplasm density with the presence of trace element deposits in both the nucleus and vacuoles, a disorganization and destruction of microvilli, and a condensation of the majority of cell organelles and mitochondria swelling. Through this study, we have confirmed that O. montagui can be a relevant model to assess trace metal element pollution in Tunisian coastal lagoons with the aim of using it in future biomonitoring programs.}, } @article {pmid30612193, year = {2019}, author = {Voříšková, A and Jansa, J and Püschel, D and Vosátka, M and Šmilauer, P and Janoušková, M}, title = {Abiotic contexts consistently influence mycorrhiza functioning independently of the composition of synthetic arbuscular mycorrhizal fungal communities.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00572-018-00878-8}, pmid = {30612193}, issn = {1432-1890}, support = {GA15-05466S//Grantov? Agentura ?esk? Republiky/ ; RVO 67985939//Institute of Botany, The Czech Academy of Sciences/ ; RVO 61388971//Institute of Microbiology, The Czech Academy of Sciences/ ; }, abstract = {The relationship between mycorrhiza functioning and composition of arbuscular mycorrhizal (AM) fungal communities is an important but experimentally still rather little explored topic. The main aim of this study was thus to link magnitude of plant benefits from AM symbiosis in different abiotic contexts with quantitative changes in AM fungal community composition. A synthetic AM fungal community inoculated to the model host plant Medicago truncatula was exposed to four different abiotic contexts, namely drought, elevated phosphorus availability, and shading, as compared to standard cultivation conditions, for two cultivation cycles. Growth and phosphorus uptake of the host plants was evaluated along with the quantitative composition of the synthetic AM fungal community. Abiotic context consistently influenced mycorrhiza functioning in terms of plant benefits, and the effects were clearly linked to the P requirement of non-inoculated control plants. In contrast, the abiotic context only had a small and transient effect on the quantitative AM fungal community composition. Our findings suggest no relationship between the degree of mutualism in AM symbiosis and the relative abundances of AM fungal species in communities in our simplified model system. The observed progressive dominance of one AM fungal species indicates an important role of different growth rates of AM fungal species for the establishment of AM fungal communities in simplified systems such as agroecosystems.}, } @article {pmid30612010, year = {2019}, author = {Cui, G and Ai, S and Chen, K and Wang, X}, title = {Arbuscular mycorrhiza augments cadmium tolerance in soybean by altering accumulation and partitioning of nutrient elements, and related gene expression.}, journal = {Ecotoxicology and environmental safety}, volume = {171}, number = {}, pages = {231-239}, doi = {10.1016/j.ecoenv.2018.12.093}, pmid = {30612010}, issn = {1090-2414}, abstract = {Arbuscular mycorrhizal (AM) fungi can protect plants against cadmium (Cd) stress, and are the most prominent symbiotic fungi for contribution to phytoremediation. However, the tolerance mechanism for AM symbiosis on Cd toxicity still remains unclear, especially the related molecular mechanisms. In this study, different Cd treatments were applied to two soybean genotypes with different Cd tolerance in the presence or absence of AM fungal inoculation. The results showed that Cd addition obviously decreased AM colonization. AM symbiosis significantly increased plant dry weight, root growth, and P acquisition in Cd-tolerant HX3 genotype at Cd addition treatments. The effectiveness was associated with a concomitant increased expression of the AM inducible phosphate (Pi) transporter genes GmPT8, GmPT9, GmPT10, and upregulated expression of P-type heavy metal ATPase gene GmHMA19. Additionally, AM fungal inoculation effectively impacted the partitioning of Mg, Cu and Zn, including increased Mg, and decreased Cu and Zn relative concentrations in shoots of Cd tolerant HX3. Taken together, these results suggest that AM symbiosis can alleviate Cd toxicity in soybean through enhanced P nutrition, up-regulated expression of AM inducible GmPTs and GmHMA19, as well as, the alteration of the partitioning of essential nutrient elements.}, } @article {pmid30611207, year = {2019}, author = {Kamm, K and Schierwater, B and DeSalle, R}, title = {Innate immunity in the simplest animals - placozoans.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {5}, doi = {10.1186/s12864-018-5377-3}, pmid = {30611207}, issn = {1471-2164}, support = {Schi-277/26//Deutsche Forschungsgemeinschaft/ ; Schi-277/27//Deutsche Forschungsgemeinschaft/ ; Schi-277/29//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our knowledge about innate immunity stems from a few animal model systems, but substantial variation between metazoan phyla has been revealed by comparative genomic studies. The exploration of more taxa is still needed to better understand the evolution of immunity related mechanisms. Placozoans are morphologically the simplest organized metazoans and the association between these enigmatic animals and their rickettsial endosymbionts has recently been elucidated. Our analyses of the novel placozoan nuclear genome of Trichoplax sp. H2 and its associated rickettsial endosymbiont genome clearly pointed to a mutualistic and co-evolutionary relationship. This discovery raises the question of how the placozoan holobiont manages symbiosis and, conversely, how it defends against harmful microorganisms. In this study, we examined the annotated genome of Trichoplax sp. H2 for the presence of genes involved in innate immune recognition and downstream signaling.

RESULTS: A rich repertoire of genes belonging to the Toll-like and NOD-like receptor pathways, to scavenger receptors and to secreted fibrinogen-related domain genes was identified in the genome of Trichoplax sp. H2. Nevertheless, the innate immunity related pathways in placozoans deviate in several instances from well investigated vertebrates and invertebrates. While true Toll- and NOD-like receptors are absent, the presence of many genes of the downstream signaling cascade suggests at least primordial Toll-like receptor signaling in Placozoa. An abundance of scavenger receptors, fibrinogen-related domain genes and Apaf-1 genes clearly constitutes an expansion of the immunity related gene repertoire specific to Placozoa.

CONCLUSIONS: The found wealth of immunity related genes present in Placozoa is surprising and quite striking in light of the extremely simple placozoan body plan and their sparse cell type makeup. Research is warranted to reveal how Placozoa utilize this immune repertoire to manage and maintain their associated microbiota as well as to fend-off pathogens.}, } @article {pmid30610167, year = {2019}, author = {Liu, J and Rutten, L and Limpens, E and Molen, TV and Velzen, RV and Chen, R and Chen, Y and Geurts, R and Kohlen, W and Kulikova, O and Bisseling, T}, title = {A Remote cis-Regulatory Region Is Required for NIN Expression in the Pericycle to Initiate Nodule Primordium Formation in Medicago truncatula.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1105/tpc.18.00478}, pmid = {30610167}, issn = {1532-298X}, abstract = {The legume-rhizobium symbiosis results in nitrogen fixing root nodules, and their formation involves both intracellular infection initiated in the epidermis and nodule organogenesis initiated in inner root cell layers. NODULE INCEPTION (NIN) is a nodule-specific transcription factor essential for both processes. These NIN-regulated processes occur at different times and locations in the root, demonstrating a complex pattern of spatiotemporal regulation. We show that regulatory sequences sufficient for the epidermal infection process are located within a 5 kb region directly upstream of the NIN start codon in Medicago truncatula. Furthermore, we identify a remote upstream cis-regulatory region required for the expression of NIN in the pericycle, and we show that this region is essential for nodule organogenesis. This region contains putative cytokinin response elements, and is conserved in eight more legume species. Both the cytokinin receptor CRE1, which is essential for nodule primordium formation, and the B-type response regulator RR1 are expressed in the pericycle in the susceptible zone of the uninoculated root. This, together with the identification of the cytokinin responsive elements in the NIN promoter, strongly suggests that NIN expression is initially triggered by cytokinin signalling in the pericycle to initiate nodule primordium formation.}, } @article {pmid30606121, year = {2019}, author = {Shinde, S and Zerbs, S and Collart, FR and Cumming, JR and Noirot, P and Larsen, PE}, title = {Pseudomonas fluorescens increases mycorrhization and modulates expression of antifungal defense response genes in roots of aspen seedlings.}, journal = {BMC plant biology}, volume = {19}, number = {1}, pages = {4}, doi = {10.1186/s12870-018-1610-0}, pmid = {30606121}, issn = {1471-2229}, abstract = {BACKGROUND: Plants, fungi, and bacteria form complex, mutually-beneficial communities within the soil environment. In return for photosynthetically derived sugars in the form of exudates from plant roots, the microbial symbionts in these rhizosphere communities provide their host plants access to otherwise inaccessible nutrients in soils and help defend the plant against biotic and abiotic stresses. One role that bacteria may play in these communities is that of Mycorrhizal Helper Bacteria (MHB). MHB are bacteria that facilitate the interactions between plant roots and symbiotic mycorrhizal fungi and, while the effects of MHB on the formation of plant-fungal symbiosis and on plant health have been well documented, the specific molecular mechanisms by which MHB drive gene regulation in plant roots leading to these benefits remain largely uncharacterized.

RESULTS: Here, we investigate the effects of the bacterium Pseudomonas fluorescens SBW25 (SBW25) on aspen root transcriptome using a tripartite laboratory community comprised of Populus tremuloides (aspen) seedlings and the ectomycorrhizal fungus Laccaria bicolor (Laccaria). We show that SBW25 has MHB activity and promotes mycorrhization of aspen roots by Laccaria. Using transcriptomic analysis of aspen roots under multiple community compositions, we identify clusters of co-regulated genes associated with mycorrhization, the presence of SBW25, and MHB-associated functions, and we generate a combinatorial logic network that links causal relationships in observed patterns of gene expression in aspen seedling roots in a single Boolean circuit diagram. The predicted regulatory circuit is used to infer regulatory mechanisms associated with MHB activity.

CONCLUSIONS: In our laboratory conditions, SBW25 increases the ability of Laccaria to form ectomycorrhizal interactions with aspen seedling roots through the suppression of aspen root antifungal defense responses. Analysis of transcriptomic data identifies that potential molecular mechanisms in aspen roots that respond to MHB activity are proteins with homology to pollen recognition sensors. Pollen recognition sensors integrate multiple environmental signals to down-regulate pollenization-associated gene clusters, making proteins with homology to this system an excellent fit for a predicted mechanism that integrates information from the rhizosphere to down-regulate antifungal defense response genes in the root. These results provide a deeper understanding of aspen gene regulation in response to MHB and suggest additional, hypothesis-driven biological experiments to validate putative molecular mechanisms of MHB activity in the aspen-Laccaria ectomycorrhizal symbiosis.}, } @article {pmid29845886, year = {2018}, author = {Cagide, C and Riviezzi, B and Minteguiaga, M and Morel, MA and Castro-Sowinski, S}, title = {Identification of Plant Compounds Involved in the Microbe-Plant Communication During the Coinoculation of Soybean with Bradyrhizobium elkanii and Delftia sp. strain JD2.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {31}, number = {11}, pages = {1192-1199}, doi = {10.1094/MPMI-04-18-0080-CR}, pmid = {29845886}, issn = {0894-0282}, mesh = {Bradyrhizobium/*physiology ; Delftia/*physiology ; *Plant Root Nodulation ; Soybeans/*microbiology ; *Symbiosis ; }, abstract = {Delftia sp. strain JD2 is a betaproteobacterium characterized as a plant growth-promoting bacterium with a 'helper' function, enhancing the performance of rhizobial inoculant strains during the coinoculation of alfalfa and clover. In this work we analyzed i) the effect of the coinoculation with Bradyrhizobium elkanii and Delftia sp. strain JD2 strains on the performance of soybean plants and ii) the production of a few secondary plant metabolites that would explain the positive effect of coinoculation on the growth and development of soybean plants. The results showed a beneficial effect of coinoculation on soybean growth, nodulation rate, and pulse yield, with the concomitant benefit for the agricultural economy. In addition, based on a metabolomics approach, we demonstrated that a different pattern of plant metabolites is being produced at different stages of plant growth. The new information suggests that the coinoculation of soybean changes the primary and secondary metabolism of the plant, including changes in the metabolic status of main and secondary nodules within the plant. The relevance of producing a different pattern of photosynthetic and photoprotective pigments, flavonoids, organic acids, and carbohydrates are discussed. Finally, we propose that JD2 could be used together with bradyrhizobia to manipulate the chemical composition of plant tissues, promoting the nutritional benefits and health of soybean.}, } @article {pmid30605473, year = {2019}, author = {Suzaki, T and Takeda, N and Nishida, H and Hoshino, M and Ito, M and Misawa, F and Handa, Y and Miura, K and Kawaguchi, M}, title = {LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonius.}, journal = {PLoS genetics}, volume = {15}, number = {1}, pages = {e1007865}, doi = {10.1371/journal.pgen.1007865}, pmid = {30605473}, issn = {1553-7404}, abstract = {Nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi (AMF) form symbioses with plant roots and these are established by precise regulation of symbiont accommodation within host plant cells. In model legumes such as Lotus japonicus and Medicago truncatula, rhizobia enter into roots through an intracellular invasion system that depends on the formation of a root-hair infection thread (IT). While IT-mediated intracellular rhizobia invasion is thought to be the most evolutionarily derived invasion system, some studies have indicated that a basal intercellular invasion system can replace it when some nodulation-related factors are genetically modified. In addition, intracellular rhizobia accommodation is suggested to have a similar mechanism as AMF accommodation. Nevertheless, our understanding of the underlying genetic mechanisms is incomplete. Here we identify a L. japonicus nodulation-deficient mutant, with a mutation in the LACK OF SYMBIONT ACCOMMODATION (LAN) gene, in which root-hair IT formation is strongly reduced, but intercellular rhizobial invasion eventually results in functional nodule formation. LjLAN encodes a protein that is homologous to Arabidopsis MEDIATOR 2/29/32 possibly acting as a subunit of a Mediator complex, a multiprotein complex required for gene transcription. We also show that LjLAN acts in parallel with a signaling pathway including LjCYCLOPS. In addition, the lan mutation drastically reduces the colonization levels of AMF. Taken together, our data provide a new factor that has a common role in symbiont accommodation process during root nodule and AM symbiosis.}, } @article {pmid30603790, year = {2019}, author = {Franzini, VI and Azcón, R and Ruiz-Lozano, JM and Aroca, R}, title = {Rhizobial symbiosis modifies root hydraulic properties in bean plants under non-stressed and salinity-stressed conditions.}, journal = {Planta}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00425-018-03076-0}, pmid = {30603790}, issn = {1432-2048}, abstract = {MAIN CONCLUSION: Rhizobial symbiosis improved the water status of bean plants under salinity-stress conditions, in part by increasing their osmotic root water flow. One of the main problems for agriculture worldwide is the increasing salinization of farming lands. The use of soil beneficial microorganisms stands up as a way to tackle this problem. One approach is the use of rhizobial N2-fixing, nodule-forming bacteria. Salinity-stress causes leaf dehydration due to an imbalance between water lost through stomata and water absorbed by roots. The aim of the present study was to elucidate how rhizobial symbiosis modulates the water status of bean (Phaseolus vulgaris) plants under salinity-stress conditions, by assessing the effects on root hydraulic properties. Bean plants were inoculated or not with a Rhizobium leguminosarum strain and subjected to moderate salinity-stress. The rhizobial symbiosis was found to improve leaf water status and root osmotic water flow under such conditions. Higher content of nitrogen and lower values of sodium concentration in root tissues were detected when compared to not inoculated plants. In addition, a drop in the osmotic potential of xylem sap and increased amount of PIP aquaporins could favour higher root osmotic water flow in the inoculated plants. Therefore, it was found that rhizobial symbiosis may also improve root osmotic water flow of the host plants under salinity stress.}, } @article {pmid30602582, year = {2019}, author = {Muñoz-Marín, MDC and Shilova, IN and Shi, T and Farnelid, H and Cabello, AM and Zehr, JP}, title = {The Transcriptional Cycle Is Suited to Daytime N2 Fixation in the Unicellular Cyanobacterium "Candidatus Atelocyanobacterium thalassa" (UCYN-A).}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02495-18}, pmid = {30602582}, issn = {2150-7511}, abstract = {Symbiosis between a marine alga and a N2-fixing cyanobacterium (Cyanobacterium UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to Braarudosphaera bigelowii N2-fixing cyanobacteria use different strategies to avoid inhibition of N2 fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N2 only at night, but, surprisingly, UCYN-A appears to fix N2 during the day. The goal of this study was to determine how the unicellular UCYN-A strain coordinates N2 fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that the transcription patterns in UCYN-A are more similar to those in marine cyanobacteria that are capable of aerobic N2 fixation in the light, such as Trichodesmium and heterocyst-forming cyanobacteria, than to those in Crocosphaera or Cyanothece species, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with that of the phototrophic eukaryotic host, thus allowing efficient coupling of N2 fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light.IMPORTANCE The symbiotic N2-fixing cyanobacterium UCYN-A, which is closely related to Braarudosphaera bigelowii, and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O2) or the O2 evolved through photosynthesis. This study showed that symbiosis between the N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N2 fixation, which is likely more energetically efficient than fixing N2 at night, as found in other unicellular marine cyanobacteria.}, } @article {pmid30602581, year = {2019}, author = {Hall, RJ and Flanagan, LA and Bottery, MJ and Springthorpe, V and Thorpe, S and Darby, AC and Wood, AJ and Thomas, GH}, title = {A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02106-18}, pmid = {30602581}, issn = {2150-7511}, abstract = {The tsetse fly is the insect vector for the Trypanosoma brucei parasite, the causative agent of human African trypanosomiasis. The colonization and spread of the trypanosome correlate positively with the presence of a secondary symbiotic bacterium, Sodalis glossinidius The metabolic requirements and interactions of the bacterium with its host are poorly understood, and herein we describe a metabolic model of S. glossinidius metabolism. The model enabled the design and experimental verification of a defined medium that supports S. glossinidius growth ex vivo This has been used subsequently to analyze in vitro aspects of S. glossinidius metabolism, revealing multiple unique adaptations of the symbiont to its environment. Continued dependence on a sugar, and the importance of the chitin monomer N-acetyl-d-glucosamine as a carbon and energy source, suggests adaptation to host-derived molecules. Adaptation to the amino acid-rich blood diet is revealed by a strong dependence on l-glutamate as a source of carbon and nitrogen and by the ability to rescue a predicted l-arginine auxotrophy. Finally, the selective loss of thiamine biosynthesis, a vitamin provided to the host by the primary symbiont Wigglesworthia glossinidia, reveals an intersymbiont dependence. The reductive evolution of S. glossinidius to exploit environmentally derived metabolites has resulted in multiple weaknesses in the metabolic network. These weaknesses may become targets for reagents that inhibit S. glossinidius growth and aid the reduction of trypanosomal transmission.IMPORTANCE Human African trypanosomiasis is caused by the Trypanosoma brucei parasite. The tsetse fly vector is of interest for its potential to prevent disease spread, as it is essential for T. brucei life cycle progression and transmission. The tsetse's mutualistic endosymbiont Sodalis glossinidius has a link to trypanosome establishment, providing a disease control target. Here, we describe a new, experimentally verified model of S. glossinidius metabolism. This model has enabled the development of a defined growth medium that was used successfully to test aspects of S. glossinidius metabolism. We present S. glossinidius as uniquely adapted to life in the tsetse, through its reliance on the blood diet and host-derived sugars. Additionally, S. glossinidius has adapted to the tsetse's obligate symbiont Wigglesworthia glossinidia by scavenging a vitamin it produces for the insect. This work highlights the use of metabolic modeling to design defined growth media for symbiotic bacteria and may provide novel inhibitory targets to block trypanosome transmission.}, } @article {pmid30602523, year = {2019}, author = {Rubin-Blum, M and Dubilier, N and Kleiner, M}, title = {Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria.}, journal = {mSphere}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSphere.00394-18}, pmid = {30602523}, issn = {2379-5042}, abstract = {Very few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest-growing invertebrate. To date, the coexistence of these two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, coexisted within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow toward the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase in the E. laminata symbiont. This electron-bifurcating complex, together with NAD(P)+ transhydrogenase and Na+ translocating Rnf membrane complexes, may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer.IMPORTANCE Primary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome, the rTCA and the CBB cycle, opens the possibility to study the potential benefits of having these two pathways and the interplay between them. Additionally, this will allow the investigation of the unusual and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.}, } @article {pmid30602367, year = {2019}, author = {Chen, YY and Chen, DQ and Chen, L and Liu, JR and Vaziri, ND and Guo, Y and Zhao, YY}, title = {Microbiome-metabolome reveals the contribution of gut-kidney axis on kidney disease.}, journal = {Journal of translational medicine}, volume = {17}, number = {1}, pages = {5}, doi = {10.1186/s12967-018-1756-4}, pmid = {30602367}, issn = {1479-5876}, support = {81673578//National Natural Science Foundation of China/ ; 81603271//National Natural Science Foundation of China/ ; 81872985//National Natural Science Foundation of China/ ; }, abstract = {Dysbiosis represents changes in composition and structure of the gut microbiome community (microbiome), which may dictate the physiological phenotype (health or disease). Recent technological advances and efforts in metagenomic and metabolomic analyses have led to a dramatical growth in our understanding of microbiome, but still, the mechanisms underlying gut microbiome-host interactions in healthy or diseased state remain elusive and their elucidation is in infancy. Disruption of the normal gut microbiota may lead to intestinal dysbiosis, intestinal barrier dysfunction, and bacterial translocation. Excessive uremic toxins are produced as a result of gut microbiota alteration, including indoxyl sulphate, p-cresyl sulphate, and trimethylamine-N-oxide, all implicated in the variant processes of kidney diseases development. This review focuses on the pathogenic association between gut microbiota and kidney diseases (the gut-kidney axis), covering CKD, IgA nephropathy, nephrolithiasis, hypertension, acute kidney injury, hemodialysis and peritoneal dialysis in clinic. Targeted interventions including probiotic, prebiotic and symbiotic measures are discussed for their potential of re-establishing symbiosis, and more effective strategies for the treatment of kidney diseases patients are suggested. The novel insights into the dysbiosis of the gut microbiota in kidney diseases are helpful to develop novel therapeutic strategies for preventing or attenuating kidney diseases and complications.}, } @article {pmid30217276, year = {2018}, author = {Rangel, SM and Paller, AS}, title = {Bacterial colonization, overgrowth, and superinfection in atopic dermatitis.}, journal = {Clinics in dermatology}, volume = {36}, number = {5}, pages = {641-647}, doi = {10.1016/j.clindermatol.2018.05.005}, pmid = {30217276}, issn = {1879-1131}, mesh = {Anti-Bacterial Agents/therapeutic use ; Dermatitis, Atopic/*immunology/microbiology ; Disease Susceptibility/immunology ; Humans ; *Immunity, Innate ; Microbiota ; Skin/microbiology ; Staphylococcal Skin Infections/drug therapy/*immunology ; *Staphylococcus aureus ; Superinfection/*immunology ; Symbiosis ; }, abstract = {Staphylococcus aureus infection is a major burden for individuals with moderate-to-severe atopic dermatitis and a known inducer of disease exacerbation. This increased susceptibility to staphylococcal infections has been attributed to abnormalities in the innate immune system of atopic dermatitis (AD) skin, including deficits in barrier proteins and lipids, and a muted response in generating antimicrobial peptides, all of which is further impaired by the activation of Th2 and Th22 immune pathways, which characterizes AD. Skewing of the immune response with a reduced Th1:Th2 ratio and increased adherence of bacteria to AD skin are also thought to contribute. Bacterial species diversity is reduced with flares, concomitant with increases in S. aureus and sometimes clinical infection, which has recently been linked to the finding that commensal bacteria produce anti-S. aureus factors that contribute to the endogenous response. S. aureus produces several virulence factors affecting the skin barrier and immune system, including promoting Th2 cell activation. Best practices for the management of staphylococcal infections include systemic antibiotics, initiation of antiseptics (particularly dilute bleach baths), and sometimes periodic intranasal mupirocin. Newer evidence suggests the possibility that treatment of the skin with commensal bacterial species could also reduce S. aureus growth and increase diversity.}, } @article {pmid30541614, year = {2018}, author = {Kanté, ST and Melachio, T and Ofon, E and Njiokou, F and Simo, G}, title = {Detection of Wolbachia and different trypanosome species in Glossina palpalis palpalis populations from three sleeping sickness foci of southern Cameroon.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {630}, doi = {10.1186/s13071-018-3229-2}, pmid = {30541614}, issn = {1756-3305}, mesh = {Animals ; Cameroon/epidemiology ; Female ; Humans ; Male ; Polymorphism, Genetic ; Symbiosis ; Trypanosoma/classification/genetics/*isolation & purification/physiology ; Trypanosomiasis, African/epidemiology/*parasitology/transmission ; Tsetse Flies/*microbiology/*parasitology/physiology ; Wolbachia/classification/genetics/*isolation & purification/physiology ; }, abstract = {BACKGROUND: African trypanosomiases are caused by trypanosomes that are cyclically transmitted by tsetse. Investigations aiming to generate knowledge on the bacterial fauna of tsetse have revealed distinct symbiotic microorganisms. Furthermore, studies addressing the tripartite association between trypanosomes-tsetse-symbionts relationship have so far been contradictory. Most studies included Sodalis glossinudius and, consequently, the association involving Wolbachia is poorly understood. Understanding the vectorial competence of tsetse requires decrypting these tripartite associations. In this study, we identified Wolbachia and trypanosomes in Glossina palpalis palpalis from three human African trypanosomiasis (HAT) foci in southern Cameroon.

METHODS: Tsetse flies were captured with pyramidal traps in the Bipindi, Campo and Fontem HAT foci. After morphological identification, DNA was extracted from whole tsetse flies and Wolbachia and trypanosomes were identified by PCR using different trypanosome-specific primers and two Wolbachia-specific primers (Wolbachia surface protein and 16S rRNA genes). Statistical analyses were performed to compare the trypanosome and Wolbachia infection rates between villages and different foci and to look for an association between these microorganisms.

RESULTS: From a total of 2122 tsetse flies, 790 G. p. palpalis were analyzed. About 25.32% of flies hosted Wolbachia and 31.84% of non-teneral flies were infected by at least one trypanosome species. There was no significant difference between the global Wolbachia prevalence revealed by the two markers while some differences were observed between HAT foci. From 248 G. p. palpalis with trypanosome infections, 62.90% were with T. vivax, 34.68% with T. congolense forest, 16.13% with T. brucei (s.l.) and 2.42% with T. congolense savannah. Of all trypanosome-infected flies, 29.84% hosted Wolbachia and no association was observed between Wolbachia and trypanosome co-infections.

CONCLUSIONS: This study revealed differences in the prevalence of Wolbachia and trypanosomes in G. p. palpalis according to HAT foci. The use of only one marker has underestimated the prevalence of Wolbachia, thus more markers in subsequent studies may improve its detection. The presence of Wolbachia seems to have no impact on the establishment of trypanosomes in G. p. palpalis. The tripartite association between tsetse, Wolbachia and trypanosomes varies according to studied areas. Studies aiming to evaluate the genetic polymorphism of Wolbachia and its density in tsetse flies could help to better understand this association.}, } @article {pmid30463128, year = {2019}, author = {Fontúrbel, FE and Bruford, MW and Salazar, DA and Cortés-Miranda, J and Vega-Retter, C}, title = {The hidden costs of living in a transformed habitat: Ecological and evolutionary consequences in a tripartite mutualistic system with a keystone mistletoe.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 2}, pages = {2740-2748}, doi = {10.1016/j.scitotenv.2018.10.125}, pmid = {30463128}, issn = {1879-1026}, mesh = {Animals ; Biodiversity ; Birds/*physiology ; *Ecosystem ; *Environmental Monitoring ; Marsupialia/*physiology ; Mistletoe/*physiology ; Seed Dispersal ; *Symbiosis ; }, abstract = {Land use change is one of the most important anthropogenic drivers of biodiversity loss. Nevertheless, the ecological and evolutionary consequences of habitat transformation remain less understood than those from habitat fragmentation. Transformed habitats are structurally simpler, altering species composition and their ecological interactions, potentially compromising gene flow and genetic diversity. We focused on a tripartite mutualistic system composed of a mistletoe (Tristerix corymbosus), its pollinator (Sephanoides sephaniodes) and its seed disperser (Dromiciops gliroides) to assess changes in their ecological and evolutionary dynamics as a result of habitat transformation. We used eight microsatellite markers to compare genetic diversity, relatedness and gene flow among five mistletoe groups inhabiting native and transformed habitats (abandoned Eucalyptus globulus plantations). We found that these groups were genetically structured, with greater allelic richness and genetic diversity in their native habitat. Also, we found higher relatedness among mistletoe individuals in transformed habitats, which varied as a function of the geographic distance among plants, probably as a result of larger resource availability, which influenced mutualist visitation rates. We did not find differences in the current migration patterns, which suggests that Tristerix corymbosus may be resilient to habitat transformation. Yet, its highly specialized interactions along with changes in its spatial configuration depict a more complex scenario, which probably impose a cost in terms of lower genetic diversity and increased relatedness that might compromise its long-term viability.}, } @article {pmid30061657, year = {2018}, author = {Butler, S and O'Dwyer, JP}, title = {Stability criteria for complex microbial communities.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2970}, pmid = {30061657}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology ; *Ecology ; *Microbiota ; Models, Biological ; Software ; *Symbiosis ; }, abstract = {Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated through the mechanism of crossfeeding. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, positive equilibria remain stable whenever mutualistic interactions are either sufficiently weak, or when all pairs of taxa reciprocate each other's assistance.}, } @article {pmid29949639, year = {2018}, author = {Melati, BG and Leal, LC}, title = {Aggressive bodyguards are not always the best: Preferential interaction with more aggressive ant species reduces reproductive success of plant bearing extrafloral nectaries.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0199764}, pmid = {29949639}, issn = {1932-6203}, mesh = {Aggression ; Animals ; Ants/*physiology ; Flowers/physiology ; Fruit/physiology ; Plant Nectar/*physiology ; Reproduction ; Seeds/physiology ; *Symbiosis ; Turnera/*physiology ; }, abstract = {Variation in partner species and frequency of interaction between species pairs are potential drivers of the net outcome of generalized mutualisms. In ant-plant mutualisms, the quality of defence provided by ants is related to ant aggressiveness. Hence, we hypothesize that the performance of plants bearing extrafloral nectaries will be higher when they interact more frequently with more aggressive ant species. We estimated ant aggressiveness in the field by observing their behaviour towards soil baits. Afterwards, we observed the frequency with which individuals from these ant species visited plants through an entire reproductive cycle. We measured the production and persistence of plants reproductive structures through this period and the total seed production. Increasing in the interaction frequency with highly aggressive ants reduced the number of floral buds and seeds produced. Increased visitation frequency by less aggressive ants increased the number of floral buds and seeds per branch. The inverse relationship between ant aggressiveness and seed production may be influenced by the costs imposed by different mutualistic partners. Thus, frequent interaction with highly aggressive ants may lead to a higher accumulation of costs through time, resulting in a negative net outcome for the plants. Our results bring new evidence highlighting the importance to incorporate temporal aspects in the study of mutualistic interactions. We suggests that the quality of mutualistic partners must be understood as a function of its per-interaction benefit and their cumulative costs to their partner over time, what puts in check our current classification regarding partner quality in mutualistic systems.}, } @article {pmid29436502, year = {2018}, author = {Hörandl, E and Speijer, D}, title = {How oxygen gave rise to eukaryotic sex.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1872}, pages = {}, pmid = {29436502}, issn = {1471-2954}, mesh = {*Biological Evolution ; Eukaryota/*physiology ; Oxygen/*metabolism ; Reactive Oxygen Species/metabolism ; *Sex ; Symbiosis/physiology ; }, abstract = {How did full meiotic eukaryotic sex evolve and what was the immediate advantage allowing it to develop? We propose that the crucial determinant can be found in internal reactive oxygen species (ROS) formation at the start of eukaryotic evolution approximately 2 × 109 years ago. The large amount of ROS coming from a bacterial endosymbiont gave rise to DNA damage and vast increases in host genome mutation rates. Eukaryogenesis and chromosome evolution represent adaptations to oxidative stress. The host, an archaeon, most probably already had repair mechanisms based on DNA pairing and recombination, and possibly some kind of primitive cell fusion mechanism. The detrimental effects of internal ROS formation on host genome integrity set the stage allowing evolution of meiotic sex from these humble beginnings. Basic meiotic mechanisms thus probably evolved in response to endogenous ROS production by the 'pre-mitochondrion'. This alternative to mitosis is crucial under novel, ROS-producing stress situations, like extensive motility or phagotrophy in heterotrophs and endosymbiontic photosynthesis in autotrophs. In multicellular eukaryotes with a germline-soma differentiation, meiotic sex with diploid-haploid cycles improved efficient purging of deleterious mutations. Constant pressure of endogenous ROS explains the ubiquitous maintenance of meiotic sex in practically all eukaryotic kingdoms. Here, we discuss the relevant observations underpinning this model.}, } @article {pmid29975783, year = {2018}, author = {Ezugwu, AE and Adeleke, OJ and Viriri, S}, title = {Symbiotic organisms search algorithm for the unrelated parallel machines scheduling with sequence-dependent setup times.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200030}, doi = {10.1371/journal.pone.0200030}, pmid = {29975783}, issn = {1932-6203}, mesh = {*Algorithms ; Heuristics ; Personnel Staffing and Scheduling ; *Symbiosis ; Time Factors ; }, abstract = {This paper addresses the problem of makespan minimization on unrelated parallel machines with sequence dependent setup times. The symbiotic organisms search (SOS) algorithm is a new and popular global optimization technique that has received wide acceptance in recent years from researchers in continuous and discrete optimization domains. An improved SOS algorithm is developed to solve the parallel machine scheduling problem. Since the standard SOS algorithm was originally developed to solve continuous optimization problems, a new solution representation and decoding procedure is designed to make the SOS algorithm suitable for the unrelated parallel machine scheduling problem (UPMSP). Similarly, to enhance the solution quality of the SOS algorithm, an iterated local search strategy based on combining variable numbers of insertion and swap moves is incorporated into the SOS algorithm. More so, to further improve the SOS optimization speed and performance, the longest processing time first (LPT) rule is used to design a machine assignment heuristic that assigns processing machines to jobs based on the machine dynamic load-balancing mechanism. Subsequently, the machine assignment scheme is incorporated into SOS algorithms and used to solve the UPMSP. The performances of the proposed methods are evaluated by comparing their solutions with other existing techniques from the literature. A number of statistical tests were also conducted to determine the variations in performance for each of the techniques. The experimental results showed that the SOS with LPT (SOS-LPT) heuristic has the best performance compared to other tested method, which is closely followed by SOS algorithm, indicating that the two proposed algorithms' solution approaches are reasonable and effective for solving large-scale UPMSPs.}, } @article {pmid30597068, year = {2018}, author = {Fukudome, M and Watanabe, E and Osuki, KI and Imaizumi, R and Aoki, T and Becana, M and Uchiumi, T}, title = {Stably-Transformed Lotus japonicus Plants Overexpressing Phytoglobin LjGlb1-1 Show Decreased Nitric Oxide Levels in Roots and Nodules as well as Delayed Nodule Senescence.}, journal = {Plant & cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcy245}, pmid = {30597068}, issn = {1471-9053}, abstract = {The class 1 phytoglobin, LjGlb1-1, is expressed in various tissues of the model legume Lotus japonicus, where it may play multiple functions by interacting with nitric oxide (NO). One of such functions is the onset of a proper symbiosis with Mesorhizobium loti resulting in the formation of actively N2-fixing nodules. Stable overexpression lines (Ox1 and Ox2) of LjGlb1-1 were generated and phenotyped. Both Ox lines showed reduced NO levels in roots and enhanced nitrogenase activity in mature and senescent nodules relative to the wild-type (WT). Physiological and cytological observations indicated that overexpression of LjGlb1-1 delayed nodule senescence. The application to WT nodules of the NO donor S-nitroso-N-acetyl-D,L-penicillamine (SNAP) or the phytohormones abscisic acid (ABA) and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) repressed nitrogenase activity, induced the expression of three senescence-associated genes, and caused cytological changes evidencing nodule senescence. These effects were almost completely reverted by the NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide. Our results reveal that overexpression of LjGlb1-1 improves the activity of mature nodules and delays nodule senescence in the L. japonicus-M. loti symbiosis. These beneficial effects are probably mediated by the participation of LjGlb1-1 in controlling the concentration of NO that may be produced downstream in the phytohormone signaling pathway in nodules.}, } @article {pmid30596477, year = {2018}, author = {Shu, L and Brock, DA and Geist, KS and Miller, JW and Queller, DC and Strassmann, JE and DiSalvo, S}, title = {Symbiont location, host fitness, and possible coadaptation in a symbiosis between social amoebae and bacteria.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, doi = {10.7554/eLife.42660}, pmid = {30596477}, issn = {2050-084X}, support = {DEB1146375//National Science Foundation/ ; 43667//John Templeton Foundation/ ; IOS1256416//National Science Foundation/ ; IOS1656756//National Science Foundation/ ; }, abstract = {Recent symbioses, particularly facultative ones, are well suited for unravelling the evolutionary give and take between partners. Here we look at variation in natural isolates of the social amoeba Dictyostelium discoideum and their relationships with bacterial symbionts, Burkholderia hayleyella and Burkholderia agricolaris. Only about a third of field-collected amoebae carry a symbiont. We cured and cross-infected amoebae hosts with different symbiont association histories and then compared host responses to each symbiont type. Before curing, field-collected clones did not vary significantly in overall fitness, but infected hosts produced morphologically different multicellular structures. After curing and reinfecting, host fitness declined. However, natural B. hayleyella hosts suffered fewer fitness costs when reinfected with B. hayleyella, indicating that they have evolved mechanisms to tolerate their symbiont. Our work suggests that amoebae hosts have evolved mechanisms to tolerate specific acquired symbionts; exploring host-symbiont relationships that vary within species may provide further insights into disease dynamics.}, } @article {pmid30528004, year = {2019}, author = {Sun, L and Zuo, W and Tian, Y and Zhang, J and Liu, J and Sun, N and Li, J}, title = {Performance and microbial community analysis of an algal-activated sludge symbiotic system: Effect of activated sludge concentration.}, journal = {Journal of environmental sciences (China)}, volume = {76}, number = {}, pages = {121-132}, doi = {10.1016/j.jes.2018.04.010}, pmid = {30528004}, issn = {1001-0742}, mesh = {Bacteria/cytology/*metabolism ; Bioreactors/*microbiology ; Extracellular Polymeric Substance Matrix/metabolism ; *Microbiota ; Nitrogen/isolation & purification/metabolism ; Phosphorus/isolation & purification/metabolism ; Sewage/chemistry/*microbiology ; *Symbiosis ; }, abstract = {It was focused on the effect of different sludge concentrations on the performances of an algal-activated sludge symbiotic system in terms of wastewater treatment, algal-activated sludge characteristics and community structure. The results showed that the highest nutrient removal efficiencies were obtained in the reactor R2 with soluble chemical oxygen demand (sCOD), ammonia nitrogen (NH4+-N) and phosphate (PO43- -P) removal efficiencies of (90.6±2.3)%, (97.69±2.6)% and (83.81±2.3)%, respectively. Further investigation exhibited that sludge concentration has a great effect on the dissolved oxygen (DO) concentration, the pH, the growth of algae and the extracellular polymeric substance (EPS) production, which resulted in influencing the settleability and the performance of symbiotic system. The denaturing gradient gel electrophoresis (DGGE) analysis demonstrated that the sludge concentration had a selective power for particular members of algae. Meantime, the stimulated algal population would selectively excite the members of bacteria benefited for the formation of algal-bacterial consortia. The variation of microbial compositions, which was influenced by the different sludge concentrations, might be ultimately responsible for the different treatment performances.}, } @article {pmid30478343, year = {2018}, author = {Regan, T and Barnett, MW and Laetsch, DR and Bush, SJ and Wragg, D and Budge, GE and Highet, F and Dainat, B and de Miranda, JR and Watson, M and Blaxter, M and Freeman, TC}, title = {Characterisation of the British honey bee metagenome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4995}, pmid = {30478343}, issn = {2041-1723}, mesh = {Animals ; Bees/*genetics/microbiology ; Contig Mapping ; Genetic Variation ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; United Kingdom ; }, abstract = {The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.}, } @article {pmid30337144, year = {2019}, author = {Váczi, P and Gauslaa, Y and Solhaug, KA}, title = {Reprint of Efficient fungal UV-screening provides a remarkably high UV-B tolerance of photosystem II in lichen photobionts.}, journal = {Plant physiology and biochemistry : PPB}, volume = {134}, number = {}, pages = {123-128}, doi = {10.1016/j.plaphy.2018.09.030}, pmid = {30337144}, issn = {1873-2690}, mesh = {Adaptation, Physiological/*radiation effects ; Ascomycota/*physiology ; Fluorometry ; Lichens/*radiation effects ; Photosystem II Protein Complex/*metabolism ; Symbiosis ; *Ultraviolet Rays ; }, abstract = {Lichen photobionts in situ have an extremely UV-B tolerant photosystem II efficiency (Fv/Fm). We have quantified the UV-B-screening offered by the mycobiont and the photobiont separately. The foliose lichens Nephroma arcticum and Umbilicaria spodochroa with 1: intact or 2: removed cortices were exposed to 0.7 Wm-2 UV-BBE for 4 h. Intact thalli experienced no reduction in Fv/Fm, whereas cortex removal lowered Fv/Fm in exposed photobiont layers by 22% for U. spodochroa and by 14% for N. arcticum. We also gave this UV-B dose to algal cultures of Coccomyxa and Trebouxia, the photobiont genera of N. arcticum and U. spodochroa, respectively. UV-B caused a 56% reduction in Fv/Fm for Coccomyxa, and as much as 98% in Trebouxia. The fluorescence excitation ratio (FER) technique comparing the fluorescence from UV-B or UV-A-excitation light with blue green excitation light using a Xe-PAM fluorometer showed that these photobiont genera did not screen any UV-B or UV-A The FER technique with a Multiplex fluorometer estimated the UV-A screening of isolated algae to be 13-16%, whereas intact lichens screened 92-95% of the UV-A. In conclusion, the cortex of N. arcticum and U. spodochroa transmitted no UV-B and little UV-A to the photobiont layer beneath. Thereby, the upper lichen cortex forms an efficient fungal solar radiation screen providing a high UV-B tolerance for studied photobionts in situ. By contrast, isolated photobionts have no UV-B screening and thus depend on their fungal partners in nature.}, } @article {pmid30266174, year = {2018}, author = {Wintermantel, WM}, title = {Integration of Omics Approaches toward Understanding Whitefly Transmission of Viruses.}, journal = {Advances in virus research}, volume = {102}, number = {}, pages = {199-223}, doi = {10.1016/bs.aivir.2018.06.005}, pmid = {30266174}, issn = {1557-8399}, mesh = {Animals ; Bacteria/growth & development/metabolism ; Begomovirus/genetics/metabolism ; Biological Coevolution ; Crinivirus/genetics/metabolism ; Gene Expression Regulation ; Hemiptera/*virology ; Host-Pathogen Interactions/*genetics ; Insect Control/methods ; Insect Proteins/classification/*genetics/metabolism ; Insect Vectors/*virology ; Metabolomics/*methods ; Plant Diseases/virology ; Plants/*virology ; Symbiosis/genetics ; Transcriptome ; }, abstract = {Viruses transmitted by whiteflies are predominantly classified as having either persistent circulative or semipersistent transmission, and the majority of studies have addressed transmission of viruses in the genera Begomovirus (family Geminiviridae) and Crinivirus (family Closteroviridae), respectively. Early studies on vector transmission primarily addressed individual aspects of transmission; however, with the breadth of new technology now available, an increasingly greater number of studies involve coordinated research that is beginning to assemble a more complete picture of how whiteflies and viruses have coevolved to facilitate transmission. In particular the integration of gene expression and metabolomic studies into broader research topics is providing knowledge of changes within the whitefly vector in response to the presence of viruses that would have been impossible to identify previously. Examples include comparative studies on the response of Bemisia tabaci to begomovirus and crinivirus infection of common host plants, evolution of whitefly endosymbiont relationships, and opportunities to evaluate responses to specific transmission-related events. Integration of metabolomics, as well as the application of electrical penetration graphing, can lead to an ability to monitor the changes that occur in vector insects associated with specific aspects of virus transmission. Through gaining more complete knowledge of the mechanisms behind whitefly transmission of viruses new control strategies will undoubtedly emerge for control of whiteflies and the viruses they transmit.}, } @article {pmid30266173, year = {2018}, author = {Carr, JP and Donnelly, R and Tungadi, T and Murphy, AM and Jiang, S and Bravo-Cazar, A and Yoon, JY and Cunniffe, NJ and Glover, BJ and Gilligan, CA}, title = {Viral Manipulation of Plant Stress Responses and Host Interactions With Insects.}, journal = {Advances in virus research}, volume = {102}, number = {}, pages = {177-197}, doi = {10.1016/bs.aivir.2018.06.004}, pmid = {30266173}, issn = {1557-8399}, mesh = {Adaptation, Physiological/genetics ; Animals ; Aphids/*virology ; Disease Resistance ; Gene Expression Regulation ; Hemiptera/virology ; Host-Pathogen Interactions/*genetics ; Insect Vectors/*virology ; Plant Diseases/virology ; Plant Viruses/*genetics/metabolism ; Plants/*virology ; Signal Transduction ; Stress, Physiological ; Symbiosis/*genetics ; Viral Proteins/genetics/metabolism ; }, abstract = {Do the alterations in plant defensive signaling and metabolism that occur in susceptible hosts following virus infection serve any purpose beyond directly aiding viruses to replicate and spread? Or indeed, are these modifications to host phenotype purely incidental consequences of virus infection? A growing body of data, in particular from studies of viruses vectored by whiteflies and aphids, indicates that viruses influence the efficiency of their own transmission by insect vectors and facilitate mutualistic relationships between viruses and their insect vectors. Furthermore, it appears that viruses may be able to increase the opportunity for transmission in the long term by providing reward to the host plants that they infect. This may be conditional, for example, by aiding host survival under conditions of drought or cold or, more surprisingly, by helping plants attract beneficial insects such as pollinators. In this chapter, we cover three main areas. First, we describe the molecular-level interactions governing viral manipulation of host plant biology. Second, we review evidence that virus-induced changes in plant phenotype enhance virus transmission. Finally, we discuss how direct and indirect manipulation of insects and plants might impact on the evolution of viruses and their hosts.}, } @article {pmid30101804, year = {2018}, author = {Pastore, M and Sforza, E}, title = {Exploiting symbiotic interactions between Chlorella protothecoides and Brevundimonas diminuta for an efficient single-step urban wastewater treatment.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {78}, number = {1-2}, pages = {216-224}, doi = {10.2166/wst.2018.155}, pmid = {30101804}, issn = {0273-1223}, mesh = {Biological Oxygen Demand Analysis ; Caulobacteraceae/*metabolism ; Chlorella/*metabolism ; Microalgae/metabolism ; Nitrogen/analysis/isolation & purification/metabolism ; Phosphorus/analysis/isolation & purification/metabolism ; Symbiosis/*physiology ; Waste Water/*chemistry ; Water Purification/*methods ; }, abstract = {The application of microalgal bacteria consortia to the treatment of wastewater is receiving increasing attention, meeting the demand for new green and efficient technologies for water remediation. The specificity of the consortium, however, may strongly affect the performance of the treatment. In fact, even though a general exploitation of the O2/CO2 exchange between microalgae and bacteria is effective, some specific interactions may increase the pollutant removal. With this aim, the co-cultivation of Chlorella protothecoides and Brevundimonas diminuta was tested, with particular attention to the removal capability of nitrogen, phosphorus and chemical oxygen demand (COD) from wastewater. Batch experiments were carried out both for the consortium and, separately, for the bacteria and microalgae alone, in order to compare their performances. B. diminuta showed a remarkable capability for removing organic substances and transforming organic nitrogen to ammonium. C. protothecoides efficiently removed nitrogen and phosphorus. As the specific growth rates of the two organisms are different, the co-cultivation was also carried out also in a continuous system, and the effect of hydraulic retention time (HRT) on the steady-state biomass concentration and nutrient removal efficiency was verified. Residence time was found as the main operating variable for obtaining a significant reduction of pollutants from wastewater.}, } @article {pmid29615108, year = {2018}, author = {Cornuault, JK and Petit, MA and Mariadassou, M and Benevides, L and Moncaut, E and Langella, P and Sokol, H and De Paepe, M}, title = {Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {65}, pmid = {29615108}, issn = {2049-2618}, mesh = {Animals ; Bacteriophages/*physiology/ultrastructure ; Biodiversity ; Colitis/etiology ; DNA Damage ; Dysbiosis ; Faecalibacterium prausnitzii/*virology ; *Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Inflammatory Bowel Diseases/etiology ; Metagenome ; Metagenomics/methods ; Mice ; Retroelements ; Symbiosis ; }, abstract = {BACKGROUND: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases.

METHODS: We identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages.

RESULTS: We show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls.

CONCLUSION: Since IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.}, } @article {pmid29288462, year = {2018}, author = {Robledo, M and García-Tomsig, NI and Jiménez-Zurdo, JI}, title = {Primary Characterization of Small RNAs in Symbiotic Nitrogen-Fixing Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1734}, number = {}, pages = {277-295}, doi = {10.1007/978-1-4939-7604-1_22}, pmid = {29288462}, issn = {1940-6029}, mesh = {Gene Expression ; *Gene Expression Regulation, Bacterial ; Genes, Reporter ; Nitrogen-Fixing Bacteria/*genetics/*metabolism ; RNA, Bacterial ; RNA, Messenger/genetics ; RNA, Small Untranslated/*genetics ; Reproducibility of Results ; *Symbiosis ; }, abstract = {High-throughput transcriptome profiling (RNAseq) has uncovered large and heterogeneous populations of small noncoding RNA species (sRNAs) with potential regulatory roles in bacteria. A large fraction of sRNAs are differentially regulated and rely on protein-assisted antisense interactions to trans-encoded target mRNAs to fine-tune posttranscriptional reprogramming of gene expression in response to external cues. However, annotation and function of sRNAs are still largely overlooked in nonmodel bacteria with complex lifestyles. Here, we describe experimental protocols successfully applied for the accurate annotation, expression profiling and target mRNA identification of trans-acting sRNAs in the nitrogen-fixing α-rhizobium Sinorhizobium meliloti. The protocols presented here can be similarly applied for the characterization of trans-sRNAs in genetically tractable α-proteobacteria of agronomical or clinical relevance interacting with eukaryotic hosts.}, } @article {pmid30592861, year = {2017}, author = {Fisinin, VI and Egorov, IA and Laptev, GY and Lenkova, TN and Nikonov, IN and Ilyina, LA and Manukyan, VA and Grozina, AA and Egorova, TA and Novikova, NI and Yildyrym, EA}, title = {[Antibiotic-free poultry production based on innovative nutritional programs with the involvement of probiotics].}, journal = {Voprosy pitaniia}, volume = {86}, number = {6}, pages = {114-124}, doi = {10.24411/0042-8833-2017-00013}, pmid = {30592861}, issn = {0042-8833}, abstract = {EU banned antibiotic growth promoters (AGP) for farm animals and poultry since 2006 in relation to the problem of drug resistance. This requires alternative products for equally efficient prevention and treatment of certain alimentary poultry diseases. One of the most actual trends is the development of innovative nutritional strategies for poultry providing an effective symbiosis between the host and its intestinal microbiota. The study presented was aimed at the comparative evaluation of productivity, nutritive value of meat, and composition of intestinal microbial populations in broiler chicks fed different diets (corn - soybean meal, wheat - sunflower cake, barley - sunflower cake) supplemented with AGP or a probiotic (cellulolytic and lactic microorganisms). In three trials straight-run Cobb 500 broilers reared from 1 to 36 days of age were fed these diets supplemented with bacitracin from 1 to 29 days of age (control) or probiotic preparation from 1 to 36 days of age (70 birds per dietary treatment in each trial). There were no differences in live bodyweight and carcass yield between the treatments in all three trials. In the two trials with sunflower cake, protein content in breast meat was significantly higher by in birds fed probiotic in compare to birds fed AGP (by 10.0 and 6.8%, p<0.05), while fat content in thigh meat was lower by 12.0% (p<0.05) and 14.1% (p<0.01), respectively. Content of amino acids in meat did not differ. Vitamin content in the poultry meat of the experimental groups was significantly higher compared to control (p<0.001). The resulting concentrations of bacitracin in meat in control treatments (no more than 0.02 U/g) did not exceed local legislative limitations. The substitution of the probiotic for AGP beneficially affected the composition of bacterial populations in the duodenum and cecae determined using T-RFLP analysis. It was concluded that the supplementation of diets with probiotic allows to produce antibiotic-free broiler meat without detrimental effects on the productive performance.}, } @article {pmid30589877, year = {2018}, author = {Thürich, J and Meichsner, D and Furch, ACU and Pfalz, J and Krüger, T and Kniemeyer, O and Brakhage, A and Oelmüller, R}, title = {Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209658}, doi = {10.1371/journal.pone.0209658}, pmid = {30589877}, issn = {1932-6203}, abstract = {Plants interact with a wide variety of fungi in a mutualistic, parasitic or neutral way. The associations formed depend on the exchange of nutrients and signalling molecules between the partners. This includes a diverse set of protein classes involved in defence, nutrient uptake or establishing a symbiotic relationship. Here, we have analysed the secretomes of the mutualistic, root-endophytic fungus Piriformospora indica and Arabidopsis thaliana when cultivated alone or in a co-culture. More than one hundred proteins were identified as differentially secreted, including proteins associated with growth, development, abiotic and biotic stress response and mucilage. While some of the proteins have been associated before to be involved in plant-microbial interaction, other proteins are newly described in this context. One plant protein found in the co-culture is PLAT1 (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase). PLAT1 has not been associated with plant-fungal-interaction and is known to play a role in abiotic stress responses. In colonised roots PLAT1 shows an altered gene expression in a stage specific manner and plat1 knock-out plants are colonised stronger. It co-localises with Brassicaceae-specific endoplasmic reticulum bodies (ER-bodies) which are involved in the formation of the defence compound scopolin. We observed degraded ER-bodies in infected Arabidopsis roots and a change in the scopolin level in response to the presence of the fungus.}, } @article {pmid30588210, year = {2018}, author = {Swain Ewald, HA and Ewald, PW}, title = {Natural Selection, The Microbiome, and Public Health.}, journal = {The Yale journal of biology and medicine}, volume = {91}, number = {4}, pages = {445-455}, pmid = {30588210}, issn = {1551-4056}, abstract = {The microbiome is composed of hundreds of interacting species that have co-evolved with the host and alterations in microbiome composition have been associated with health and disease. Insights from evolutionary ecology may aid efforts to ameliorate microbiome-associated diseases. One step toward this goal involves recognition that the idea of commensalism has been applied too broadly to human/microbe symbioses. Commensalism is most accurately viewed on a symbiosis continuum as a dividing line that separates a spectrum of mutualisms of decreasing positive interdependence from parasitisms of increasing severity. Insights into the evolution of the gut microbial symbiosis continuum will help distinguish between human actions that will advance or hinder health. Theory and research indicate that a major benefit of mutualistic microbes will be protection against pathogens. Mismatches between current and ancestral diets may disfavor mutualists, resulting in microbiome effects on health problems, including obesity, diabetes, autism, and childhood allergy. Evolutionary theory indicates that mutualisms will be favored when symbionts depend on resources that are not used by the host. These resources, which are referred to as human-inaccessible microbiota-accessible carbohydrates (HIMACs), can be supplied naturally through diet. Public health interventions need to consider the position of gut microbes on the mutualist-parasite continuum and the specific associations between prebiotics, such as HIMACs, and the mutualists they support. Otherwise interventions may fail to restore the match between human adaptations, diet, and microbiome function and may thereby fail to improve health and even inadvertently promote illness.}, } @article {pmid30583741, year = {2018}, author = {Lebon, C and Benlali, A and Atyame, C and Mavingui, P and Tortosa, P}, title = {Construction of a genetic sexing strain for Aedes albopictus: a promising tool for the development of sterilizing insect control strategies targeting the tiger mosquito.}, journal = {Parasites & vectors}, volume = {11}, number = {Suppl 2}, pages = {658}, doi = {10.1186/s13071-018-3212-y}, pmid = {30583741}, issn = {1756-3305}, abstract = {BACKGROUND: Aedes albopictus is an invasive mosquito species of global medical concern as its distribution has recently expanded to Africa, the Americas and Europe. In the absence of prophylaxis protecting human populations from emerging arboviruses transmitted by this mosquito species, the most straightforward control measures rely on the suppression or manipulation of vector natural populations. A number of environmental-friendly methods using mass releases of sterilizing males are currently under development. However, these strategies are still lacking an efficient sexing method required for production of males at an industrial scale.

RESULTS: We present the first Genetic Sexing Strain (GSS) in Ae. albopictus, hereafter referred as Tikok, obtained by sex linkage of the rdl gene conferring dieldrin resistance. Hatch rate, larval survival and sex ratio were followed during twelve generations. The use of dieldrin at the third larval stage allowed selecting 98 % of males on average.

CONCLUSION: A good production rate of Tikok males makes this GSS suitable for any control method based on mass production of Ae. albopictus males. Despite limitations resulting from reduced egg hatch as well as the nature of the used insecticide, the construction of this GSS paves the way for industrial sex separation of Ae. albopictus.}, } @article {pmid30583535, year = {2018}, author = {Blaz, J and Barrera-Redondo, J and Vázquez-Rosas-Landa, M and Canedo-Téxon, A and Aguirre von Wobeser, E and Carrillo, D and Stouthamer, R and Eskalen, A and Villafán, E and Alonso-Sánchez, A and Lamelas, A and Ibarra-Juarez, LA and Pérez-Torres, CA and Ibarra-Laclette, E}, title = {Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes.}, journal = {Life (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/life9010002}, pmid = {30583535}, issn = {2075-1729}, support = {265677//Comisión Nacional Forestal (CONAFOR)/ ; 292399//Fondo Nacional de Desarrollo Científico y Tecnológico (FORDECYT)/ ; }, abstract = {Mutualistic symbiosis and eusociality have developed through gradual evolutionary processes at different times in specific lineages. Like some species of termites and ants, ambrosia beetles have independently evolved a mutualistic nutritional symbiosis with fungi, which has been associated with the evolution of complex social behaviors in some members of this group. We sequenced the transcriptomes of two ambrosia complexes (Euwallacea sp. near fornicatus⁻Fusarium euwallaceae and Xyleborus glabratus⁻Raffaelea lauricola) to find evolutionary signatures associated with mutualism and behavior evolution. We identified signatures of positive selection in genes related to nutrient homeostasis; regulation of gene expression; development and function of the nervous system, which may be involved in diet specialization; behavioral changes; and social evolution in this lineage. Finally, we found convergent changes in evolutionary rates of proteins across lineages with phylogenetically independent origins of sociality and mutualism, suggesting a constrained evolution of conserved genes in social species, and an evolutionary rate acceleration related to changes in selective pressures in mutualistic lineages.}, } @article {pmid30247121, year = {2018}, author = {Bünger, W and Grönemeyer, JL and Sarkar, A and Reinhold-Hurek, B}, title = {Bradyrhizobium ripae sp. nov., a nitrogen-fixing symbiont isolated from nodules of wild legumes in Namibia.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {12}, pages = {3688-3695}, doi = {10.1099/ijsem.0.002955}, pmid = {30247121}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Bradyrhizobium/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Intergenic/genetics ; Fabaceae/*microbiology ; Genes, Bacterial ; Multilocus Sequence Typing ; Namibia ; *Nitrogen Fixation ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Root-nodule bacteria were isolated from wild legumes growing in the Kavango region, Namibia. Using a polyphasic approach, four strains belonging to the genus Bradyrhizobium (WR4T, WR87, T10 and T12) were further characterized to clarify the taxonomic status of this group. On the basis of 16S rRNA gene sequences, the four strains showed highest similarity to Bradyrhizobium elkanii USDA 76T (99.9 %), Bradyrhizobium pachyrhizi PAC48T (identical) and to Bradyrhizobiumbrasilense UFLA03-321T (identical). Multilocus sequence analysis of concatenated glnII-recA-gyrB-dnaK-rpoB sequences and comparison of the intergenic transcribed spacer (ITS) sequences confirmed that the novel group belongs to a distinct lineage of the genus Bradyrhizobium, with <96.7 % (MLSA) and 97.25 % (ITS) nucleotide identity with B. elkanii USDA 76T. Results from the sequence-based analysis were validated by DNA-DNA hybridization experiments and suggested a novel species. Several phenotypic features including carbon compound utilization and growth characteristics supported the phylogenetic data, thus it is concluded that the strains represent a novel species, for which the name Bradyrhizobium ripae sp. nov. is proposed, with type strain WR4T [LMG 30283, DSM 105795, NTCCM 0019 (Windhoek)].}, } @article {pmid29355408, year = {2018}, author = {Burne, RA}, title = {Getting to Know "The Known Unknowns": Heterogeneity in the Oral Microbiome.}, journal = {Advances in dental research}, volume = {29}, number = {1}, pages = {66-70}, pmid = {29355408}, issn = {1544-0737}, support = {R01 DE013239/DE/NIDCR NIH HHS/United States ; R01 DE025832/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Physiological Phenomena ; Dental Caries/*microbiology/*prevention & control ; Dysbiosis/physiopathology ; Humans ; Metabolomics ; Microbiota/*physiology ; Mouth/*microbiology ; *Oral Health ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Symbiosis/physiology ; }, abstract = {Technological advances in DNA sequencing have provided unprecedented insights into the composition of the oral microbiome in health and disease, and RNA-sequencing and metabolomics-related technologies are beginning to yield information on the activities of these organisms. Importantly, progress in this area has brought the scientific community closer to an understanding of what constitutes a health-associated microbiome and is supporting the notion that the microbiota in healthy sites assumes an active role in promoting health and suppressing the acquisition, persistence, and activities of overt and opportunistic pathogens. It is also becoming clear that a significant impediment to developing a conclusive body of evidence that defines a healthy microbiome and the mechanisms by which beneficial bacteria promote health is that an inherent characteristic of the most abundant members of the oral flora, those that potentially play the greatest roles in health and disease, is intraspecies genomic diversity. In particular, individual isolates of abundant commensal and pathogenic streptococci show tremendous variability in gene content, and this variability manifests in tremendous phenotypic heterogeneity. Analysis of the consequences of this diversity has been complicated by the exquisite sensitivity these bacteria have evolved to environmental inputs, inducing rapid and substantial fluctuations in behaviors, and often only within subpopulations of the organisms. Thus, the conditions under which the oral microbiota is studied can produce widely different results within and between species. Fortunately, continually diminishing costs and ongoing refinements in sequencing and metabolomics are making it practical to study the oral microbiome at a level that will create a sufficiently robust understanding of the functions of individual organisms and reveal the complex interrelationships of these microbes ("the known unknowns") in a way that researchers will be able to engage in the rational design of reliable and economical risk assessments and preventive therapies.}, } @article {pmid29187569, year = {2018}, author = {Reid, D and Liu, H and Kelly, S and Kawaharada, Y and Mun, T and Andersen, SU and Desbrosses, G and Stougaard, J}, title = {Dynamics of Ethylene Production in Response to Compatible Nod Factor.}, journal = {Plant physiology}, volume = {176}, number = {2}, pages = {1764-1772}, pmid = {29187569}, issn = {1532-2548}, mesh = {Ethylenes/*analysis/metabolism ; Lotus/microbiology/*physiology ; Mesorhizobium/*physiology ; Mutation ; *Nitrogen Fixation ; Plant Growth Regulators/*analysis/metabolism ; Plant Proteins/genetics/metabolism ; Rhizobium/physiology ; Seedlings/microbiology/physiology ; *Signal Transduction ; Symbiosis ; Transcription Factors/genetics/metabolism ; }, abstract = {Establishment of symbiotic nitrogen-fixation in legumes is regulated by the plant hormone ethylene, but it has remained unclear whether and how its biosynthesis is regulated by the symbiotic pathway. We established a sensitive ethylene detection system for Lotus japonicus and found that ethylene production increased as early as 6 hours after inoculation with Mesorhizobium loti This ethylene response was dependent on Nod factor production by compatible rhizobia. Analyses of nodulation mutants showed that perception of Nod factor was required for ethylene emission, while downstream transcription factors including CYCLOPS, NIN, and ERN1 were not required for this response. Activation of the nodulation signaling pathway in spontaneously nodulating mutants was also sufficient to elevate ethylene production. Ethylene signaling is controlled by EIN2, which is duplicated in L. japonicus We obtained a L. japonicus Ljein2a Ljein2b double mutant that exhibits complete ethylene insensitivity and confirms that these two genes act redundantly in ethylene signaling. Consistent with this redundancy, both LjEin2a and LjEin2b are required for negative regulation of nodulation and Ljein2a Ljein2b double mutants are hypernodulating and hyperinfected. We also identified an unexpected role for ethylene in the onset of nitrogen fixation, with the Ljein2a Ljein2b double mutant showing severely reduced nitrogen fixation. These results demonstrate that ethylene production is an early and sustained nodulation response that acts at multiple stages to regulate infection, nodule organogenesis, and nitrogen fixation in L. japonicus.}, } @article {pmid30583042, year = {2018}, author = {Elias-Costa, AJ and Confalonieri, VA and Lanteri, AA and Rodriguero, MS}, title = {Game of Clones: Is Wolbachia inducing speciation in a weevil with a mixed reproductive mode?.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ympev.2018.12.027}, pmid = {30583042}, issn = {1095-9513}, abstract = {Parthenogenesis is widely distributed in Metazoa but it is especially frequent in weevils (Coleoptera, Curculionidae) with one fifth of all known cases. Previous studies have shown that in the tribe Naupactini parthenogenetic reproduction most likely originated with an infection of the endoparasitic bacterium Wolbachia pipientis. In particular, Pantomorus postfasciatus possess a mixed reproductive mode: some populations have males while in others they are absent, and females produce clones by thelytoky. To better understand this scenario, we studied the population structure and infection status in 64 individuals of P. postfasciatus from Argentina and Brazil. We sequenced two mitochondrial (COI and COII) and one nuclear (ITS-1) fragments and obtained two very divergent haplogroups, one corresponding to the sexual populations uninfected with Wolbachia, and another conforming a monophyletic parthenogenetic (or presumptively parthenogenetic) and infected clade. Each of these haplogroups was identified as an independently evolutionary unit by all species delimitation analyses accomplished: multilocus *BEAST and BP&P, and single locus GMYC and K/θ rule. Additionally, present evidence suggests that Wolbachia infection occurred at least twice in all-female populations of P. postfasciatus with two different bacterial strains. Speciation mediated by Wolbachia is a recently described phenomenon and the case of P. postfasciatus is the first known case in a diplo-diploid insect. A model that describes how thelytoky-inducing phenotypes of Wolbachia could generate new lineages is discussed.}, } @article {pmid30581847, year = {2018}, author = {Burlaka, AP and Ganusevich, II and Vovk, AV and Burlaka, AA and Gafurov, MR and Lukin, SN}, title = {Colorectal Cancer and Mitochondrial Dysfunctions of the Adjunct Adipose Tissues: A Case Study.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {2169036}, doi = {10.1155/2018/2169036}, pmid = {30581847}, issn = {2314-6141}, abstract = {Excess body weight has been causally linked to an increased risk of different cancer types, including colorectal cancer (CRC) but the mechanisms underlying this association are practically unknown. We investigate redox state-superoxide (SO) generation rate, activity of complex I in electron transport chain (ETC) of mitochondria and of dinitrosyl iron complexes by electron paramagnetic resonance; activity of matrix metalloproteinase (gelatinase) MMP-2 and MMP-9 by gel zymography of adipose tissues (AT) from 46 patients (64.0 ± 1.6 y.o.) with CRC (II-III stages, pT2-3N0-2M0) in the AT adjacent to tumor (ATAT) and at a distance of 3 cm from the tumor (ATD) to follow the connection of the AT redox state with some of the tumor microenvironment indicators. We have incubated the AT species with the tumor necrosis factor α (TNF-α) to follow its influence on the measured values. As a control, normal AT (NAT) obtained during the liposuction is used. Tumor-induced changes in mitochondrial ETC of ATAT, particularly for Complex I, lead to the enhanced SO generation and consequent oxidative modifications of DNA in ATAT (up to 6.1 times higher than that in NAT and 3.7 times higher than that in ATD, p < 0.05). Gelatinase activity in ATAT is significantly higher than in ATD. A considerable effect of TNF-α on ATAT and ATD (but not on NAT, i.e., only on the tissues where the reprogramming of metabolism has already occurred under the influence of tumor) manifested in increase of cellular hypoxia, gelatinase activity, and SO generation rate is observed. The results can be used for better understanding the mechanism(s) of metabolic symbiosis of tumor and AT as well as serving as a basis for new therapeutic approaches.}, } @article {pmid30420495, year = {2018}, author = {Farrell, JM and Brown, SP}, title = {Evolution of bacterial trade in a two-species community.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {47}, pages = {11874-11875}, pmid = {30420495}, issn = {1091-6490}, mesh = {Bacteria ; *Biological Evolution ; *Symbiosis ; }, } @article {pmid29704246, year = {2019}, author = {Hennion, N and Durand, M and Vriet, C and Doidy, J and Maurousset, L and Lemoine, R and Pourtau, N}, title = {Sugars en route to the roots. Transport, metabolism and storage within plant roots and towards microorganisms of the rhizosphere.}, journal = {Physiologia plantarum}, volume = {165}, number = {1}, pages = {44-57}, doi = {10.1111/ppl.12751}, pmid = {29704246}, issn = {1399-3054}, support = {//University of Poitiers/ ; //The Centre National de la Recherche Scientifique (CNRS)/ ; //The French Ministry for Research and Higher Education/ ; //2015-2020 State-Region Planning Contracts (CPER)/ ; //European Regional Development Fund (FEDER)/ ; }, mesh = {Biological Transport ; Carbon/metabolism ; Minerals/metabolism ; Mycorrhizae ; Phloem/metabolism ; Plant Proteins/metabolism ; Plant Roots/*metabolism/microbiology ; *Rhizosphere ; Starch/metabolism ; Sucrose/metabolism ; Sugars/*metabolism ; Symbiosis ; }, abstract = {In plants, the root is a typical sink organ that relies exclusively on the import of sugar from the aerial parts. Sucrose is delivered by the phloem to the most distant root tips and, en route to the tip, is used by the different root tissues for metabolism and storage. Besides, a certain portion of this carbon is exuded in the rhizosphere, supplied to beneficial microorganisms and diverted by parasitic microbes. The transport of sugars toward these numerous sinks either occurs symplastically through cell connections (plasmodesmata) or is apoplastically mediated through membrane transporters (MST, mononsaccharide tranporters, SUT/SUC, H+/sucrose transporters and SWEET, Sugar will eventually be exported transporters) that control monosaccharide and sucrose fluxes. Here, we review recent progresses on carbon partitioning within and outside roots, discussing membrane transporters involved in plant responses to biotic and abiotic factors.}, } @article {pmid30578745, year = {2018}, author = {Watts-Williams, SJ and Emmett, BD and Levesque-Tremblay, V and MacLean, AM and Sun, X and Satterlee, JW and Fei, Z and Harrison, MJ}, title = {Diverse Sorghum bicolor accessions show marked variation in growth and transcriptional responses to arbuscular mycorrhizal fungi.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13509}, pmid = {30578745}, issn = {1365-3040}, abstract = {Sorghum is an important crop grown world-wide for feed and fibre. Like most plants, it has the capacity to benefit from symbioses with arbuscular mycorrhizal (AM) fungi and its diverse genotypes likely vary in their responses. Currently, the genetic basis of mycorrhiza-responsiveness is largely unknown. Here we investigated transcriptional and physiological responses of sorghum accessions, founders of a bioenergy nested association mapping panel, for their responses to four species of AM fungi. Transcriptome comparisons across four accessions identified mycorrhiza-inducible genes; stringent filtering criteria revealed 278 genes that show mycorrhiza-inducible expression independent of genotype and 55 genes whose expression varies with genotype. The latter suggests variation in phosphate transport and defence across these accessions. The mycorrhiza growth and nutrient responses of eighteen sorghum accessions varied tremendously, ranging from mycorrhiza-dependent to negatively mycorrhiza-responsive. Additionally, accessions varied in the number of AM fungi to which they showed positive responses; from one to several fungal species. Mycorrhiza growth and phosphorus responses were positively correlated, while expression of two mycorrhiza-inducible phosphate transporters, SbPT8 and SbPT9, correlated negatively with mycorrhizal growth responses. AM fungi improve growth and mineral nutrition of sorghum and the substantial variation between lines provides the potential to map loci influencing mycorrhiza responses.}, } @article {pmid30578387, year = {2018}, author = {Ghosh, B and Gaike, AH and Pyasi, K and Brashier, B and Das, VV and Londhe, JD and Juvekar, S and Shouche, YS and Donnelly, LE and Salvi, SS and Barnes, PJ}, title = {Bacterial load and defective monocyte-derived macrophage bacterial phagocytosis in biomass-smoke COPD.}, journal = {The European respiratory journal}, volume = {}, number = {}, pages = {}, doi = {10.1183/13993003.02273-2017}, pmid = {30578387}, issn = {1399-3003}, abstract = {Lower airway colonisation with potentially pathogenic bacterial species (PPBs) is associated with defective bacterial phagocytosis, in monocyte-derived macrophages (MDMs) and alveolar macrophages, from tobacco-smoke associated COPD (S-COPD) subjects. In developing world, COPD among non-smokers is largely due to biomass-smoke (BMS) exposure. Yet, little is known about PPBs colonisation and its association with impaired innate immunity in these subjects.We investigated the PPBs load (Streptococcus pneumoniae, SP; Haemophilus influenzae, HI; Moraxella catarrhalis, MC; and Pseudomonas aeruginosa, PA) in BMS-exposed COPD (BMS-COPD) compared with S-COPD and spirometrically normal subjects. We also examined the association between load of PPBs with phagocytic activity of MDMs and lung function.Induced sputum and peripheral venous blood samples were collected from 18 healthy non-smokers, 15 smokers without COPD, 16 BMS-exposed healthy, 19 S-COPD and 23 BMS-COPD subjects. PPBs load in induced sputum and MDMs phagocytic activity were determined using qPCR and fluorimetry respectively.Higher bacterial load of SP, HI, and PA were observed in BMS-COPD. Increased PPBs load in BMS-exposed subjects was significantly negatively associated with defective phagocytosis in MDMs, and spirometric lung function indices (p<0.05).Increased load of PPBs in airways of BMS-COPD subjects is inversely associated with defective bacterial phagocytosis and lung function.}, } @article {pmid30576511, year = {2018}, author = {Xu, X and Fang, P and Zhang, H and Chi, C and Song, L and Xia, X and Shi, K and Zhou, Y and Zhou, J and Yu, J}, title = {Strigolactones positively regulate defense against root-knot nematodes in tomato.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/ery439}, pmid = {30576511}, issn = {1460-2431}, abstract = {Strigolactones (SLs) are carotenoid-derived phytohormones well known to influence various aspects of plant growth and development. As root-derived signals, SLs can enhance symbiosis between plants and arbuscular mycorrhizal fungi (AMF). However, little is known about the roles of SLs in plant defense against soil-borne pathogens. Here, we demonstrated that root-knot nematodes (RKNs; Meloidogyne incognita) infection induced SL biosynthesis in tomato roots. Silencing of SL biosynthesis genes compromised the defense, whilst the application of the SL analog racGR24 enhanced the defense against RKN. Endogenous jasmonic acid (JA) and abscisic acid (ABA) accumulation in the roots were enhanced by silencing of SLs biosynthetic genes but was suppressed by application of racGR24 in response to RKN infection. Genetic evidence showed that JA was a positive regulator while ABA was a negative regulator of RKN defense in tomato. Furthermore, racGR24 enhanced the defense against nematode in JA-deficient mutant but not in ABA-deficient mutant. In addition, silencing of SLs biosynthetic genes resulted in upregulation of MYC2, which negatively regulated the resistance. Our results demonstrated that SLs play a positive role in nematode defense. MYC2 negatively regulate nematode defense potentially by mediating the hormone crosstalk among SLs, ABA and JA.}, } @article {pmid30576446, year = {2018}, author = {Ballinger, MJ and Gawryluk, RMR and Perlman, SJ}, title = {Toxin and genome evolution in a Drosophila defensive symbiosis.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evy272}, pmid = {30576446}, issn = {1759-6653}, abstract = {Defenses conferred by microbial symbionts play a vital role in the health and fitness of their animal hosts. An important outstanding question in the study of defensive symbiosis is what determines long term stability and effectiveness against diverse natural enemies. In this study, we combine genome and transcriptome sequencing, symbiont transfection and parasite protection experiments, and toxin activity assays to examine the evolution of the defensive symbiosis between Drosophila flies and their vertically transmitted Spiroplasma bacterial symbionts, focusing in particular on ribosome-inactivating proteins (RIPs), symbiont-encoded toxins that have been implicated in protection against both parasitic wasps and nematodes. While many strains of Spiroplasma, including the male-killing symbiont (sMel) of D. melanogaster, protect against parasitic wasps, only the strain (sNeo) that infects the mycophagous fly D. neotestacea appears to protect against parasitic nematodes. We find that RIP repertoire is a major differentiating factor between strains that do and do not offer nematode protection, and that sMel RIPs do not show activity against nematode ribosomes in vivo. We also discovered a strain of Spiroplasma infecting a mycophagous phorid fly, Megaselia nigra. Although both the host and its Spiroplasma are distantly related to D. neotestacea and its symbiont, genome sequencing revealed that the M. nigra symbiont encodes abundant and diverse RIPs, including plasmid-encoded toxins that are closely related to the RIPs in sNeo. Our results suggest that distantly related Spiroplasma RIP toxins may perform specialized functions with regard to parasite specificity and suggest an important role for horizontal gene transfer in the emergence of novel defensive phenotypes.}, } @article {pmid30576265, year = {2018}, author = {Wippel, K and Long, SR}, title = {Symbiotic performance of Sinorhizobium meliloti lacking ppGpp depends on the Medicago host species.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-11-18-0306-R}, pmid = {30576265}, issn = {0894-0282}, abstract = {Host specificity in the root nodule symbiosis between legumes and rhizobia is crucial for the establishment of a successful interaction and ammonia provision to the plant. The specificity is mediated by plant-bacterial signal exchange during early stages of interaction. We observed that a Sinorhizobium meliloti mutant ∆relA, which is deficient in initiating the bacterial stringent response, fails to nodulate Medicago sativa (alfalfa), but successfully infects Medicago truncatula. We used biochemical, histological, transcriptomic, and imaging approaches to compare the behavior of the S. meliloti ∆relA mutant and wild type on the two plant hosts. ∆relA performed almost wild type-like on M. truncatula, except for reduced nitrogen fixation capacity and a disorganized positioning of bacteroids within nodule cells. In contrast, ∆relA showed impaired root colonization on alfalfa, and failed to infect nodule primordia. Global transcriptome analyses of ∆relA cells treated with the alfalfa flavonoid luteolin, and of mature nodules induced by the mutant on M. truncatula, revealed normal nod gene expression but overexpression of exopolysaccharide biosynthesis genes, and a slight suppression of plant defense-like reactions. Many RelA-dependent transcripts overlap with the hypo-osmolarity-related FeuP regulon or are characteristic of stress responses. Based on our findings, we suggest that RelA is not essential until the late stages of symbiosis with M. truncatula, where it may be involved in processes that optimize nitrogen fixation.}, } @article {pmid30575731, year = {2018}, author = {Lutzoni, F and Nowak, MD and Alfaro, ME and Reeb, V and Miadlikowska, J and Krug, M and Arnold, AE and Lewis, LA and Swofford, DL and Hibbett, D and Hilu, K and James, TY and Quandt, D and Magallón, S}, title = {Contemporaneous radiations of fungi and plants linked to symbiosis.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5451}, doi = {10.1038/s41467-018-07849-9}, pmid = {30575731}, issn = {2041-1723}, abstract = {Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant embryophytes occurred ca. 480 Ma. This was followed by the origin of extant lichens. Saprotrophic mushrooms diversified in the Late Paleozoic as forests of seed plants started to dominate the landscape. The subsequent diversification and explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal mushrooms, were associated with the evolution of Pinaceae in the Mesozoic, and establishment of angiosperm-dominated biomes in the Cretaceous.}, } @article {pmid30575161, year = {2018}, author = {Haselkorn, TS and DiSalvo, S and Miller, JW and Bashir, U and Brock, DA and Queller, DC and Strassmann, JE}, title = {The specificity of Burkholderia symbionts in the social amoeba farming symbiosis: prevalence, species, genetic and phenotypic diversity.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.14982}, pmid = {30575161}, issn = {1365-294X}, abstract = {The establishment of symbioses between eukaryotic hosts and bacterial symbionts in nature is a dynamic process. The formation of such relationships depends on the life history of both partners. Bacterial symbionts of amoebae may have unique evolutionary trajectories to the symbiont lifestyle, because bacteria are typically ingested as prey. To persist after ingestion, bacteria must first survive phagocytosis. In the social amoeba Dictyostelium discoideum, certain strains of Burkholderia bacteria are able to resist amoebal digestion and maintain a persistent relationship that includes carriage throughout the amoeba's social cycle that culminates in spore formation. Some Burkholderia strains allow their host to carry other bacteria, as food. This carried food is released in new environments in a trait called farming. To better understand the diversity and prevalence of Burkholderia symbionts and the traits they impart to their amoebae hosts, we first screened 700 natural isolates of D. discoideum and found 25% infected with Burkholderia. We next used a multilocus phylogenetic analysis and identified two independent transitions by Burkholderia to the symbiotic lifestyle. Finally, we tested the ability of 38 strains of Burkholderia from D. discoideum, as well as strains isolated from other sources, for traits relevant to symbiosis in D. discoideum. Only D. discoideum native isolates belonging to the B. agricolaris, B. hayleyella, and B. bonniea species were able to form persistent symbiotic associations with D. discoideum. The Burkholderia-Dictyostelium relationship provides a promising arena for further studies of the pathway to symbiosis in a unique system. This article is protected by copyright. All rights reserved.}, } @article {pmid30575076, year = {2019}, author = {Foyer, CH and Nguyen, H and Lam, HM}, title = {Legumes-The art and science of environmentally sustainable agriculture.}, journal = {Plant, cell & environment}, volume = {42}, number = {1}, pages = {1-5}, doi = {10.1111/pce.13497}, pmid = {30575076}, issn = {1365-3040}, support = {BB/N004914/1//BBSRC (UK)/ ; //Worldwide University Network (WUN)/ ; }, abstract = {Symbiotic nitrogen fixation, which is carried out by the legume-rhizobia partnership, is a major source of nitrogen acquisition in natural ecosystems and in agriculture. The benefits to the plant gained through the rhizobial-legume symbiosis can be further enhanced by associations of the legume with arbuscular mycorrhiza. The progressive engagement of the legume host with the rhizobial bacteria and mycorrhizal fungi requires an extensive exchange of signalling molecules. These signals alter the transcriptional profiles of the partners, guiding and enabling extensive microbial and fungal proliferation in the roots. Such interactions and associations are greatly influenced by environmental stresses, which also severely limit the productivity of legume crops. Part II of the Special Issue on Legumes provides new insights into the mechanisms that underpin sustainable symbiotic partnerships, as well as the effects of abiotic stresses, such as drought, waterlogging, and salinity on legume biology. The requirement for germplasm and new breeding methods is discussed as well as the future of legume production in the face of climate change.}, } @article {pmid30573737, year = {2018}, author = {Mohammed, M and Jaiswal, SK and Dakora, FD}, title = {Distribution and correlation between phylogeny and functional traits of cowpea (Vigna unguiculata L. Walp.)-nodulating microsymbionts from Ghana and South Africa.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {18006}, doi = {10.1038/s41598-018-36324-0}, pmid = {30573737}, issn = {2045-2322}, abstract = {Cowpea (Vigna unguiculata L. Walp.) is indigenous to Africa, and highly valued for its N2-fixing trait and the nutritional attributes of its grain and leaves. The species' ability to establish effective symbiosis with diverse rhizobial populations gives it survival and growth advantage in N-limited environments. To explore the functional diversity and phylogenetic positions of rhizobia nodulating cowpea in Africa, nodules were collected from various cowpea varieties grown in soils from the Guinea savanna and Sudano-sahelian agroecologies of Northern Ghana, and from the lowveld and middleveld areas of Mpumalanga Province in South Africa. Box-PCR profiling and multilocus sequence analysis revealed the presence of diverse microsymbionts responsible for cowpea nodulation across the study sites. BOX-PCR amplifications yielded variable band sizes, ranging from 618 bp to 5354 bp, which placed the isolates in six major clusters (Cluster A-F). Phylogenetic analysis based on 16S rRNA, atpD, glnII, gyrB, rpoB, nifH and nodC genes revealed the presence of diverse Bradyrhizobium sp. closely related to Bradyrhizobium daqingense, Bradyrhizobium subterraneum, Bradyrhizobium yuanmingense, Bradyrhizobium embrapense, Bradyrhizobium pachyrhizi, Bradyrhizobium elkanii and novel Bradyrhizobium species in the soils studied, a finding that could be attributed to the unique edapho-climatic conditions of the contrasting environments. The test isolates exhibited distinct symbiotic efficiencies, and also induced variable (p ≤ 0.001) photosynthetic rates, leaf transpiration, total chlorophyll and shoot biomass accumulation on cowpea (their homologous host). Canonical correspondence analysis showed that the distribution of these microsymbionts was influenced by the concentrations of macro- and micronutrients in soils. The pairwise genetic distances derived from phylogenies and nodule functioning showed significant (p < 0.05) correlation, which suggests that local environmental factors played a major role in the cowpea-Bradyrhizobium symbiosis.}, } @article {pmid29205604, year = {2018}, author = {Aung, K and Jiang, Y and He, SY}, title = {The role of water in plant-microbe interactions.}, journal = {The Plant journal : for cell and molecular biology}, volume = {93}, number = {4}, pages = {771-780}, pmid = {29205604}, issn = {1365-313X}, support = {K99 GM115766/GM/NIGMS NIH HHS/United States ; R01 GM109928/GM/NIGMS NIH HHS/United States ; }, mesh = {*Droughts ; Gene Expression Regulation, Plant ; Homeostasis ; *Host Microbial Interactions ; *Host-Pathogen Interactions ; Humidity ; Plant Diseases/microbiology ; Plant Leaves ; Plant Stomata/microbiology/physiology ; Plants/*microbiology ; Rhizosphere ; Symbiosis ; *Water/metabolism ; }, abstract = {Throughout their life plants are associated with various microorganisms, including commensal, symbiotic and pathogenic microorganisms. Pathogens are genetically adapted to aggressively colonize and proliferate in host plants to cause disease. However, disease outbreaks occur only under permissive environmental conditions. The interplay between host, pathogen and environment is famously known as the 'disease triangle'. Among the environmental factors, rainfall events, which often create a period of high atmospheric humidity, have repeatedly been shown to promote disease outbreaks in plants, suggesting that the availability of water is crucial for pathogenesis. During pathogen infection, water-soaking spots are frequently observed on infected leaves as an early symptom of disease. Recent studies have shown that pathogenic bacteria dedicate specialized virulence proteins to create an aqueous habitat inside the leaf apoplast under high humidity. Water availability in the apoplastic environment, and probably other associated changes, can determine the success of potentially pathogenic microbes. These new findings reinforce the notion that the fight over water may be a major battleground between plants and pathogens. In this article, we will discuss the role of water availability in host-microbe interactions, with a focus on plant-bacterial interactions.}, } @article {pmid30569615, year = {2019}, author = {Genre, A and Timmers, T}, title = {The symbiotic role of the actin filament cytoskeleton.}, journal = {The New phytologist}, volume = {221}, number = {2}, pages = {611-613}, doi = {10.1111/nph.15506}, pmid = {30569615}, issn = {1469-8137}, } @article {pmid30569614, year = {2019}, author = {}, title = {Sally E. Smith.}, journal = {The New phytologist}, volume = {221}, number = {2}, pages = {648-649}, doi = {10.1111/nph.15569}, pmid = {30569614}, issn = {1469-8137}, } @article {pmid30568663, year = {2018}, author = {Lehnert, H and Serfling, A and Friedt, W and Ordon, F}, title = {Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat (Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1728}, doi = {10.3389/fpls.2018.01728}, pmid = {30568663}, issn = {1664-462X}, abstract = {In the majority of wheat growing areas worldwide, the incidence of drought stress has increased significantly resulting in a negative impact on plant development and grain yield. Arbuscular mycorrhizal symbiosis is known to improve drought stress tolerance of wheat. However, quantitative trait loci (QTL) involved in the response to drought stress conditions in the presence of mycorrhizae are largely unknown. Therefore, a diverse set consisting of 94 bread wheat genotypes was phenotyped under drought stress and well watered conditions in the presence and absence of mycorrhizae. Grain yield and yield components, drought stress related traits as well as response to mycorrhizae were assessed. In parallel, wheat accessions were genotyped by using the 90k iSelect chip, resulting in a set of 15511 polymorphic and mapped SNP markers, which were used for genome-wide association studies (GWAS). In general, drought stress tolerance of wheat was significantly increased in the presence of mycorrhizae compared to drought stress tolerance in the absence of mycorrhizae. However, genotypes differed in their response to mycorrhizae under drought stress conditions. Several QTL regions on different chromosomes were detected associated with grain yield and yield components under drought stress conditions. Furthermore, two genome regions on chromosomes 3D and 7D were found to be significantly associated with the response to mycorrhizae under drought stress conditions. Overall, the results reveal that inoculation of wheat with mycorrhizal fungi significantly improves drought stress tolerance and that QTL regions associated with the response to mycorrhizae under drought stress conditions exist in wheat. Further research is necessary to validate detected QTL regions. However, this study may be the starting point for the identification of candidate genes associated with drought stress tolerance and response to mycorrhizae under drought stress conditions. Maybe in future, these initial results will help to contribute to use mycorrhizal fungi effectively in agriculture and combine new approaches i.e., use of genotypic variation in response to mycorrhizae under drought stress conditions with existing drought tolerance breeding programs to develop new drought stress tolerant genotypes.}, } @article {pmid30566798, year = {2017}, author = {Mizuno, S and Kanai, T}, title = {Fecal microbiota transplantation.}, journal = {Nihon rinsho. Japanese journal of clinical medicine}, volume = {75}, number = {3}, pages = {492-497}, pmid = {30566798}, issn = {0047-1852}, abstract = {Various strains of microorganisms inhabit the human intestinal tract, and disturbance of intestinal flora, dysbiosis, is thought to be pathogenesis of various diseases. Inducing symbiosis of intestinal flora has therapeutic potential for gastrointestinal diseases, but there are limited therapeutic options including probiotics.'Previous reports suggested that fecal microbiota transplantation (FMT) was a very useful choice in treatment for recurrent Clostridium difficile infection. FMT for ulcerative colitis (UC) patients is proposed as a potential treatment for resolving dysbiosis. There is some debate as to whether FMT for UC patients is effective or not. It remains a challenge for future research to make more sophisticated and convenient methods of FMT.}, } @article {pmid29442372, year = {2018}, author = {Hoye, BJ and Fenton, A}, title = {Animal host-microbe interactions.}, journal = {The Journal of animal ecology}, volume = {87}, number = {2}, pages = {315-319}, doi = {10.1111/1365-2656.12788}, pmid = {29442372}, issn = {1365-2656}, mesh = {Animals ; Host Microbial Interactions/*physiology ; Host-Pathogen Interactions ; Symbiosis ; }, } @article {pmid28502120, year = {2018}, author = {Kohl, KD and Varner, J and Wilkening, JL and Dearing, MD}, title = {Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets.}, journal = {The Journal of animal ecology}, volume = {87}, number = {2}, pages = {323-330}, doi = {10.1111/1365-2656.12692}, pmid = {28502120}, issn = {1365-2656}, mesh = {*Adaptation, Physiological ; Animals ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Diet ; Gastrointestinal Tract/*microbiology ; Herbivory ; Host Microbial Interactions/*physiology ; Host Specificity ; Lagomorpha/classification/*microbiology ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; United States ; }, abstract = {Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high-elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fibre and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss. Here, we inventoried the microbial communities of pika caecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets. Microbial communities varied significantly across populations, and differences in microbial community structure were congruent with genetic differences in host population structure, a pattern known as "phylosymbiosis." Several microbial members (Ruminococcus, Prevotella, Oxalobacter and Coprococcus) were detected across all samples, and thus likely represent a "core microbiome." These genera are known to perform a number of services for herbivorous hosts such as fibre fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreover, pikas that feed on moss harboured microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fibre for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss. These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fibre-degrading microbes. Last, we discuss the implications of population-specific microbial communities for conservation efforts in this species.}, } @article {pmid30565261, year = {2018}, author = {Dreyer, I and Spitz, O and Kanonenberg, K and Montag, K and Handrich, M and Ahmad, S and Schott-Verdugo, S and Navarro-Retamal, C and Rubio-Meléndez, ME and Gomez-Porras, JL and Riedelsberger, J and Molina-Montenegro, MA and Succurro, A and Zuccaro, A and Gould, SB and Bauer, P and Schmitt, L and Gohlke, H}, title = {Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15646}, pmid = {30565261}, issn = {1469-8137}, abstract = {To get insights into the dynamics of nutrient exchange in arbuscular mycorrhizal (AM) symbiosis, we modelled mathematically the two-membrane system at the plant-fungus interface and simulated its dynamics. In computational cell biology experiments, the full range of nutrient transport pathways was tested for their ability to exchange phosphorus (P) / carbon (C) / nitrogen (N) sources. As a result, we obtained a thermodynamically justified, independent, and comprehensive model of the dynamics of the nutrient exchange at the plant-fungus contact zone. The predicted optimal transporter network coincides with the transporter set independently confirmed in wet-lab experiments previously, indicating that all essential transporter types have been discovered. The thermodynamic analyses suggest that phosphate is released from the fungus via proton-coupled phosphate transporters rather than anion channels. Optimal transport pathways, such as cation channels or proton-coupled symporters, shuttle nutrients along with a positive charge across the membranes. Only in exceptional cases, also the electroneutral transport via diffusion facilitators appears plausible. The thermodynamic models presented here can be generalised and adapted to other forms of mycorrhiza and open the door for future studies combining wet-lab experiments with computational simulations to obtain a deeper understanding of the investigated phenomena. This article is protected by copyright. All rights reserved.}, } @article {pmid30563061, year = {2018}, author = {Alloing, G and Mandon, K and Boncompagni, E and Montrichard, F and Frendo, P}, title = {Involvement of Glutaredoxin and Thioredoxin Systems in the Nitrogen-Fixing Symbiosis between Legumes and Rhizobia.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {7}, number = {12}, pages = {}, doi = {10.3390/antiox7120182}, pmid = {30563061}, issn = {2076-3921}, support = {ANR-11-LABX-0027-01//Agence Nationale de la Recherche/ ; }, abstract = {Leguminous plants can form a symbiotic relationship with Rhizobium bacteria, during which plants provide bacteria with carbohydrates and an environment appropriate to their metabolism, in return for fixed atmospheric nitrogen. The symbiotic interaction leads to the formation of a new organ, the root nodule, where a coordinated differentiation of plant cells and bacteria occurs. The establishment and functioning of nitrogen-fixing symbiosis involves a redox control important for both the plant-bacteria crosstalk and the regulation of nodule metabolism. In this review, we discuss the involvement of thioredoxin and glutaredoxin systems in the two symbiotic partners during symbiosis. The crucial role of glutathione in redox balance and S-metabolism is presented. We also highlight the specific role of some thioredoxin and glutaredoxin systems in bacterial differentiation. Transcriptomics data concerning genes encoding components and targets of thioredoxin and glutaredoxin systems in connection with the developmental step of the nodule are also considered in the model system Medicago truncatula⁻Sinorhizobium meliloti.}, } @article {pmid30446651, year = {2018}, author = {Albrecht, J and Hagge, J and Schabo, DG and Schaefer, HM and Farwig, N}, title = {Reward regulation in plant-frugivore networks requires only weak cues.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4838}, pmid = {30446651}, issn = {2041-1723}, mesh = {Animal Migration/physiology ; Animal Nutritional Physiological Phenomena ; Animals ; Antioxidants/chemistry ; Birds/classification/*physiology ; Color ; *Cues ; Food Preferences/*physiology ; Fruit/anatomy & histology/*chemistry ; Herbivory/physiology ; Immunity, Innate ; Lipids/chemistry ; Plants/anatomy & histology/chemistry ; *Reward ; Seasons ; Symbiosis/*physiology ; }, abstract = {Theory assumes that fair trade among mutualists requires highly reliable communication. In plant-animal mutualisms the reliability of cues that indicate reward quality is often low. Therefore, it is controversial whether communication allows animal mutualists to regulate their reward intake. Here we show that even loose relationships between fruit brightness and nutritional rewards (r2 = 0.11-0.35) allow birds to regulate their nutrient intake across distinct European plant-frugivore networks. Resident, over-wintering generalist frugivores that interact with diverse plant species select bright, lipid-rich fruits, whereas migratory birds select dark, sugar- and antioxidant-rich fruits. Both nutritional strategies are consistent with previous physiological experiments suggesting that over-wintering generalists aim to maximize their energy intake, whereas migrants aim to enhance the build-up of body fat, their immune response and oxidative status during migration. Our results suggest that animal mutualists require only weak cues to regulate their reward intake according to specific nutritional strategies.}, } @article {pmid29864164, year = {2018}, author = {Palmer, WH and Medd, NC and Beard, PM and Obbard, DJ}, title = {Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses.}, journal = {PLoS pathogens}, volume = {14}, number = {6}, pages = {e1007050}, pmid = {29864164}, issn = {1553-7374}, support = {WT085064//Wellcome Trust/United Kingdom ; WT095831//Wellcome Trust/United Kingdom ; WT104915MA//Wellcome Trust/United Kingdom ; BB/J004324/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; DNA Virus Infections/genetics/immunology/*virology ; DNA Viruses/*isolation & purification/physiology ; Drosophila melanogaster/growth & development/*immunology/microbiology/virology ; Female ; Genetic Variation ; Host-Pathogen Interactions/*immunology ; Male ; Symbiosis ; Viral Proteins/*genetics ; Virus Replication ; Wolbachia/*growth & development/immunology/isolation & purification ; }, abstract = {Drosophila melanogaster has played a key role in our understanding of invertebrate immunity. However, both functional and evolutionary studies of host-virus interaction in Drosophila have been limited by a dearth of native virus isolates. In particular, despite a long history of virus research, DNA viruses of D. melanogaster have only recently been described, and none have been available for experimental study. Here we report the isolation and comprehensive characterisation of Kallithea virus, a large double-stranded DNA virus, and the first DNA virus to have been reported from wild populations of D. melanogaster. We find that Kallithea virus infection is costly for adult flies, reaching high titres in both sexes and disproportionately reducing survival in males, and movement and late fecundity in females. Using the Drosophila Genetic Reference Panel, we quantify host genetic variance for virus-induced mortality and viral titre and identify candidate host genes that may underlie this variation, including Cdc42-interacting protein 4. Using full transcriptome sequencing of infected males and females, we examine the transcriptional response of flies to Kallithea virus infection and describe differential regulation of virus-responsive genes. This work establishes Kallithea virus as a new tractable model to study the natural interaction between D. melanogaster and DNA viruses, and we hope it will serve as a basis for future studies of immune responses to DNA viruses in insects.}, } @article {pmid29343832, year = {2018}, author = {Itoh, H and Hori, T and Sato, Y and Nagayama, A and Tago, K and Hayatsu, M and Kikuchi, Y}, title = {Infection dynamics of insecticide-degrading symbionts from soil to insects in response to insecticide spraying.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {909-920}, pmid = {29343832}, issn = {1751-7370}, mesh = {Animals ; Biological Evolution ; Burkholderia/*drug effects/genetics/physiology ; DNA, Bacterial/analysis ; Digestive System/*microbiology ; Fenitrothion/*pharmacology ; Heteroptera/*microbiology ; Insecticide Resistance/*physiology ; Insecticides/*pharmacology ; Microbiota/*drug effects ; Saccharum ; Sequence Analysis, DNA ; *Soil Microbiology ; Symbiosis/drug effects/physiology ; }, abstract = {Insecticide resistance is a serious concern in modern agriculture, and an understanding of the underlying evolutionary processes is pivotal to prevent the problem. The bean bug Riptortus pedestris, a notorious pest of leguminous crops, acquires a specific Burkholderia symbiont from the environment every generation, and harbors the symbiont in the midgut crypts. The symbiont's natural role is to promote insect development but the insect host can also obtain resistance against the insecticide fenitrothion (MEP) by acquiring MEP-degrading Burkholderia from the environment. To understand the developing process of the symbiont-mediated MEP resistance in response to the application of the insecticide, we investigated here in parallel the soil bacterial dynamics and the infected gut symbionts under different MEP-spraying conditions by culture-dependent and culture-independent analyses, in conjunction with stinkbug rearing experiments. We demonstrate that MEP application did not affect the total bacterial soil population but significantly decreased its diversity while it dramatically increased the proportion of MEP-degrading bacteria, mostly Burkholderia. Moreover, we found that the infection of stinkbug hosts with MEP-degrading Burkholderia is highly specific and efficient, and is established after only a few times of insecticide spraying at least in a field soil with spraying history, suggesting that insecticide resistance could evolve in a pest bug population more quickly than was thought before.}, } @article {pmid30562535, year = {2018}, author = {Gutjahr, C}, title = {Symbiosis: Plasmodesmata Link Root-Nodule Organogenesis with Infection.}, journal = {Current biology : CB}, volume = {28}, number = {24}, pages = {R1400-R1403}, doi = {10.1016/j.cub.2018.11.013}, pmid = {30562535}, issn = {1879-0445}, abstract = {During the establishment of root-nodule symbioses between plants and nitrogen-fixing rhizobia, nodule organogenesis in the inner cortex needs to be precisely coordinated with the rhizobial infection site at the root epidermis. A new study shows that rhizobia induce localized callose turnover at plasmodesmata to allow spatiotemporal synchronization of the two processes through symplastic connections.}, } @article {pmid30561420, year = {2018}, author = {Manfredi, M and Gaiani, F and Kayali, S and Bizzarri, B and Iuliano, S and Minelli, R and Leandro, G and Di Mario, F and De' Angelis, GL}, title = {How and when investigating and treating Helicobacter pylori infection in children.}, journal = {Acta bio-medica : Atenei Parmensis}, volume = {89}, number = {8-S}, pages = {65-71}, pmid = {30561420}, issn = {0392-4203}, abstract = {For thousands of years humans have lived in symbiosis with Helicobacter pylori. This infection is acquired mainly during childhood and, despite it represents one of the most common infections in humans, only a minority of infected people may develop health issues and life-threatening diseases. For diagnosing Helicobacter pylori infection in children we can use, at first, non-invasive diagnostic tests, if clinical pattern and/or history are of suspicion. Then, invasive tests i.e. gastroscopy are necessary to confirm the infection. As antibiotics are not widely available in children affected by Helicobacter pylori infection, they should be chosen based on individual antibiotic susceptibility testing obtained by gastric biopsy specimens or the local antibiotic resistance pattern, in empirical treatment is chosen. Test and treat strategy in children should be avoided. In this brief review we summarize how and in which children the infection should be investigate and which the most appropriate eradication treatment should be chosen.}, } @article {pmid30561093, year = {2018}, author = {Cherkasov, SV and Popova, LY and Vivtanenko, TV and Demina, RR and Khlopko, YA and Balkin, AS and Plotnikov, AO}, title = {Oral microbiomes in children with asthma and dental caries.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.13020}, pmid = {30561093}, issn = {1601-0825}, abstract = {OBJECTIVE: Recently, a significant association between dental caries and the severity of bronchial asthma in children has been revealed. This finding indicates a possible relationship between the oral microbiome and the pathogenesis of asthma. The purpose of our study was to estimate differences in the dental plaque microbiota of asthmatic children with and without dental caries by 16S rDNA sequencing.

MATERIAL AND METHODS: Dental plaque samples were obtained with a spoon excavator from the occlusal surface of one deciduous tooth (the second mandibular left molar in caries-free children and the most affected tooth in caries-affected children). Total DNA was extracted from dental plaque. DNA libraries were analysed by 16S rRNA gene sequencing on the MiSeq (Illumina) platform.

RESULTS: There were no significant differences in the composition of bacterial communities from both caries-affected and caries-free children with asthma. The 'caries-enriched' genus was Veillonella (Veillonellaceae, Selenomonadales, Negativicutes). Relative abundance of Neisseria was significantly higher in caries-free children with asthma (p<0.05).

CONCLUSIONS: The most significant difference in compared bacterial communities was a higher relative abundance of Veillonella in caries-affected plaques that suggests its involvement in pathogenesis of caries. Potential respiratory pathogens are present in oral cavity of both caries-affected and caries-free asthmatic children. This article is protected by copyright. All rights reserved.}, } @article {pmid30451902, year = {2018}, author = {Kruse, S and Goris, T and Westermann, M and Adrian, L and Diekert, G}, title = {Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4872}, pmid = {30451902}, issn = {2041-1723}, mesh = {Acetic Acid/metabolism ; Anaerobiosis/drug effects/physiology ; Campylobacteraceae/drug effects/growth & development/*metabolism ; Coculture Techniques ; Fermentation/drug effects/*physiology ; Fumarates/metabolism/pharmacology ; Hydrogen/*metabolism ; Kinetics ; Lactic Acid/metabolism ; Methanococcus/drug effects/growth & development/*metabolism ; Oxidation-Reduction ; Pyruvic Acid/metabolism/pharmacology ; Succinic Acid/metabolism ; Symbiosis/*physiology ; }, abstract = {Hydrogen-producing bacteria are of environmental importance, since hydrogen is a major electron donor for prokaryotes in anoxic ecosystems. Epsilonproteobacteria are currently considered to be hydrogen-oxidizing bacteria exclusively. Here, we report hydrogen production upon pyruvate fermentation for free-living Epsilonproteobacteria, Sulfurospirillum spp. The amount of hydrogen produced is different in two subgroups of Sulfurospirillum spp., represented by S. cavolei and S. multivorans. The former produces more hydrogen and excretes acetate as sole organic acid, while the latter additionally produces lactate and succinate. Hydrogen production can be assigned by differential proteomics to a hydrogenase (similar to hydrogenase 4 from E. coli) that is more abundant during fermentation. A syntrophic interaction is established between Sulfurospirillum multivorans and Methanococcus voltae when cocultured with lactate as sole substrate, as the former cannot grow fermentatively on lactate alone and the latter relies on hydrogen for growth. This might hint to a yet unrecognized role of Epsilonproteobacteria as hydrogen producers in anoxic microbial communities.}, } @article {pmid30451829, year = {2018}, author = {Zélé, F and Magalhães, S and Kéfi, S and Duncan, AB}, title = {Ecology and evolution of facilitation among symbionts.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4869}, pmid = {30451829}, issn = {2041-1723}, mesh = {Animals ; Bacteria/growth & development ; *Biological Evolution ; Ecosystem ; Fungi/physiology ; Humans ; Parasites/physiology ; Plants/microbiology/parasitology/virology ; Symbiosis/*physiology ; Viruses/growth & development ; }, abstract = {Facilitation occurs when one species positively impacts the fitness of another, and has predominantly been studied in free-living species like plants. Facilitation can also occur among symbiont (mutualistic or parasitic) species or strains, but equivalent studies are scarce. To advance an integrated view of the effect of facilitation on symbiont ecology and evolution, we review empirical evidence and their underlying mechanisms, explore the factors favouring its emergence, and discuss its consequences for virulence and transmission. We argue that the facilitation concept can improve understanding of the evolutionary forces shaping symbiont communities and their effects on hosts.}, } @article {pmid30073404, year = {2018}, author = {Bezerra, RHS and Bocchiglieri, A}, title = {Association of ectoparasites (Diptera and Acari) on bats (Mammalia) in a restinga habitat in northeastern Brazil.}, journal = {Parasitology research}, volume = {117}, number = {11}, pages = {3413-3420}, pmid = {30073404}, issn = {1432-1955}, mesh = {Animals ; Brazil/epidemiology ; Chiroptera/classification/*parasitology ; Cold Temperature ; Diptera/*classification ; Ecosystem ; Ectoparasitic Infestations/*epidemiology ; Female ; Host-Parasite Interactions ; Male ; Mites/*classification ; Prevalence ; Seasons ; Symbiosis ; Temperature ; Ticks/*classification ; }, abstract = {In Brazil, 124 species of ectoparasites of bats are known from the families Streblidae, Nycteribiidae, and Spinturnicidae. This study aimed to characterize the ectoparasites associated with bats in a restinga habitat in Sergipe, northeastern Brazil. Sampling occurred between October 2016 and September 2017 in the Reserva Particular do Patrimônio Natural do Caju through the capture of bats, using 10 mist nets. The ectoparasites collected were stored in 70% alcohol and subsequently identified. For the hosts, the parasitological indexes were calculated and, for the most abundant ones, the influences of the sex of the host and of seasonality on these indexes were evaluated. We collected 430 parasites, of which 77.90% belonged to the Streblidae family. The influence of host sex was observed only in terms of the prevalence between Periglischrus iheringi and Artibeus lituratus, with the highest values observed for females. This may be associated with the highest susceptibility of females to parasitism by the greater permanency in the shelter. In terms of the influence of seasonality, only the interaction between Carollia perspicillata and Trichobius joblingi was affected by temperature, with an increase in prevalence rates and mean intensity during the season with lower temperatures. This relationship may be associated with biological differences among parasites species. The present study identified six new species of ectoparasites and the occurrence of ticks on bats for Sergipe, in addition to registering 11 new bat-ectoparasite associations for the state and two for Brazil, contributing to an increase in our knowledge about bat-ectoparasite interactions.}, } @article {pmid29976144, year = {2018}, author = {Li, H and Harwood, JD and Liu, T and Chu, D}, title = {Novel proteome and acetylome of Bemisia tabaci Q in response to Cardinium infection.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {523}, pmid = {29976144}, issn = {1471-2164}, support = {31572064//National Natural Science Foundation of China/ ; }, mesh = {Acetylation ; Animals ; Bacteroidetes/*physiology ; Chromatography, High Pressure Liquid ; Hemiptera/*metabolism/microbiology ; Insect Proteins/genetics/metabolism ; Lysine/metabolism ; Peptides/analysis ; Protein Interaction Maps/genetics ; Proteome/*metabolism ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: It has become increasingly clear that symbionts have crucial evolutionary and ecological ramifications for their host arthropods. However, little is known whether these symbiont infections influence the proteome and lysine acetylome of their host arthropods. Here we performed experiments to investigate the proteomes and acetylomes of Cardinium-infected (C*+) and -uninfected (C-) Bemisia tabaci Q with identical backgrounds, through the combination of affinity enrichment and high-resolution LC-MS/MS analysis.

RESULTS: Of the 3353 proteins whose levels were quantitated in proteome, a total of 146 proteins dividing into 77 up-regulated and 69 down-regulated proteins were discovered to be differentially expressed as having at least a 1.2-fold change when C*+ strain was compared with C- strain. Furthermore, a total of 528 lysine acetylation sites in 283 protein groups were identified, among which 356 sites in 202 proteins were quantified. The comparison of acetylomes revealed 30 sites in 26 lysine acetylation proteins (Kac) were quantified as up-regulated targets and 35 sites in 29 Kac proteins were quantified as down-regulated targets. Functional analysis showed that these differentially expressed proteins and Kac proteins were mainly involved in diverse physiological processes related to development, immune responses and energy metabolism, such as retinol metabolism, methane metabolism and fatty acid degradation. Notably, protein interaction network analyses demonstrated widespread interactions modulated by protein acetylation.

CONCLUSION: Here we show the proteome and acetylom of B. tabaci Q in response to the symbiont Cardinium infection. This is the first study to utilize the tool of acetylome analysis for revealing physiological responses of arthropods to its symbiont infection, which will provide an important resource for exploring the arthropod-symbiont interaction.}, } @article {pmid29801436, year = {2018}, author = {Opatovsky, I and Santos-Garcia, D and Ruan, Z and Lahav, T and Ofaim, S and Mouton, L and Barbe, V and Jiang, J and Zchori-Fein, E and Freilich, S}, title = {Modeling trophic dependencies and exchanges among insects' bacterial symbionts in a host-simulated environment.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {402}, pmid = {29801436}, issn = {1471-2164}, support = {1481/13//Israel Science Foundation/ ; 484/17//Israel Science Foundation/ ; }, mesh = {Animals ; Bacteria/*genetics/*metabolism ; *Environment ; Genome, Bacterial/genetics ; Hemiptera/*microbiology ; Metabolic Networks and Pathways ; *Models, Biological ; *Symbiosis ; }, abstract = {BACKGROUND: Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. In phloem-feeding insects such metabolic interactions with bacteria enable complementation of their deprived nutrition. The phloem-feeding whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. This well-defined bacterial community in B. tabaci serves here as a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented occurrences of bacterial combinations. We first reconstructed the metabolic networks of five common B. tabaci symbionts genera (Portiera, Rickettsia, Hamiltonella, Cardinium and Wolbachia), and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species' combinations, and (3) dependencies of each species on different media components.

RESULTS: The predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggests several previously un-reported routes for complementary interactions and estimated the dependency of each symbiont in specific host metabolites. No clear association was detected between metabolic co-dependencies and co-occurrence patterns.

CONCLUSIONS: The analysis generated predictions for testable hypotheses of metabolic exchanges and co-dependencies in bacterial communities and by crossing them with co-occurrence profiles, contextualized interaction patterns into a wider ecological perspective.}, } @article {pmid30556901, year = {2018}, author = {Balyan, R and Gund, R and Chawla, AS and Khare, SP and Pradhan, SJ and Rane, S and Galande, S and Durdik, JM and George, A and Bal, V and Rath, S}, title = {Correlation of Cell-Surface CD8 Levels with Function, Phenotype and Transcriptome of Naive CD8 T Cells.}, journal = {Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imm.13036}, pmid = {30556901}, issn = {1365-2567}, abstract = {We have previously demonstrated co-receptor level-associated functional heterogeneity in apparently homogenous naive peripheral CD4 T cells, dependent on MHC-mediated tonic signals. Since maturation pathways can differ between naive CD4 and naive CD8 cells, we tested whether the latter showed similar co-receptor level-associated functional heterogeneity. We report that, when either polyclonal and TCR-transgenic monoclonal peripheral naive CD8 T cells from young mice were separated into CD8hi and CD8lo subsets, CD8lo cells responded poorly, but CD8hi and CD8lo subsets of CD8 single-positive (SP) thymocytes responded similarly. CD8lo naive CD8 T cells were smaller and showed lower levels of some cell-surface molecules, but higher levels of the negative regulator CD5. In addition to the expected peripheral decline in CD8 levels on transferred naive CD8 T cells in wild-type but not in MHC class I (MHCI)-deficient recipient mice, short-duration naive T cell-dendritic cell (DC) co-cultures in vitro also caused coreceptor downmodulation in CD8 T cells but not in CD4 T cells. Constitutive pZAP70/pSyk and pERK levels ex vivo were lower in CD8lo naive CD8 T cells and dual-specific phosphatase (DUSP) inhibition partially rescued their hypo-responsiveness. Bulk mRNA sequencing showed major differences in the transcriptional landscapes of CD8hi and CD8lo naive CD8 T cells. CD8hi naive CD8 T cells showed enrichment of genes involved in positive regulation of cell cycle and survival. Thus, our data show that naive CD8 T cells show major differences in their signaling, transcriptional and functional landscapes associated with subtly altered CD8 levels, consistent with the possibility of peripheral cellular aging. This article is protected by copyright. All rights reserved.}, } @article {pmid30555063, year = {2018}, author = {Thakur, J and Dwivedi, MD and Uniyal, PL}, title = {Ultrastructural studies and molecular characterization of root-associated fungi, of Crepidium acuminatum (D.Don) Szlach.: a threatened and medicinally important taxon.}, journal = {Journal of genetics}, volume = {97}, number = {5}, pages = {1139-1146}, pmid = {30555063}, issn = {0973-7731}, abstract = {Crepidium acuminatum (Orchidaceae) is a threatened medicinal orchid that grows under shady and moist forest floor where light remains for a very short period of time. Mycorrhizal association is known to be essential for seed germination and seedling establishment in amajority of orchids. Identification of fungi that form mycorrhizae with orchids is of crucial importance for orchid conservation. We used both morphological as well as molecular approaches to study this plant-fungal interaction. Scanning electron microscopy showed that fungi grow and proliferate in the middle layers of the cortex. Also, spiral-root hairs were foundalong with root hairs, which is an unusual observation. Spiral-root hairs provide more surface area for fluid absorption and entrance of colonizers. Further, total root genomic DNA was isolated and fungal internal-transcribed spacer (ITS) regions were polymerase chain reaction (PCR)-amplified using specific primer combinations ITS1F/ITS4 and ITS1/ITS4tul. ITS sequences were obtainedand analysed to know the closest sequence matche in the GenBank using BLASTn hosted by NLM-NCBI. Subject sequences were identified to be belonging to three main genera, namely, Tulasnella, Aspergillus and Penicillium. Results indicate that mycorrhizal association is necessary for the growth and development of the plant. In addition, this symbiosis influences the distribution and rarity of this medicinally valuable taxon. Specific fungal partners may lead to an enhanced seed germination rate and increased efficiency of nutrient exchange between both the partners. Hence, knowledge of mycorrhizal fungi is essential for future in vitro germination and seedling establishment programmes, because they rely on fungi for germination. Identification of mycorrhizal fungi can be usedfor orchid propagation and conservation programmes.}, } @article {pmid30301086, year = {2018}, author = {Parsaian, M and Shokri, MR and Pazooki, J}, title = {The response of benthic foraminifera to aquaculture and industrial pollution: A case study from the Northern Persian Gulf.}, journal = {Marine pollution bulletin}, volume = {135}, number = {}, pages = {682-693}, doi = {10.1016/j.marpolbul.2018.07.073}, pmid = {30301086}, issn = {1879-3363}, mesh = {Animals ; Anthozoa ; Aquaculture ; Biodiversity ; *Coral Reefs ; Environmental Biomarkers ; Environmental Monitoring/methods ; Foraminifera/*physiology ; Geologic Sediments ; Indian Ocean ; Sewage ; Symbiosis ; Water Pollution/*adverse effects ; Water Quality ; }, abstract = {The aquaculture and industrial sewage impacts on benthic foraminifera investigated at two reefs across the northern Persian Gulf. The foraminifera assemblages at a single sewaged reef were compared with two non-sewaged reefs. A low-diversity assemblage, dominated by stress-tolerant species Quinqueloculina sp. and larger symbiont-bearing Amphistegina sp., was characteristic of the industrial sewaged reef. The opportunistic species Ammonia sp. and Elphidium sp. were common in aquaculture sewaged reef. The density of foraminifera in sewaged reefs was lower than non-sewaged reefs. The lower diversity was only detected in the industrial sewaged reef. Assemblage structure was significantly different between sewaged and non-sewaged reefs. The industrial sewaged reef displayed high FORAM Index values (>4.0), reflecting favorable environments for supporting relatively healthy reefs. FORAM Index in aquaculture sewaged reef ranged from 2.0 to 4.0 indicated that the water with organic pollution may support living coral community, but any damage would not be followed by recovery.}, } @article {pmid30231855, year = {2018}, author = {Zeng, Z and Fu, Y and Guo, D and Wu, Y and Ajayi, OE and Wu, Q}, title = {Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {688}, pmid = {30231855}, issn = {1471-2164}, support = {XDB11040400//Chinese Academy of Sciences/ ; 2014CB138405//Ministry of Science and Technology of the People's Republic of China/ ; 31571305//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacterial Proteins/*genetics ; Cytophagaceae/*physiology ; *Genome, Bacterial ; Genomics ; Hemiptera/*genetics/growth & development/*microbiology ; Phylogeny ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Sogatella furcifera is a migratory pest that damages rice plants and causes severe economic losses. Due to its ability to annually migrate long distances, S. furcifera has emerged as a major pest of rice in several Asian countries. Symbiotic relationships of inherited bacteria with terrestrial arthropods have significant implications. The genus Cardinium is present in many types of arthropods, where it influences some host characteristics. We present a report of a newly identified strain of the bacterial endosymbiont Cardinium cSfur in S. furcifera.

RESULT: From the whole genome of S. furcifera previously sequenced by our laboratory, we assembled the whole genome sequence of Cardinium cSfur. The sequence comprised 1,103,593 bp with a GC content of 39.2%. The phylogenetic tree of the Bacteroides phylum to which Cardinium cSfur belongs suggests that Cardinium cSfur is closely related to the other strains (Cardinium cBtQ1 and cEper1) that are members of the Amoebophilaceae family. Genome comparison between the host-dependent endosymbiont including Cardinium cSfur and free-living bacteria revealed that the endosymbiont has a smaller genome size and lower GC content, and has lost some genes related to metabolism because of its special environment, which is similar to the genome pattern observed in other insect symbionts. Cardinium cSfur has limited metabolic capability, which makes it less contributive to metabolic and biosynthetic processes in its host. From our findings, we inferred that, to compensate for its limited metabolic capability, Cardinium cSfur harbors a relatively high proportion of transport proteins, which might act as the hub between it and its host. With its acquisition of the whole operon related to biotin synthesis and glycolysis related genes through HGT event, Cardinium cSfur seems to be undergoing changes while establishing a symbiotic relationship with its host.

CONCLUSION: A novel bacterial endosymbiont strain (Cardinium cSfur) has been discovered. A genomic analysis of the endosymbiont in S. furcifera suggests that its genome has undergone certain changes to facilitate its settlement in the host. The envisaged potential reproduction manipulative ability of the new endosymbiont strain in its S. furcifera host has vital implications in designing eco-friendly approaches to combat the insect pest.}, } @article {pmid29891837, year = {2018}, author = {Clerissi, C and Touchon, M and Capela, D and Tang, M and Cruveiller, S and Genthon, C and Lopez-Roques, C and Parker, MA and Moulin, L and Masson-Boivin, C and Rocha, EPC}, title = {Parallels between experimental and natural evolution of legume symbionts.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2264}, pmid = {29891837}, issn = {2041-1723}, support = {ANR-12-ADAP-0014-01//Agence Nationale de la Recherche (French National Research Agency)/International ; ANR-16-CE20-0011-01//Agence Nationale de la Recherche (French National Research Agency)/International ; ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/International ; ANR-10-LABX-41//Agence Nationale de la Recherche (French National Research Agency)/International ; }, mesh = {Adaptation, Physiological/genetics ; Cupriavidus/genetics/physiology ; *Directed Molecular Evolution ; *Evolution, Molecular ; Fabaceae/*microbiology ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Mimosa/microbiology ; Mutation ; Plasmids/genetics ; Ralstonia solanacearum/genetics/physiology ; Symbiosis/*genetics/physiology ; }, abstract = {The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes remain unknown. Here we compare the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with the experimental evolution of symbiotic Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time span, environment, genetic background, and phenotypic achievement, both processes resulted in rapid genetic diversification dominated by purifying selection. We observe no adaptation in the plasmid carrying the genes responsible for the ecological transition. Instead, adaptation was associated with positive selection in a set of genes that led to the co-option of the same quorum-sensing system in both processes. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to understand symbiogenesis.}, } @article {pmid29608935, year = {2018}, author = {Wang, X and Liu, D and Luo, Y and Zhao, L and Liu, Z and Chou, M and Wang, E and Wei, G}, title = {Comparative analysis of rhizobial chromosomes and plasmids to estimate their evolutionary relationships.}, journal = {Plasmid}, volume = {96-97}, number = {}, pages = {13-24}, doi = {10.1016/j.plasmid.2018.03.001}, pmid = {29608935}, issn = {1095-9890}, mesh = {Chromosomes, Bacterial/*chemistry ; *Evolution, Molecular ; Genetic Variation ; *Phylogeny ; Plant Root Nodulation/physiology ; Plants/*microbiology ; Plasmids/*chemistry/classification/metabolism ; Replicon ; Rhizobium/classification/*genetics ; Selection, Genetic ; Symbiosis/physiology ; }, abstract = {In the present study, complete genomic sequences retrieved from 57 rhizobial strains that covered four genera including 11 species were analyzed comprehensively. The four types of replicons: chromosomes, chromids, nonsymbiotic plasmids, and symbiotic plasmids were investigated and compared among these strains. Results showed that co-evolution occurred among these four replicons based on the similarities in average nucleotide identity. High correlation coefficient r values were observed between chromosomes and chromids, as well as between chromosomes and nonsymbiotic plasmids. Chromosomes and symbiotic plasmids showed different phylogenetic topology based on their core genes. Population structure analyses were performed to extrapolate the evolutionary histories of the test strains based on their chromosomal and symbiotic plasmid background. This resulted in seven ancestral types for chromosomal genes and three ancestral types for symbiotic plasmid genes. Rhizobial strains containing chromosome genes with ancestral type E tend to contain symbiotic plasmid genes with ancestral type II, while rhizobial strains containing chromosome genes with ancestral type G tend to contain symbiotic plasmid genes with ancestral type III. Seventeen strains associated with different host plant species which harbored the symbiotic genes with ancestral type I, exhibited high genetic diversity. In addition, Fu's test of the symbiotic plasmid genes with ancestral type III had undergone an expansion event, implying the influence of negative selection on these symbiotic plasmid genes.}, } @article {pmid29440372, year = {2018}, author = {Ma, M and Powell, DA and Weyand, NJ and Rhodes, KA and Rendón, MA and Frelinger, JA and So, M}, title = {A Natural Mouse Model for Neisseria Colonization.}, journal = {Infection and immunity}, volume = {86}, number = {5}, pages = {}, pmid = {29440372}, issn = {1098-5522}, support = {R56 AI124665/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Disease Models, Animal ; Gram-Negative Bacterial Infections/*immunology/*transmission ; *Host-Pathogen Interactions ; *Immunity, Innate ; Mice/*microbiology ; Neisseria/*pathogenicity ; *Symbiosis ; }, abstract = {Commensals are important for the proper functioning of multicellular organisms. How a commensal establishes persistent colonization of its host is little understood. Studies of this aspect of microbe-host interactions are impeded by the absence of an animal model. We have developed a natural small animal model for identifying host and commensal determinants of colonization and of the elusive process of persistence. Our system couples a commensal bacterium of wild mice, Neisseria musculi, with the laboratory mouse. The pairing of a mouse commensal with its natural host circumvents issues of host restriction. Studies are performed in the absence of antibiotics, hormones, invasive procedures, or genetic manipulation of the host. A single dose of N. musculi, administered orally, leads to long-term colonization of the oral cavity and gut. All mice are healthy. Susceptibility to colonization is determined by host genetics and innate immunity. For N. musculi, colonization requires the type IV pilus. Reagents and powerful tools are readily available for manipulating the laboratory mouse, allowing easy dissection of host determinants controlling colonization resistance. N. musculi is genetically related to human-dwelling commensal and pathogenic Neisseria and encodes host interaction factors and vaccine antigens of pathogenic Neisseria Our system provides a natural approach for studying Neisseria-host interactions and is potentially useful for vaccine efficacy studies.}, } @article {pmid28539635, year = {2017}, author = {Onuma, R and Mishra, N and Miyagishima, SY}, title = {Regulation of chloroplast and nucleomorph replication by the cell cycle in the cryptophyte Guillardia theta.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2345}, pmid = {28539635}, issn = {2045-2322}, mesh = {Algal Proteins/genetics/metabolism ; Amino Acid Sequence ; *Cell Cycle ; Cell Division ; Cell Nucleus/genetics/*metabolism ; Chloroplasts/genetics/*metabolism ; Cryptophyta/classification/genetics/*metabolism ; *DNA Replication ; Gene Expression ; Histones/genetics/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Symbiosis/genetics ; Time Factors ; }, abstract = {The chloroplasts of cryptophytes arose through a secondary endosymbiotic event in which a red algal endosymbiont was integrated into a previously nonphotosynthetic eukaryote. The cryptophytes retain a remnant of the endosymbiont nucleus (nucleomorph) that is replicated once in the cell cycle along with the chloroplast. To understand how the chloroplast, nucleomorph and host cell divide in a coordinated manner, we examined the expression of genes/proteins that are related to nucleomorph replication and chloroplast division as well as the timing of nuclear and nucleomorph DNA synthesis in the cryptophyte Guillardia theta. Nucleus-encoded nucleomorph HISTONE H2A mRNA specifically accumulated during the nuclear S phase. In contrast, nucleomorph-encoded genes/proteins that are related to nucleomorph replication and chloroplast division (FtsZ) are constantly expressed throughout the cell cycle. The results of this study and previous studies on chlorarachniophytes suggest that there was a common evolutionary pattern in which an endosymbiont lost its replication cycle-dependent transcription while cell-cycle-dependent transcriptional regulation of host nuclear genes came to restrict the timing of nucleomorph replication and chloroplast division.}, } @article {pmid30554405, year = {2018}, author = {Le Marquer, M and Bécard, G and Frei Dit Frey, N}, title = {Arbuscular mycorrhizal fungi possess a CLAVATA3/Endosperm surrounding region-related gene that positively regulates symbiosis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15643}, pmid = {30554405}, issn = {1469-8137}, abstract = {The arbuscular mycorrhizal (AM) symbiosis is a beneficial association established between land plants and the members of a subphylum of fungi, the Glomeromycotina. How the two symbiotic partners regulate their association is still enigmatic. Secreted fungal peptides are candidates for regulating this interaction. We searched for fungal peptides with similarities with known plant signaling peptides. We identified CLAVATA (CLV)/EMBRYO SURROUNDING REGION (ESR)-RELATED PROTEIN (CLE) genes in phylogenetically distant AM fungi: four Rhizophagus species and one Gigaspora species. These CLE genes encode a signal peptide for secretion and the conserved CLE C-terminal motif. They seem to be absent in the other fungal clades. R. irregularis and G. rosea CLE genes (RiCLE1 and GrCLE1) are transcriptionally induced in symbiotic versus asymbiotic conditions. Exogenous application of synthetic RiCLE1 peptide on Medicago truncatula affects root architecture, by slowing the apical growth of primary roots and stimulating the formation of lateral roots. In addition, pre-treatement of seedlings with RiCLE1 peptide stimulates mycorrhization. Our findings demonstrate for the first time that in addition to plants and nematodes, AM fungi also possess CLE genes. These results pave the way for deciphering new mechanisms by which AM fungi modulate plant cellular responses during the establishment of AM symbiosis. This article is protected by copyright. All rights reserved.}, } @article {pmid30554292, year = {2018}, author = {Vasilchenko, AS and Valyshev, AV}, title = {Pore-forming bacteriocins: structural-functional relationships.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-018-1610-3}, pmid = {30554292}, issn = {1432-072X}, support = {18-7-8-26//The Program of fundamental research at the Ural Branch of the Russian Academy of Sciences/ ; }, abstract = {Peptides and proteins are important bioorganic compounds in nature, among which a special place is occupied by antimicrobial substances. There are more than 2000 different antimicrobial peptides (AMPs) produced by a variety of living organisms. Bacteriocins produced by bacteria are the minor group, whose chemical structures are most complicated among all AMPs. The review summarized the main points related to antimicrobial action of the bacteriocins including steps of peptide's interaction with bacterial membranes and details of membrane damaging. The membrane-disordered bacteriocins were described in accordance with structural-functional relationships.}, } @article {pmid30552673, year = {2018}, author = {Sudová, R and Kohout, P and Kolaříková, Z and Rydlová, J and Voříšková, J and Suda, J and Španiel, S and Müller-Schärer, H and Mráz, P}, title = {Sympatric diploid and tetraploid cytotypes of Centaurea stoebe s.l. do not differ in arbuscular mycorrhizal communities and mycorrhizal growth response.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {}, doi = {10.1002/ajb2.1206}, pmid = {30552673}, issn = {1537-2197}, support = {SNF 31003A_125314//Swiss National Science Foundation/ ; NPUI LO1417//Charles University/ ; //The Czech Academy of Sciences/ ; }, abstract = {PREMISE OF THE STUDY: Genome duplication is associated with multiple changes at different levels, including interactions with pollinators and herbivores. Yet little is known whether polyploidy may also shape belowground interactions.

METHODS: To elucidate potential ploidy-specific interactions with arbuscular mycorrhizal fungi (AMF), we compared mycorrhizal colonization and assembly of AMF communities in roots of diploid and tetraploid Centaurea stoebe s.l. (Asteraceae) co-occurring in a Central European population. In a follow-up greenhouse experiment, we tested inter-cytotype differences in mycorrhizal growth response by combining ploidy, substrate, and inoculation with native AMF in a full-factorial design.

KEY RESULTS: All sampled plants were highly colonized by AMF, with the Glomeraceae predominating. AMF-community composition revealed by 454-pyrosequencing reflected the spatial distribution of the hosts, but not their ploidy level or soil characteristics. In the greenhouse experiment, the tetraploids produced more shoot biomass than the diploids did when grown in a more fertile substrate, while no inter-cytotype differences were found in a less fertile substrate. AMF inoculation significantly reduced plant growth and improved P uptake, but its effects did not differ between the cytotypes.

CONCLUSIONS: The results do not support our hypotheses that the cytotype structure in a mixed-ploidy population of C. stoebe is mirrored in AMF-community composition and that ploidy-specific fungal communities contribute to cytotype co-existence. Causes and implications of the observed negative growth response to AMF are discussed.}, } @article {pmid30552481, year = {2018}, author = {Shah, A and Prasad, S and Rastogi, B and Dash, S and Saini, J and Pal, PK and Ingalhalikar, M}, title = {Altered structural connectivity of the motor subnetwork in multiple system atrophy with cerebellar features.}, journal = {European radiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00330-018-5874-4}, pmid = {30552481}, issn = {1432-1084}, support = {ECR/2016/000808//Science and Engineering Research Board/ ; }, abstract = {OBJECTIVES: To investigate the structural connectivity of the motor subnetwork in multiple system atrophy with cerebellar features (MSA-C), a distinct subtype of MSA, characterized by predominant cerebellar symptoms.

METHODS: Twenty-three patients with MSA-C and 25 age- and gender-matched healthy controls were recruited for the study. Disease severity was quantified using the Unified Multiple System Atrophy Rating Scale (UMSARS). Diffusion MRI images were acquired and used to compute the structural connectomes (SCs) using probabilistic fiber tracking. The motor network with 12 brain regions and 26 cerebellar regions was extracted and was compared between the groups using analysis of variance at a global (network-wide), nodal (at each node), and edge (at each connection) levels, and was corrected for multiple comparisons. In addition, the acquired connectivity measures were correlated with duration of illness, total Unified MSA Rating Scale (UMSARS), and the motor component score.

RESULTS: Significantly lower global network metrics-global density, transitivity, clustering coefficient, and characteristic path length-were observed in MSA-C (corrected p < 0.05). Reduced nodal strength was observed in the bilateral ventral diencephalon, the left thalamus, and several cerebellar regions. Network-based statistics revealed significant abnormal edge-wise connectivity in 40 connections (corrected p < 0.01), with majority of deficits observed in the cerebellum. Finally, significant negative correlations were observed between UMSARS scores and thalamic and cerebellar connectivity (p < 0.05) as well as between duration of illness and cerebellar connectivity.

CONCLUSIONS: Abnormal connectivity of the basal ganglia and cerebellar network may be causally implicated for the motor features observed in MSA-C.

KEY POINTS: • Structural connectivity of the motor subnetwork was explored in patients with multiple system atrophy with cerebellar features (MSA-C) using probabilistic tractography. • The motor subnetwork in MSA-C has significant alterations in both basal ganglia and cerebellar connectivity, with a higher extent of abnormality in the cerebellum. • These findings may be causally implicated for the motor features of cerebellar dysfunction and parkinsonism observed in MSA-C.}, } @article {pmid30551119, year = {2018}, author = {McClave, SA and Martindale, RG}, title = {Why do current strategies for optimal nutritional therapy neglect the microbiome?.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {60}, number = {}, pages = {100-105}, doi = {10.1016/j.nut.2018.09.024}, pmid = {30551119}, issn = {1873-1244}, abstract = {Strategies for providing optimal nutritional therapy have evolved over time, with the emphasis on specific directives (such as route, use of immunonutrition, high protein, organ-specific formulas, etc.), achieving variable degrees of success for improving outcomes in the intensive care unit. As the largest immune organ in the body comprising the largest interface between the host and the external environment, the gut can have an amplifying effect on a pattern of dysbiosis, immune dysregulation, and multiple organ failure seen in the critically ill patient. Conversely, maintenance of gut integrity can serve to restore a pattern of homeostasis, appropriate immune responses, symbiosis, and clinical recovery. Simply providing refined polymeric formulas as enteral nutrition may not take full advantage of the potential for optimal outcome that could be derived by giving therapy designed to directly stimulate gut defenses and support the intestinal microbiota. This article describes a series of strategies (such as use of intact whole food formulas, soluble fiber, fecal microbial transplantation, serum bovine immunoglobulin, or agents to promote commensal behavior) that should modulate the gut microbiome and shift the critically ill patient toward a pattern of health and recovery.}, } @article {pmid30550604, year = {2018}, author = {Sinnesael, A and Eeckhout, S and Janssens, SB and Smets, E and Panis, B and Leroux, O and Verstraete, B}, title = {Detection of Burkholderia in the seeds of Psychotria punctata (Rubiaceae) - Microscopic evidence for vertical transmission in the leaf nodule symbiosis.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209091}, doi = {10.1371/journal.pone.0209091}, pmid = {30550604}, issn = {1932-6203}, abstract = {BACKGROUND AND AIMS: The bacterial leaf nodule symbiosis is a close interaction between endophytes and their plant hosts, mainly within the coffee family. The interaction between Rubiaceae species and Burkholderia bacteria is unique due to its obligate nature, high specificity, and predominantly vertical transmission of the endophytes to the next generation of host plants. This vertical transmission is intriguing since it is the basis for the uniqueness of the symbiosis. However, unequivocal evidence of the location of the endophytes in the seeds is lacking. The aim of this paper is therefore to demonstrate the presence of the host specific endophyte in the seeds of Psychotria punctata and confirm its precise location. In addition, the suggested location of the endophyte in other parts of the host plant is investigated.

METHODS: To identify and locate the endophyte in Psychotria punctata, a two-level approach was adopted using both a molecular screening method and fluorescent in situ hybridisation microscopy.

KEY RESULTS: The endophytes, molecularly identified as Candidatus Burkholderia kirkii, were detected in the leaves, vegetative and flower buds, anthers, gynoecium, embryos, and young twigs. In addition, they were in situ localised in leaves, flowers and shoot apical meristems, and, for the first time, in between the cotyledons of the embryos.

CONCLUSIONS: Both independent techniques detected the host specific endophyte in close proximity to the shoot apical meristem of the embryo, which confirms for the first time the exact location of the endophytes in the seeds. This study provides reliable proof that the endophytes are maintained throughout the growth and development of the host plant and are transmitted vertically to the offspring.}, } @article {pmid30546856, year = {2018}, author = {Brodl, E and Winkler, A and Macheroux, P}, title = {Molecular Mechanisms of Bacterial Bioluminescence.}, journal = {Computational and structural biotechnology journal}, volume = {16}, number = {}, pages = {551-564}, doi = {10.1016/j.csbj.2018.11.003}, pmid = {30546856}, issn = {2001-0370}, abstract = {Bioluminescence refers to the production of light by living organisms. Bioluminescent bacteria with a variety of bioluminescence emission characteristics have been identified in Vibrionaceae, Shewanellaceae and Enterobacteriaceae. Bioluminescent bacteria are mainly found in marine habitats and they are either free-floating, sessile or have specialized to live in symbiosis with other marine organisms. On the molecular level, bioluminescence is enabled by a cascade of chemical reactions catalyzed by enzymes encoded by the lux operon with the gene order luxCDABEG. The luxA and luxB genes encode the α- and β- subunits, respectively, of the enzyme luciferase producing the light emitting species. LuxC, luxD and luxE constitute the fatty acid reductase complex, responsible for the synthesis of the long-chain aldehyde substrate and luxG encodes a flavin reductase. In bacteria, the heterodimeric luciferase catalyzes the monooxygenation of long-chain aliphatic aldehydes to the corresponding acids utilizing reduced FMN and molecular oxygen. The energy released as a photon results from an excited state flavin-4a-hydroxide, emitting light centered around 490 nm. Advances in the mechanistic understanding of bacterial bioluminescence have been spurred by the structural characterization of protein encoded by the lux operon. However, the number of available crystal structures is limited to LuxAB (Vibrio harveyi), LuxD (Vibrio harveyi) and LuxF (Photobacterium leiognathi). Based on the crystal structure of LuxD and homology models of LuxC and LuxE, we provide a hypothetical model of the overall structure of the LuxCDE fatty acid reductase complex that is in line with biochemical observations.}, } @article {pmid30546353, year = {2018}, author = {Nagel, R and Bieber, JE and Schmidt-Dannert, MG and Nett, RS and Peters, RJ}, title = {A Third Class: Functional Gibberellin Biosynthetic Operon in Beta-Proteobacteria.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2916}, doi = {10.3389/fmicb.2018.02916}, pmid = {30546353}, issn = {1664-302X}, abstract = {The ability of plant-associated microbes to produce gibberellin A (GA) phytohormones was first described for the fungal rice pathogen Gibberella fujikuroi in the 1930s. Recently the capacity to produce GAs was shown for several bacteria, including symbiotic alpha-proteobacteria (α-rhizobia) and gamma-proteobacteria phytopathogens. All necessary enzymes for GA production are encoded by a conserved operon, which appears to have undergone horizontal transfer between and within these two phylogenetic classes of bacteria. Here the operon was shown to be present and functional in a third class, the beta-proteobacteria, where it is found in several symbionts (β-rhizobia). Conservation of function was examined by biochemical characterization of the enzymes encoded by the operon from Paraburkholderia mimosarum LMG 23256T. Despite the in-frame gene fusion between the short-chain alcohol dehydrogenase/reductase and ferredoxin, the encoded enzymes exhibited the expected activity. Intriguingly, together these can only produce GA9, the immediate precursor to the bioactive GA4, as the cytochrome P450 (CYP115) that catalyzes the final hydroxylation reaction is missing, similar to most α-rhizobia. However, phylogenetic analysis indicates that the operon from β-rhizobia is more closely related to examples from gamma-proteobacteria, which almost invariably have CYP115 and, hence, can produce bioactive GA4. This indicates not only that β-rhizobia acquired the operon by horizontal gene transfer from gamma-proteobacteria, rather than α-rhizobia, but also that they independently lost CYP115 in parallel to the α-rhizobia, further hinting at the possibility of detrimental effects for the production of bioactive GA4 by these symbionts.}, } @article {pmid30544498, year = {2018}, author = {Franck, S and Strodtman, KN and Qiu, J and Emerich, DW}, title = {Transcriptomic 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/ijms19123918}, pmid = {30544498}, issn = {1422-0067}, support = {2004-35604-14708//United States Department of Agriculture Cooperative State Research Education and Extension Service Natonal Research Initiative/ ; }, abstract = {The transcriptional activity of Bradyrhizobium diazoefficens isolated from soybean nodules was monitored over the period from symbiosis to late plant nodule senescence. The bacteria retained a near constant level of RNA throughout this period, and the variation in genes demonstrating increased, decreased, and/or patterned transcriptional activity indicates that the bacteria are responding to the changing environment within the nodule as the plant cells progress from an organized cellular structure to an unorganized state of internal decay. The transcriptional variation and persistence of the bacteria suggest that the bacteria are adapting to their environment and acting similar to hemibiotrophs, which survive both as saprophytes on live plant tissues and then as necrophytes on decaying plant tissues. The host plant restrictions of symbiosis make B. diazoefficiens a highly specialized, restricted hemibiotroph.}, } @article {pmid30544020, year = {2018}, author = {Saito, R and Kabeya, M and Nemoto, Y and Oomachi, H}, title = {Monitoring 137Cs concentrations in bird species occupying different ecological niches; game birds and raptors in Fukushima Prefecture.}, journal = {Journal of environmental radioactivity}, volume = {197}, number = {}, pages = {67-73}, doi = {10.1016/j.jenvrad.2018.10.016}, pmid = {30544020}, issn = {1879-1700}, abstract = {This study was conducted to assess radiocesium accumulation in birds after the accident at Tokyo Electric Power Company's Fukushima Daiichi Nuclear Power Station in 2011, with a particular focus on 137Cs, which has a long physical half-life. Results of 137Cs monitoring in four game bird species including two pheasant species and two duck species (copper pheasant, green pheasant, spot-billed duck and mallard) were assessed in Fukushima Prefecture. We also obtained samples from rescued raptors that died during treatment or rehabilitation at the Wildlife Symbiosis Centre in Fukushima Prefecture because of severe injury. We measured the muscle concentrations of 137Cs in four of these raptor species (black kite, northern goshawk, peregrine falcon and ural owl). Comparison of the two pheasant species showed that the copper pheasants inhabiting forested areas had higher 137Cs concentrations in muscle (Bq/kg, fresh mass) than the green pheasants inhabiting mountainous areas near human habitation (i.e., Satoyama). No clear tendencies were observed in 137Cs concentration in muscle of copper pheasants over time, but a tendency to decrease was observed in green pheasants over time. The difference in tendencies between species may be attributable to differences in their food habits and its 137Cs concentration, and also differences in the situation of 137Cs accumulation in their habitat. No significant differences were observed in 137Cs concentration in muscle between the resident spot-billed duck and migratory mallard because of the comparatively short biological of effective half-life of radiocesium. Analysis of 137Cs concentration in muscle of raptor revealed that the concentration was similar to, or lower than, those of pheasants and ducks.}, } @article {pmid30542338, year = {2018}, author = {Campos, C and Carvalho, M and Brígido, C and Goss, MJ and Nobre, T}, title = {Symbiosis Specificity of the Preceding Host Plant Can Dominate but Not Obliterate the Association Between Wheat and Its Arbuscular Mycorrhizal Fungal Partners.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2920}, doi = {10.3389/fmicb.2018.02920}, pmid = {30542338}, issn = {1664-302X}, abstract = {The symbiosis established between arbuscular mycorrhizal fungi (AMF) and roots of most land plants plays a key role in plant nutrient acquisition and alleviation of environmental stresses. Despite the ubiquity of the symbiosis, AMF and host species display significant specificity in their interactions. To clarify preferential associations between wheat (Triticum aestivum) and AMF, we characterized root AMF communities in the transition from two first host species, ryegrass (Lolium rigidum) and yellow-serradella (Ornithopus compressus), grown separately or together, to a second host (wheat), by sequencing the large subunit ribosomal DNA (LSU rDNA) gene. The response of AMF communities in wheat to prior soil disturbance - and consequently of the mycelial network [intact extraradical mycelium (ERM) vs. disrupted mycelium] established with either of the first hosts - was also investigated. Since the outcome of a specific host-symbiont interaction depends on the molecular responses of the host plant upon microbial colonization, we studied the expression of six key symbiosis-related genes in wheat roots. AMF communities on L. rigidum and O. compressus roots were clearly distinct. Within an undisturbed ERM, wheat AMF communities were similar to that of previous host, and O. compressus-wheat-AMF interactions supported a greater growth of wheat than L. rigidum-wheat-AMF interactions. This effect declined when ERM was disrupted, but generated a greater activation of symbiotic genes in wheat, indicating that plant symbiotic program depends on some extent on the colonizing symbiont propagule type. When a mixture of L. rigidum and O. compressus was planted, the wheat colonization pattern resembled that of O. compressus, although this was not reflected in a greater growth. These results show a lasting effect of previous hosts in shaping wheat AMF communities through an efficient use of the established ERM, although not completely obliterating host-symbiont specificity.}, } @article {pmid30285612, year = {2018}, author = {Sánchez-Rangel, D and Hernández-Domínguez, EE and Pérez-Torres, CA and Ortiz-Castro, R and Villafán, E and Rodríguez-Haas, B and Alonso-Sánchez, A and López-Buenfil, A and Carrillo-Ortiz, N and Hernández-Ramos, L and Ibarra-Laclette, E}, title = {Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {721}, pmid = {30285612}, issn = {1471-2164}, support = {2016-1//Secretaría de Agricultura, Ganadería, Desarrollo Rural, Pesca y Alimentación (SAGARPA) - Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA)/ ; 292399//Fondo Institucional de Fomento Regional para el Desarrollo Científico, Tecnológico y de Innovación (FORDECYT)/ ; }, mesh = {Animals ; *Environment ; Fusaric Acid/biosynthesis ; Fusarium/*genetics/growth & development/metabolism/*physiology ; *Gene Expression Profiling ; Hydrogen-Ion Concentration ; Molecular Sequence Annotation ; Phylogeny ; Sequence Homology, Nucleic Acid ; Symbiosis ; Weevils/*microbiology ; }, abstract = {BACKGROUND: The Ambrosia Fusarium Clade phytopathogenic Fusarium fungi species have a symbiotic relationship with ambrosia beetles in the genus Euwallacea (Coleoptera: Curculionidae). Related beetle species referred to as Euwallacea sp. near fornicatus have been spread in California, USA and are recognized as the causal agents of Fusarium dieback, a disease that causes mortality of many plant species. Despite the importance of this fungi, no transcriptomic resources have been generated. The datasets described here represent the first ever transcripts available for these species. We focused our study on the isolated species of Fusarium that is associated with one of the cryptic species referred to as Kuroshio Shot Hole Borer (KSHB) Euwallacea sp. near fornicatus.

RESULTS: Hydrogen concentration is a critical signal in fungi for growth and host colonization, the aim of this study was to evaluate the effect of different pH conditions on growth and gene expression of the fungus Fusarium sp. associated with KSHB. An RNA-seq approach was used to compare the gene expression of the fungus grown for 2 weeks in liquid medium at three different pH levels (5.0, 6.0, and 7.0). An unbuffered treatment was included to evaluate the capability of the fungus to change the pH of its environment and the impact in gene expression. The results showed that the fungus can grow and modulate its genetic expression at different pH conditions; however, growth was stunted in acidic pH in comparison with neutral pH. The results showed a differential expression pattern in each pH condition even when acidic conditions prevailed at the end of the experiment. After comparing transcriptomics data from the three treatments, we found a total of 4,943 unique transcripts that were differentially expressed.

CONCLUSIONS: We identified transcripts related to pH signaling such as the conserved PAL/RIM pathway, some transcripts related to secondary metabolism and other transcripts that were differentially expressed. Our analysis suggests possible mechanisms involved in pathogenicity in this novel Fusarium species. This is the first report that shows transcriptomic data of this pathogen as well as the first report of genes and proteins involved in their metabolism identifying potential virulence factors.}, } @article {pmid29597292, year = {2018}, author = {Bok, E and Mazurek, J and Myc, A and Stosik, M and Wojciech, M and Baldy-Chudzik, K}, title = {Comparison of Commensal Escherichia coli Isolates from Adults and Young Children in Lubuskie Province, Poland: Virulence Potential, Phylogeny and Antimicrobial Resistance.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {4}, pages = {}, pmid = {29597292}, issn = {1660-4601}, mesh = {Adolescent ; Adult ; Age Factors ; Anti-Bacterial Agents/pharmacology ; Child, Preschool ; Drug Resistance, Bacterial/*genetics ; *Escherichia coli/drug effects/genetics/isolation & purification/pathogenicity ; Female ; *Gastrointestinal Microbiome/drug effects/genetics ; *Genetic Variation ; Humans ; Infant ; Male ; Middle Aged ; Phenotype ; *Phylogeny ; Poland ; *Symbiosis ; Virulence/*genetics ; Virulence Factors/genetics ; Young Adult ; }, abstract = {Commensal Escherichia coli population is a dynamic structure which may be important in the pathogenesis of extraintestinal infections. The aim of this study was the comparison of genetic diversity of commensal E. coli isolates from two age group-adults and young children. E. coli strains were isolated on MacConkey agar and identified by biochemical tests. Determination of four major phylogenetic groups, identification of virulence genes and antimicrobial resistance determinants were performed by using multiplex or simplex PCR. Phenotypic analysis of resistance was based on disc-diffusion method. The prevalence of virulence genes was significantly higher among isolates from adults than from young children. Phylogroup B2 predominated among E. coli from adults, whereas phylogroup A was the most common in isolates from young children. The analyses of antimicrobial resistance revealed that resistance to at least one antimicrobial agent and multidrug-resistance were detected significantly more frequent in the isolates from adults than from young children. This study documented that the commensal E. coli isolates from adults showed greater genetic diversity than from young children and constitutes a substantial reservoir of the virulence genes typical for extraintestinal pathogenic E. coli.}, } @article {pmid29286547, year = {2018}, author = {Moog, D and Maier, UG}, title = {Explaining the Origin of Three-Membrane-Bound Plastids in Dinoflagellates and Euglenophytes: Kleptoplastidy via Myzocytosis?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {2}, pages = {}, doi = {10.1002/bies.201700224}, pmid = {29286547}, issn = {1521-1878}, mesh = {Cell Membrane ; Ciliophora ; *Dinoflagellida ; *Euglenida ; Phylogeny ; Plastids ; Symbiosis ; }, } @article {pmid28566699, year = {2017}, author = {Steinert, G and Rohde, S and Janussen, D and Blaurock, C and Schupp, PJ}, title = {Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2542}, pmid = {28566699}, issn = {2045-2322}, mesh = {Animals ; Atlantic Ocean ; Bacteria/classification/*genetics ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; Microbiota/*genetics ; *Phylogeny ; Porifera/*microbiology ; Prokaryotic Cells/classification ; RNA, Ribosomal, 16S/genetics ; Seawater ; Sequence Analysis, DNA ; Sweden ; Symbiosis/physiology ; }, abstract = {Sponges (Porifera) are abundant and diverse members of benthic filter feeding communities in most marine ecosystems, from the deep sea to tropical reefs. A characteristic feature is the associated dense and diverse prokaryotic community present within the sponge mesohyl. Previous molecular genetic studies revealed the importance of host identity for the community composition of the sponge-associated microbiota. However, little is known whether sponge host-specific prokaryotic community patterns observed at 97% 16S rRNA gene sequence similarity are consistent at high taxonomic ranks (from genus to phylum level). In the present study, we investigated the prokaryotic community structure and variation of 24 sponge specimens (seven taxa) and three seawater samples from Sweden. Results show that the resemblance of prokaryotic communities at different taxonomic ranks is consistent with patterns present at 97% operational taxonomic unit level.}, } @article {pmid30538693, year = {2018}, author = {George, F and Daniel, C and Thomas, M and Singer, E and Guilbaud, A and Tessier, FJ and Revol-Junelles, AM and Borges, F and Foligné, B}, title = {Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2899}, doi = {10.3389/fmicb.2018.02899}, pmid = {30538693}, issn = {1664-302X}, abstract = {Lactic acid bacteria (LAB) are representative members of multiple ecosystems on earth, displaying dynamic interactions within animal and plant kingdoms in respect with other microbes. This highly heterogeneous phylogenetic group has coevolved with plants, invertebrates, and vertebrates, establishing either mutualism, symbiosis, commensalism, or even parasitism-like behavior with their hosts. Depending on their location and environment conditions, LAB can be dominant or sometimes in minority within ecosystems. Whatever their origins and relative abundance in specific anatomic sites, LAB exhibit multifaceted ecological and functional properties. While some resident LAB permanently inhabit distinct animal mucosal cavities, others are provided by food and may transiently occupy the gastrointestinal tract. It is admitted that the overall gut microbiome has a deep impact on health and diseases. Here, we examined the presence and the physiological role of LAB in the healthy human and several animal microbiome. Moreover, we also highlighted some dysbiotic states and related consequences for health, considering both the resident and the so-called "transionts" microorganisms. Whether LAB-related health effects act collectively or follow a strain-specificity dogma is also addressed. Besides the highly suggested contribution of LAB to interplay with immune, metabolic, and even brain-axis regulation, the possible involvement of LAB in xenobiotic detoxification processes and metal equilibrium is also tackled. Recent technological developments such as functional metagenomics, metabolomics, high-content screening and design in vitro and in vivo experimental models now open new horizons for LAB as markers applied for disease diagnosis, susceptibility, and follow-up. Moreover, identification of general and more specific molecular mechanisms based on antioxidant, antimicrobial, anti-inflammatory, and detoxifying properties of LAB currently extends their selection and promising use, either as probiotics, in traditional and functional foods, for dedicated treatments and mostly for maintenance of normobiosis and homeostasis.}, } @article {pmid30538687, year = {2018}, author = {Paymaneh, Z and Gryndler, M and Konvalinková, T and Benada, O and Borovička, J and Bukovská, P and Püschel, D and Řezáčová, V and Sarcheshmehpour, M and Jansa, J}, title = {Soil Matrix Determines the Outcome of Interaction Between Mycorrhizal Symbiosis and Biochar for Andropogon gerardii Growth and Nutrition.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2862}, doi = {10.3389/fmicb.2018.02862}, pmid = {30538687}, issn = {1664-302X}, abstract = {Biochar has been heralded as a multipurpose soil amendment to sustainably increase soil fertility and crop yields, affect soil hydraulic properties, reduce nutrient losses, and sequester carbon. Some of the most spectacular results of biochar (and organic nutrient) inputs are the terra preta soils in the Amazon, dark anthropogenic soils with extremely high fertility sustained over centuries. Such soil improvements have been particularly difficult to achieve on a short run, leading to speculations that biochar may need to age (weather) in soil to show its best. Further, interaction of biochar with arbuscular mycorrhizal fungi (AMF), important root symbionts of a great majority of terrestrial plants including most agricultural crops, remains little explored. To study the effect of aged biochar on highly mycotrophic Andropogon gerardii plants and their associated AMF, we made use of softwood biochar, collected from a historic charcoal burning site. This biochar (either untreated or chemically activated, the latter serving as a proxy for freshly prepared biochar) was added into two agricultural soils (acid or alkaline), and compared to soils without biochar. These treatments were further crossed with inoculation with a synthetic AMF community to address possible interactions between biochar and the AMF. Biochar application was generally detrimental for growth and mineral nutrition of our experimental plants, but had no effect on the extent of their root colonized by the AMF, nor did it affect composition of their root-borne AMF communities. In contrast, biochar affected development of two out of five AMF (Claroideoglomus and Funneliformis) in the soil. Establishment of symbiosis with AMF largely mitigated biochar-induced suppression of plant growth and mineral nutrition, mainly by improving plant acquisition of phosphorus. Both mycorrhizal and non-mycorrhizal plants grew well in the acid soil without biochar application, whereas non-mycorrhizal plants remained stunted in the alkaline soils under all situations (with or without biochar). These different and strong effects indicate that response of plants to biochar application are largely dependent on soil matrix and also on microbes such as AMF, and call for further research to enable qualified predictions of the effects of different biochar applications on field-grown crops and soil processes.}, } @article {pmid30538275, year = {2018}, author = {Nicolás, C and Martin-Bertelsen, T and Floudas, D and Bentzer, J and Smits, M and Johansson, T and Troein, C and Persson, P and Tunlid, A}, title = {The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0331-6}, pmid = {30538275}, issn = {1751-7370}, support = {2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, abstract = {Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.}, } @article {pmid30538206, year = {2018}, author = {Harding, K and Turk-Kubo, KA and Sipler, RE and Mills, MM and Bronk, DA and Zehr, JP}, title = {Symbiotic unicellular cyanobacteria fix nitrogen in the Arctic Ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1813658115}, pmid = {30538206}, issn = {1091-6490}, abstract = {Biological dinitrogen (N2) fixation is an important source of nitrogen (N) in low-latitude open oceans. The unusual N2-fixing unicellular cyanobacteria (UCYN-A)/haptophyte symbiosis has been found in an increasing number of unexpected environments, including northern waters of the Danish Straight and Bering and Chukchi Seas. We used nanoscale secondary ion mass spectrometry (nanoSIMS) to measure 15N2 uptake into UCYN-A/haptophyte symbiosis and found that UCYN-A strains identical to low-latitude strains are fixing N2 in the Bering and Chukchi Seas, at rates comparable to subtropical waters. These results show definitively that cyanobacterial N2 fixation is not constrained to subtropical waters, challenging paradigms and models of global N2 fixation. The Arctic is particularly sensitive to climate change, and N2 fixation may increase in Arctic waters under future climate scenarios.}, } @article {pmid30384908, year = {2018}, author = {Fan, M and Liu, Z and Nan, L and Wang, E and Chen, W and Lin, Y and Wei, G}, title = {Isolation, characterization, and selection of heavy metal-resistant and plant growth-promoting endophytic bacteria from root nodules of Robinia pseudoacacia in a Pb/Zn mining area.}, journal = {Microbiological research}, volume = {217}, number = {}, pages = {51-59}, doi = {10.1016/j.micres.2018.09.002}, pmid = {30384908}, issn = {1618-0623}, mesh = {Acclimatization ; Agrobacterium tumefaciens/drug effects/isolation & purification/metabolism ; Bacteria/classification/*drug effects/*isolation & purification/metabolism ; Biodegradation, Environmental ; Biomass ; Carbon-Carbon Lyases/metabolism ; DNA, Bacterial/analysis ; Endophytes/classification/*drug effects/*isolation & purification/metabolism ; Indoleacetic Acids/metabolism ; Lead/toxicity ; Mesorhizobium/drug effects/isolation & purification/metabolism ; Metals, Heavy/*toxicity ; Microbial Sensitivity Tests ; *Mining ; Phylogeny ; *Plant Development ; RNA, Ribosomal, 16S/genetics ; Rhizobium ; Robinia/growth & development/*microbiology ; Root Nodules, Plant/*microbiology ; Seedlings/growth & development ; Siderophores/metabolism ; Soil Microbiology ; Soil Pollutants/metabolism ; Symbiosis ; Zinc/toxicity ; }, abstract = {Multiple heavy metals (HMs) commonly coexist in mining areas, which highlights the necessity to select multiple HM-resistant plant growth-promoting bacteria for improving phytoremediation efficiency. In this study, we isolated and characterized 82 endophytic bacteria from the root nodules of black locust (Robinia pseudoacacia) grown in a Pb-Zn mining area. There were 80 isolates showing resistance to four HMs, 0.01-18.0 mM/L for Cd, 0.2-40.0 mM/L for Zn, 0.3-2.2 mM/L for Pb, and 0.2-1.4 mM/L for Cu. Indole-3-acetic acid production, siderophore production, and 1-aminocyclopropane-1-carboxylate deaminase activity were detected in 43, 50, and 17 isolates, respectively. Two symbiotic isolates selected with the highest potential for HM resistance and PGP traits, designated Mesorhizobium loti HZ76 and Agrobacterium radiobacter HZ6, were evaluated for promotion of plant growth and metal uptake by R. pseudoacacia seedlings grown in pots containing different levels of Cd, Zn, Pb, or Cu. HZ76 significantly increased plant shoot biomass, while HZ6 did not, compared with non-inoculated controls. The results indicate that inoculation with HZ76 or HZ6 relieved HM stress in the plants, depending on the type and concentration of HM in the treatment. Mesorhizobium loti HZ76 may be a better candidate for application in phytoremediation than A. radiobacter HZ6. The microsymbiosis between HM-resistant rhizobia and R. pseudoacacia is an interesting mutualistic system for phytoremediation in mining areas contaminated with multiple HMs.}, } @article {pmid30384903, year = {2018}, author = {Huang, X and Zhu, J and Cai, Z and Lao, Y and Jin, H and Yu, K and Zhang, B and Zhou, J}, title = {Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach.}, journal = {Microbiological research}, volume = {217}, number = {}, pages = {1-13}, doi = {10.1016/j.micres.2018.08.015}, pmid = {30384903}, issn = {1618-0623}, mesh = {Acyltransferases/genetics/metabolism ; Bacteria/classification/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Carbon-Sulfur Lyases/genetics/metabolism ; China ; Dinoflagellida/growth & development/*microbiology ; Eutrophication/physiology ; Marine Biology ; Metagenomics/*methods ; Microbiota/*genetics/*physiology ; Phylogeny ; Proteobacteria/genetics/metabolism ; Quorum Sensing/*genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis ; Sequence Analysis, Protein ; Sequence Homology ; Symbiosis ; Transcription Factors/genetics/metabolism ; }, abstract = {The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.}, } @article {pmid29282064, year = {2017}, author = {Gerardo, N and Hurst, G}, title = {Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {126}, pmid = {29282064}, issn = {1741-7007}, mesh = {Animals ; *Biological Evolution ; Host-Pathogen Interactions/*physiology ; Microbiota/*physiology ; *Symbiosis ; }, abstract = {Over the past decade, there has been a pronounced shift in the study of host-microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes).}, } @article {pmid29173838, year = {2017}, author = {Martino, ME and Leulier, F}, title = {Guest editorial: Microbiota: Microbiota and animal ecology, evolution and physiology: back to the future.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {viii-x}, doi = {10.1016/j.mib.2017.09.017}, pmid = {29173838}, issn = {1879-0364}, mesh = {Animals ; Bacteria/metabolism ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Caenorhabditis elegans/metabolism/microbiology ; Drosophila melanogaster/metabolism/microbiology ; *Environmental Microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Host Microbial Interactions/genetics/*physiology ; Humans ; Plants/metabolism/microbiology ; Symbiosis ; }, } @article {pmid30536933, year = {2018}, author = {Brown, A and Akçay, E}, title = {Evolution of transmission mode in conditional mutualisms with spatial variation in symbiont quality.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1111/evo.13656}, pmid = {30536933}, issn = {1558-5646}, abstract = {Many symbioses have costs and benefits to their hosts that vary with the environmental context, which itself may vary in space. The same symbiont may be a mutualist in one location and a parasite in another. Such spatially conditional mutualisms pose a dilemma for hosts, who might evolve (higher or lower) horizontal or vertical transmission to increase their chances of being infected only where the symbiont is beneficial. To determine how transmission in hosts might evolve, we modeled transmission evolution where the symbiont had a spatially conditional effect on either host lifespan or fecundity. We found that over ecological time, symbionts that affected lifespan but not fecundity led to high frequencies of infected hosts in areas where the symbiont was beneficial and low frequencies elsewhere. In response, hosts evolved increased horizontal transmission only when the symbiont affected lifespan. We also modeled transmission evolution in symbionts, which evolved high horizontal and vertical transmission, indicating a possible host-symbiont conflict over transmission mode. Our results suggest an eco-evolutionary feedback where the component of host fitness affected by a conditionally mutualistic symbiont in turn determines its distribution in the population, and, through this, the transmission mode that evolves. This article is protected by copyright. All rights reserved.}, } @article {pmid30535938, year = {2018}, author = {Tullio, LD and Nakatani, AS and Gomes, DF and Ollero, FJ and Megías, M and Hungria, M}, title = {Revealing the roles of y4wF and tidC genes in Rhizobium tropici CIAT 899: biosynthesis of indolic compounds and impact on symbiotic properties.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-018-1607-y}, pmid = {30535938}, issn = {1432-072X}, support = {CNPq 465133/2014-2, Fundação Araucária-STI, CAPES//INCT-Plant-Growth Promoting Microorganisms for Agricultural Sustainability and Environmental Responsibility/ ; 02.13.08.001.00.00//Empresa Brasileira de Pesquisa Agropecuária/ ; 400468/2016-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; MINECO, AGL2016-77163-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; }, abstract = {Rhizobium tropici CIAT 899 is a strain known by its ability to nodulate a broad range of legume species, to synthesize a variety of Nod factors, its tolerance of abiotic stresses, and its high capacity to fix atmospheric N2, especially in symbiosis with common bean (Phaseolus vulgaris L.). Genes putatively related to the synthesis of indole acetic acid (IAA) have been found in the symbiotic plasmid of CIAT 899, in the vicinity of the regulatory nodulation gene nodD5, and, in this study, we obtained mutants for two of these genes, y4wF and tidC (R. tropici indole-3-pyruvic acid decarboxylase), and investigated their expression in the absence and presence of tryptophan (TRP) and apigenin (API). In general, mutations of both genes increased exopolysaccharide (EPS) synthesis and did not affect swimming or surface motility; mutations also delayed nodule formation, but increased competitiveness. We found that the indole-3-acetamide (IAM) pathway was active in CIAT 899 and not affected by the mutations, and-noteworthy-that API was required to activate the tryptamine (TAM) and the indol-3-pyruvic acid (IPyA) pathways in all strains, particularly in the mutants. High up-regulation of y4wF and tidC genes was observed in both the wild-type and the mutant strains in the presence of API. The results obtained revealed an intriguing relationship between IAA metabolism and nod-gene-inducing activity in R. tropici CIAT 899. We discuss the IAA pathways, and, based on our results, we attribute functions to the y4wF and tidC genes of R. tropici.}, } @article {pmid30535374, year = {2018}, author = {Chang, Y and Liu, H and Liu, M and Liao, X and Sahu, SK and Fu, Y and Song, B and Cheng, S and Kariba, R and Muthemba, S and Hendre, PS and Mayes, S and Ho, WK and Kendabie, P and Wang, S and Li, L and Muchugi, A and Jamnadass, R and Lu, H and Peng, S and Van Deynze, A and Simons, A and Yana-Shapiro, H and Xu, X and Yang, H and Wang, J and Liu, X}, title = {The draft genomes of five agriculturally important African orphan crops.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giy152}, pmid = {30535374}, issn = {2047-217X}, abstract = {Background: Continuous growth of the world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries current face a serious burden of malnutrition, especially in Africa and South and South-East Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize and rice provide the majority of calories. Therefore, to diversify and stabilize global food supply, enhance agricultural productivity and tackle malnutrition, greater use of neglected or underutilized local plants (so-called "orphan crops," but also including a few plants of special significance to agriculture, agroforestry and nutrition) could be a partial solution.

Results: Here, we present draft genome information from five agriculturally, biologically, medicinally and economically important underutilized plants native to Africa; Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea and M. oleifera we have predicted 31707, 20946, 28979, 18937, 18451 protein-coding genes, respectively. By further analysing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors and starch biosynthesis-related genes in these genomes.

Conclusions: These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused and predictable crop improvement programs.}, } @article {pmid30534962, year = {2018}, author = {Gutiérrez-García, K and Bustos-Díaz, ED and Corona-Gómez, JA and Ramos-Aboites, HE and Sélem-Mojica, N and Cruz-Morales, P and Pérez-Farrera, MA and Barona-Gómez, F and Cibrián-Jaramillo, A}, title = {Cycad coralloid roots contain bacterial communities including cyanobacteria and Caulobacter spp that encode niche-specific biosynthetic gene clusters.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evy266}, pmid = {30534962}, issn = {1759-6653}, abstract = {Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Rhizobium and Nostoc species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities. This data was used for whole-genome inferences that suggest two Dioon-specific monophyletic groups, and a level of specialization characteristic of co-evolved symbiotic relationships. Furthermore, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with detection of pigment emissions using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.}, } @article {pmid30534351, year = {2018}, author = {Liang, J and Hoffrichter, A and Brachmann, A and Marín, M}, title = {Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont.}, journal = {Standards in genomic sciences}, volume = {13}, number = {}, pages = {36}, doi = {10.1186/s40793-018-0336-9}, pmid = {30534351}, issn = {1944-3277}, abstract = {Rhizobia bacteria engage in nitrogen-fixing root nodule symbiosis, a mutualistic interaction with legume plants in which a bidirectional nutrient exchange takes place. Occasionally, this interaction is suboptimal resulting in the formation of ineffective nodules in which little or no atmospheric nitrogen fixation occurs. Rhizobium leguminosarum Norway induces ineffective nodules in a wide range of Lotus hosts. To investigate the basis of this phenotype, we sequenced the complete genome of Rl Norway and compared it to the genome of the closely related strain R. leguminosarum bv. viciae 3841. The genome comprises 7,788,085 bp, distributed on a circular chromosome containing 63% of the genomic information and five large circular plasmids. The functionally classified bacterial gene set is distributed evenly among all replicons. All symbiotic genes (nod, fix, nif) are located on the pRLN3 plasmid. Whole genome comparisons revealed differences in the metabolic repertoire and in protein secretion systems, but not in classical symbiotic genes.}, } @article {pmid30533911, year = {2018}, author = {Montecillo, AD and Raymundo, AK and Papa, IA and Aquino, GMB and Rosana, ARR}, title = {Complete Genome Sequence of Rhizobium sp. Strain 11515TR, Isolated from Tomato Rhizosphere in the Philippines.}, journal = {Microbiology resource announcements}, volume = {7}, number = {7}, pages = {}, doi = {10.1128/MRA.00903-18}, pmid = {30533911}, issn = {2576-098X}, abstract = {Rhizobium sp. strain 11515TR was isolated from the rhizosphere of tomato in Laguna, Philippines. The 7.07-Mb complete genome comprises three replicons, one chromosome, and two plasmids, with a G+C content of 59.4% and 6,720 protein-coding genes. The genome encodes gene clusters supporting rhizosphere processes, plant symbiosis, and secondary bioactive metabolites.}, } @article {pmid30533842, year = {2018}, author = {Nguyen, HDT and Cloutier, S and Bromfield, ESP}, title = {Complete Genome Sequence of Bradyrhizobium ottawaense OO99T, an Efficient Nitrogen-Fixing Symbiont of Soybean.}, journal = {Microbiology resource announcements}, volume = {7}, number = {21}, pages = {}, doi = {10.1128/MRA.01477-18}, pmid = {30533842}, issn = {2576-098X}, abstract = {We present the complete genome sequence of Bradyrhizobium ottawaense strain OO99T, a nitrogen-fixing bacterium from root nodules of soybean. The genome consists of a single 8.6-Mb chromosome and includes a symbiosis island. Genes involved in symbiotic nitrogen fixation, stress response, resistance to antibiotics, and toxic compounds were detected.}, } @article {pmid30533769, year = {2018}, author = {Andryuschenko, SV and Ivanova, EV and Perunova, NB and Zdvizhkova, IA and Bekpergenova, AV and Bukharin, OV}, title = {Draft Genome Sequence of Bifidobacterium bifidum Strain ICIS-310, Isolated from the Feces of a Healthy 5-Year-Old Child from Orenburg, Russia.}, journal = {Microbiology resource announcements}, volume = {7}, number = {18}, pages = {}, doi = {10.1128/MRA.01271-18}, pmid = {30533769}, issn = {2576-098X}, abstract = {This report describes the draft genome sequence of Bifidobacterium bifidum strain ICIS-310, isolated from the feces of a healthy 5-year-old child from Orenburg, Russia. The size of the genome was 2,219,632 bp (62.4% G+C content). Annotation revealed 1,886 coding sequences, including 1,718 proteins, 6 rRNA genes, and 52 tRNA genes.}, } @article {pmid30533398, year = {2018}, author = {Brock, DA and Haselkorn, TS and Garcia, JR and Bashir, U and Douglas, TE and Galloway, J and Brodie, F and Queller, DC and Strassmann, JE}, title = {Diversity of Free-Living Environmental Bacteria and Their Interactions With a Bactivorous Amoeba.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {411}, doi = {10.3389/fcimb.2018.00411}, pmid = {30533398}, issn = {2235-2988}, abstract = {A small subset of bacteria in soil interact directly with eukaryotes. Which ones do so can reveal what is important to a eukaryote and how eukaryote defenses might be breached. Soil amoebae are simple eukaryotic organisms and as such could be particularly good for understanding how eukaryote microbiomes originate and are maintained. One such amoeba, Dictyostelium discoideum, has both permanent and temporary associations with bacteria. Here we focus on culturable bacterial associates in order to interrogate their relationship with D. discoideum. To do this, we isolated over 250 D. discoideum fruiting body samples from soil and deer feces at Mountain Lake Biological Station. In one-third of the wild D. discoideum we tested, one to six bacterial species were found per fruiting body sorus (spore mass) for a total of 174 bacterial isolates. The remaining two-thirds of D. discoideum fruiting body samples did not contain culturable bacteria, as is thought to be the norm. A majority (71.4%) of the unique bacterial haplotypes are in Proteobacteria. The rest are in either Actinobacteria, Bacteriodetes, or Firmicutes. The highest bacterial diversity was found in D. discoideum fruiting bodies originating from deer feces (27 OTUs), greater than either of those originating in shallow (11 OTUs) or in deep soil (4 OTUs). Rarefaction curves and the Chao1 estimator for species richness indicated the diversity in any substrate was not fully sampled, but for soil it came close. A majority of the D. discoideum-associated bacteria were edible by D. discoideum and supported its growth (75.2% for feces and 81.8% for soil habitats). However, we found several bacteria genera were able to evade phagocytosis and persist in D. discoideum cells through one or more social cycles. This study focuses not on the entire D. discoideum microbiome, but on the culturable subset of bacteria that have important eukaryote interactions as prey, symbionts, or pathogens. These eukaryote and bacteria interactions may provide fertile ground for investigations of bacteria using amoebas to gain an initial foothold in eukaryotes and of the origins of symbiosis and simple microbiomes.}, } @article {pmid30533318, year = {2018}, author = {Kenkel, CD and Bay, LK}, title = {Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6047}, doi = {10.7717/peerj.6047}, pmid = {30533318}, issn = {2167-8359}, abstract = {The coral symbiosis is the linchpin of the reef ecosystem, yet the mechanisms that promote and maintain cooperation between hosts and symbionts have not been fully resolved. We used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism in which symbionts are inherited directly from parents, predicted to enhance cooperation and holobiont fitness. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, which exhibit environmental acquisition of symbionts, were fragmented and subjected to a 2-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological performance and cooperation. All species exhibited similar decreases in symbiont cell density and net photosynthesis in response to elevated temperature, consistent with the onset of bleaching. Yet baseline cooperation, or translocation of photosynthate, in ambient conditions and the reduction in cooperation in response to elevated temperature differed among species. Although Porites lobata and Galaxea acrhelia did exhibit the highest levels of baseline cooperation, we did not observe universally higher levels of cooperation in vertically transmitting species. Post hoc sequencing of the Symbiodinium ITS-2 locus was used to investigate the potential role of differences in symbiont community composition. Interestingly, reductions in cooperation at the onset of bleaching tended to be associated with increased symbiont community diversity among coral species. The theoretical benefits of evolving vertical transmission are based on the underlying assumption that the host-symbiont relationship becomes genetically uniform, thereby reducing competition among symbionts. Taken together, our results suggest that it may not be vertical transmission per se that influences host-symbiont cooperation, but genetic uniformity of the symbiont community, although additional work is needed to test this hypothesis.}, } @article {pmid30533314, year = {2018}, author = {Kariman, K and Barker, SJ and Tibbett, M}, title = {Structural plasticity in root-fungal symbioses: diverse interactions lead to improved plant fitness.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6030}, doi = {10.7717/peerj.6030}, pmid = {30533314}, issn = {2167-8359}, abstract = {Root-fungal symbioses such as mycorrhizas and endophytes are key components of terrestrial ecosystems. Diverse in trophy habits (obligate, facultative or hemi-biotrophs) and symbiotic relations (from mutualism to parasitism), these associations also show great variability in their root colonization and nutritional strategies. Specialized interface structures such as arbuscules and Hartig nets are formed by certain associations while others are restricted to non-specialized intercellular or intracellular hyphae in roots. In either case, there are documented examples of active nutrient exchange, reinforcing the fact that specialized structures used to define specific mycorrhizal associations are not essential for reciprocal exchange of nutrients and plant growth promotion. In feremycorrhiza (with Austroboletus occidentalis and eucalypts), the fungal partner markedly enhances plant growth and nutrient acquisition without colonizing roots, emphasizing that a conventional focus on structural form of associations may have resulted in important functional components of rhizospheres being overlooked. In support of this viewpoint, mycobiome studies using the state-of-the-art DNA sequencing technologies have unearthed much more complexity in root-fungal relationships than those discovered using the traditional morphology-based approaches. In this review, we explore the existing literature and most recent findings surrounding structure, functioning, and ecology of root-fungal symbiosis, which highlight the fact that plant fitness can be altered by taxonomically/ecologically diverse fungal symbionts regardless of root colonization and interface specialization. Furthermore, transition from saprotrophy to biotrophy seems to be a common event that occurs in diverse fungal lineages (consisting of root endophytes, soil saprotrophs, wood decayers etc.), and which may be accompanied by development of specialized interface structures and/or mycorrhiza-like effects on plant growth and nutrition.}, } @article {pmid30533255, year = {2018}, author = {Koné, NA and Soro, B and Vanié-Léabo, LPL and Konaté, S and Bakayoko, A and Koné, D}, title = {Diversity, phenology and distribution of Termitomyces species in Côte d'Ivoire.}, journal = {Mycology}, volume = {9}, number = {4}, pages = {307-315}, doi = {10.1080/21501203.2018.1500498}, pmid = {30533255}, issn = {2150-1203}, abstract = {The mutualistic symbiosis between termites of the Macrotermitinae subfamily (Isoptera: Termitidae) and fungi of the genus Termitomyces (Basidiomycota: Lyophyllaceae) is of great ecological and socio-economic importance. Seasonal fruit bodies of the symbiotic fungi are regularly collected and sold in Côte d'Ivoire. However, there are very few studies on their diversity, phenology, distribution and especially the socio-economic scope of the fruit bodies of these fungi at a national scale. This study aims at (i) assessing the diversity of Termitomyces fruit bodies in Côte d'Ivoire and (ii) mapping their fructification areas through a determination of their spatiotemporal distribution according to a climatic and phytogeographic gradients. Using ethnomycological surveys all over the Ivorian territory, information was collected from rural populations on the fructification of Termitomyces and their socio-economic importance. Based on these surveys, sampling efforts of these fungi were properly structured and oriented. The results revealed a diversity of 16 species of Termitomyces, including 9 species new to Côte d'Ivoire and 2 probably new to science. Five species were found in the forest zone, nine in theGuinean savannah zone and four in the Sudano-Guinean zone. Termitomyces's fructifications were observed throughout the year, with specific period for each species. All listed species are regularly consumed by populations. However, only Termitomyces letestui (Pat.) R. Heim and Termitomyces schimperi (Pat.) R. Heim are marketed on a relatively large scale.}, } @article {pmid30530738, year = {2018}, author = {Newman-Griffis, AH and Del Cerro, P and Charpentier, M and Meier, I}, title = {Medicago LINC complexes function in nuclear morphology, nuclear movement, and root nodule symbiosis.}, journal = {Plant physiology}, volume = {}, number = {}, pages = {}, doi = {10.1104/pp.18.01111}, pmid = {30530738}, issn = {1532-2548}, abstract = {Nuclear movement is involved in cellular and developmental processes across eukaryotic life, often driven by Linker of Nucleoskeleton and Cytoskeleton (LINC) complexes, which bridge the nuclear envelope (NE) via the interaction of Klarsicht/ANC-1/Syne-1 Homology (KASH) and Sad1/UNC-84 (SUN) proteins. Arabidopsis (Arabidopsis thaliana) LINC complexes are involved in nuclear movement and positioning in several cell types. Observations since the 1950s have described targeted nuclear movement and positioning during symbiosis initiation between legumes and rhizobia, but it has never been established whether these movements are functional or incidental. Here, we identify and characterize LINC complexes in the model legume Medicago truncatula. We show that LINC complex characteristics such as NE localization, dependence of KASH proteins on SUN protein binding for NE enrichment, and direct SUN-KASH binding are conserved between plant species. Using a SUN dominant-negative strategy, we demonstrate that LINC complexes are necessary for proper nuclear shaping and movement in Medicago root hairs, and are important for infection thread initiation and nodulation.}, } @article {pmid30530198, year = {2018}, author = {Hu, D and Baskin, JM and Baskin, CC and Wang, Z and Zhang, S and Yang, X and Huang, Z}, title = {Arbuscular mycorrhizal symbiosis and achene mucilage have independent functions in seedling growth of a desert shrub.}, journal = {Journal of plant physiology}, volume = {232}, number = {}, pages = {1-11}, doi = {10.1016/j.jplph.2018.11.010}, pmid = {30530198}, issn = {1618-1328}, abstract = {Arbuscular mycorrhizal (AM) symbiosis can play a role in improving seedling establishment in deserts, and it has been suggested that achene mucilage facilitates seedling establishment in sandy deserts and that mucilage biodegradation products may improve seedling growth. We aimed to determine if AM symbiosis interacts with achene mucilage in regulating seedling growth in sand dunes. Up to 20 A M fungal taxa colonized Artemisia sphaerocephala roots in the field, and mycorrhizal frequency and colonization intensity exhibited seasonal dynamics. In the greenhouse, total biomass of AM fungal-colonized plants decreased, whereas the root/shoot ratio increased. AM symbiosis resulted in increased concentrations of nutrients and chlorophyll and decreased concentrations of salicylic acid (SA) and abscisic acid (ABA). Achene mucilage had a weaker effect on biomass and on nutrient, chlorophyll, and phytohormone concentration than did AM symbiosis. We suggest that AM symbiosis and achene mucilage act independently in enhancing seedling establishment in sandy deserts.}, } @article {pmid30527539, year = {2018}, author = {Hanachi, M and Manichanh, C and Schoenenberger, A and Pascal, V and Levenez, F and Cournède, N and Doré, J and Melchior, JC}, title = {Altered host-gut microbes symbiosis in severely malnourished anorexia nervosa (AN) patients undergoing enteral nutrition: An explicative factor of functional intestinal disorders?.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnu.2018.10.004}, pmid = {30527539}, issn = {1532-1983}, abstract = {BACKGROUND: Functional intestinal disorders (FIDs) are frequently observed in patients with anorexia nervosa (AN). Relationship between FIDs and a potential gut microbiota dysbiosis has been poorly explored.

OBJECTIVE: We aimed to determine an association between FIDs severity and dysbiosis of the intestinal microbiota in a severely malnourished patient population with AN undergoing enteral nutrition.

DESIGN: Faecal microbiota of AN (DSM IVr criteria) female inpatients were collected and compared to healthy controls based on 16S rRNA profiling. The severity of FIDs was evaluated in patients and healthy controls using Francis Score.

RESULTS: Thirty-three patients (BMI: 11,7 ± 1,5; Age: 32 ± 12) and 22 healthy controls (BMI: 21 ± 2; age: 36 ± 12) were included. A marked dysbiosis was identified in AN patients compared to healthy controls (p = 0.03). Some potentially pathogenic bacterial genera (Klebsiella, Salmonella) were more abundant in AN patients whereas, other bacterial symbionts (Eubacterium and Roseburia) involved in immune balance were significantly less abundant in patients than controls. Severity of FIDs was strongly correlated with several microbial genera (r = -0.581 for an unknown genus belonging to Peptostreptococcaceae family; r = 0.392 for Dialister, r = 0.444 for Robinsoniella and r = 0.488 for Enterococcus). Other associations between dysbiosis, clinical and biological characteristics were identified including severity of undernutrition (BMI).

CONCLUSION: Observed gut microbiota dysbiosis in malnourished patients with anorexia nervosa is correlated with the severity of FIDs and other metabolic disturbances, which strongly suggests an altered host-microbe symbiosis.}, } @article {pmid30311875, year = {2018}, author = {Barelli, L and Moreira, CC and Bidochka, MJ}, title = {Initial stages of endophytic colonization by Metarhizium involves rhizoplane colonization.}, journal = {Microbiology (Reading, England)}, volume = {164}, number = {12}, pages = {1531-1540}, doi = {10.1099/mic.0.000729}, pmid = {30311875}, issn = {1465-2080}, abstract = {Here we assessed the time course of rhizoplane colonization by the endophytic insect pathogenic fungus Metarhizium robertsii. We describe a method of quantifying root colonization of bean plants by M. robertsii using quantitative polymerase chain reaction (qPCR). Results of this method were compared to the standard plate count method using colony-forming units (c.f.u.). Both the c.f.u. and qPCR methods were used to monitor the time-course of haricot bean (Phaseolus vulgaris) colonization by a strain of M. robertsii that expresses the green fluorescent protein (ARSEF 2575-GFP) for colony verification. There was a strong correlation between the results of the c.f.u. and qPCR methods, indicating that both methods are well suited for the determination of colonization of P. vulgaris roots by M. robertsii. Primers for a catalase gene (cat) amplified DNA from M. robertsii, M. brunneum and M. guizhouense. Primers for a nitrogen response-regulator (nrr) additionally detected M. acridum and M. flavoviride, whereas Metarhizium perilipin-like protein (mpl) primers were specific to M. robertsii alone. However, cat was the only target that specifically amplified Metarhizium in experiments utilizing non-sterile soil. Endophytic colonization of P. vulgaris at 60 days post-inoculation with M. robertsii was detected from surface-sterilized roots with more sensitivity using our qPCR technique over the c.f.u. method. Our results suggest that there is a prolonged period of rhizoplane colonization by Metarhizium with transient, low-level endophytic colonization of the root system of P. vulgaris that persists for the entirety of the plant life cycle.}, } @article {pmid30291510, year = {2018}, author = {Inagaki, T and Matsuura, K}, title = {Extended mutualism between termites and gut microbes: nutritional symbionts contribute to nest hygiene.}, journal = {Die Naturwissenschaften}, volume = {105}, number = {9-10}, pages = {52}, pmid = {30291510}, issn = {1432-1904}, support = {25221206//Japan Society for the Promotion of Science/ ; }, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; *Bacterial Physiological Phenomena ; Gastrointestinal Tract/microbiology ; Isoptera/*microbiology ; *Symbiosis ; }, abstract = {All higher eukaryotes have established symbiotic relationships with diverse microorganisms. One of the most well-characterized symbiotic systems is that of termites and their intestinal microorganisms, which digest cellulose. Recently, diverse types of symbioses between gut microbes and host organisms including humans have received growing attention for various features of their complex interactions beyond nutrition. In termites, researchers are beginning to explore such function of gut symbionts, but only the contribution to internal immunity against entomopathogen is known in a few species. Here, we report that gut symbionts of the dampwood termite Zootermopsis nevadensis protect nests from the spread of the commensal bacterium Serratia marcescens, which has pathogenic potential. Defaunated termites dispersed S. marcescens in the surrounding environment by feeding on the bacteria, which then survived passage through their alimentary tracts, while non-defaunated termites did not. Loss of gut symbionts caused a significant reduction in intestinal acetate, which is an important carbon source for termites. Culture experiments showed that acetate had significant inhibitory effects on S. marcescens at a concentration as low as 12 mM, which indicated that the intestinal acetate of non-defaunated termites (40-130 mM) was capable of suppressing this bacterium. These results suggest that digestive derivatives produced by intestinal symbionts play an essential role in nest hygiene in addition to their nutritional function for termites. Our study provides a better understanding of the multifunctionality of symbiotic relationships in diverse organisms beyond nutrition.}, } @article {pmid30193163, year = {2018}, author = {Lei, YJ and Tian, Y and Zhang, J and Sun, L and Kong, XW and Zuo, W and Kong, LC}, title = {Microalgae cultivation and nutrients removal from sewage sludge after ozonizing in algal-bacteria system.}, journal = {Ecotoxicology and environmental safety}, volume = {165}, number = {}, pages = {107-114}, doi = {10.1016/j.ecoenv.2018.08.096}, pmid = {30193163}, issn = {1090-2414}, mesh = {Ammonium Compounds/analysis ; Bacteria/*growth & development ; *Biomass ; Bioreactors/*microbiology ; Microalgae/*growth & development ; Nitrogen/analysis ; Oxygen/metabolism ; Ozone ; Phosphorus/analysis ; Sewage/*chemistry/microbiology ; Symbiosis ; Waste Disposal, Fluid/methods ; }, abstract = {The feasibility of growing algae in concentrated wastewater generated from sludge ozonation for simultaneous nutrients removal and biomass production was studied. The effects of bacteria addition into microalgae on nutrients removal, biomass yield and settleability, the growth rate of algae and concentrations of extracellular polymeric substances (EPS) and soluble microbial products (SMP) were investigated. The results showed that the growth rate of algae in algal-bacteria system (0.2182) was improved than in algae-only system (0.1852), while both of them are comparable with others reported previously. And the addition of bacteria enhanced COD, NH4+-N, TN and TP removal rate by 23.9 ± 3.3%, 27.7 ± 3.6%, 16.6 ± 1.8% and 14.9 ± 2.2%, respectively. And 32.8 ± 0.7% of the TN and 50.3 ± 1.8% of the TP were recycled from ozonated sludge-supernatant (OSS) being absorbed into algal-bacterial biomass. The algal-bacteria system also demonstrated advantages on biomass settleability and heavy metals removal. Finally, the mechanism involving matter exchange and algal-bacteria system on OSS treatment in this study were discussed through evaluation of nutrients, SMP and EPS contents, nitrogen and phosphorus balance.}, } @article {pmid30150426, year = {2018}, author = {Kostaropoulos, T and Papageorgiou, L and Champeris Tsaniras, S and Vlachakis, D and Eliopoulos, E}, title = {Carcinogenic Pesticide Control via Hijacking Endosymbiosis; The Paradigm of DSB-A from Wolbachia pipientis for the Management of Otiorhynchus singularis.}, journal = {In vivo (Athens, Greece)}, volume = {32}, number = {5}, pages = {1051-1062}, pmid = {30150426}, issn = {1791-7549}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; *Carcinogens/toxicity ; *Chemical Safety ; Coleoptera/*microbiology ; Conserved Sequence ; Drug Design ; *Insect Control ; Models, Molecular ; *Pesticides/adverse effects ; Phylogeny ; Protein Conformation ; Protein Disulfide-Isomerases/chemistry/classification/genetics/*metabolism ; Structure-Activity Relationship ; *Symbiosis ; Wolbachia/enzymology/genetics/*metabolism ; }, abstract = {BACKGROUND/AIM: Pesticides have little, if any specificity, to the pathogen they target in most cases. Wide spectrum toxic chemicals are being used to remove pestcides and salvage crops and economies linked to agriculture. The burden on the environment, public health and economy is huge. Traditional pestcide control is based on administering heavy loads of highly toxic compounds and elements that essentially strip all life from the field. Those chemicals are a leading cause of increased cancer related deaths in countryside. Herein, the Trojan horse of endosymbiosis was used, in an effort to control pests using high specificity compounds in reduced quantities.

MATERIALS AND METHODS: Our pipeline has been applied on the case of Otiorhynchus singularis, which is a very widespread pest, whose impact is devastating on a repertoire of crops. To date, there is no specific pesticide nor agent to control it. The deployed strategy involves the inhibition of the key DSB-A enzyme of its endosymbiotic Wolbachia pipientis bacterial strain.

RESULTS: Our methodology, provides the means to design, test and identify highly specific pestcide control substances that minimize the impact of toxic chemicals on health, economy and the environment.

CONCLUSION: All in all, in this study a radical computer-based pipeline is proposed that could be adopted under many other similar scenarios and pave the way for precision agriculture via optimized pest control.}, } @article {pmid30142922, year = {2018}, author = {Stabili, L and Parisi, MG and Parrinello, D and Cammarata, M}, title = {Cnidarian Interaction with Microbial Communities: From Aid to Animal's Health to Rejection Responses.}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30142922}, issn = {1660-3397}, mesh = {Animals ; Biotechnology/methods ; Cnidaria/microbiology/*physiology ; Homeostasis/immunology ; *Immunity, Innate ; Microbiota/*immunology ; Mucous Membrane/immunology/microbiology ; Phylogeny ; Symbiosis/*immunology ; }, abstract = {The phylum Cnidaria is an ancient branch in the tree of metazoans. Several species exert a remarkable longevity, suggesting the existence of a developed and consistent defense mechanism of the innate immunity capable to overcome the potential repeated exposure to microbial pathogenic agents. Increasing evidence indicates that the innate immune system in Cnidarians is not only involved in the disruption of harmful microorganisms, but also is crucial in structuring tissue-associated microbial communities that are essential components of the Cnidarian holobiont and useful to the animal's health for several functions, including metabolism, immune defense, development, and behavior. Sometimes, the shifts in the normal microbiota may be used as "early" bio-indicators of both environmental changes and/or animal disease. Here the Cnidarians relationships with microbial communities and the potential biotechnological applications are summarized and discussed.}, } @article {pmid30132152, year = {2018}, author = {Hinojosa-Vidal, E and Marco, F and Martínez-Alberola, F and Escaray, FJ and García-Breijo, FJ and Reig-Armiñana, J and Carrasco, P and Barreno, E}, title = {Characterization of the responses to saline stress in the symbiotic green microalga Trebouxia sp. TR9.}, journal = {Planta}, volume = {248}, number = {6}, pages = {1473-1486}, pmid = {30132152}, issn = {1432-2048}, support = {CGL2016-391 79158-P//Ministerio de Economía y Competitividad/ ; BES-2013-065511//Ministerio de Economía y Competitividad/ ; PROMETEO/2017/039)//Generalitat Valenciana/ ; }, mesh = {Abscisic Acid/metabolism ; Ascomycota/genetics/*physiology/ultrastructure ; Chlorophyta/genetics/microbiology/*physiology/ultrastructure ; Lichens/genetics/microbiology/*physiology/ultrastructure ; Microalgae/genetics/microbiology/*physiology/ultrastructure ; Photosynthesis/drug effects ; Plant Growth Regulators/metabolism ; Salinity ; Sodium Chloride/pharmacology ; Stress, Physiological ; *Symbiosis ; }, abstract = {MAIN CONCLUSION: For the first time we provide a study on the physiological, ultrastructural and molecular effects of salt stress on a terrestrial symbiotic green microalga, Trebouxia sp. TR9. Although tolerance to saline conditions has been thoroughly studied in plants and, to an extent, free-living microalgae, scientific data regarding salt stress on symbiotic lichen microalgae is scarce to non-existent. Since lichen phycobionts are capable of enduring harsh, restrictive and rapidly changing environments, it is interesting to study the metabolic machinery operating under these extreme conditions. We aim to determine the effects of prolonged exposure to high salt concentrations on the symbiotic phycobiont Trebouxia sp. TR9, isolated from the lichen Ramalina farinacea. Our results suggest that, when this alga is confronted with extreme saline conditions, the cellular structures are affected to an extent, with limited chlorophyll content loss and photosynthetic activity remaining after 72 h of exposure to 5 M NaCl. Furthermore, this organism displays a rather different molecular response compared to land plants and free-living halophile microalgae, with no noticeable increase in ABA levels and ABA-related gene expression until the external NaCl concentration is raised to 3 M NaCl. Despite this, the ABA transduction pathway seems functional, since the ABA-related genes tested are responsive to exogenous ABA. These observations could suggest that this symbiotic green alga may have developed alternative molecular pathways to cope with highly saline environments.}, } @article {pmid30059700, year = {2018}, author = {Kraberger, S and Hofstetter, RW and Potter, KA and Farkas, K and Varsani, A}, title = {Genomoviruses associated with mountain and western pine beetles.}, journal = {Virus research}, volume = {256}, number = {}, pages = {17-20}, doi = {10.1016/j.virusres.2018.07.019}, pmid = {30059700}, issn = {1872-7492}, mesh = {Animals ; Arizona ; Ascomycota/growth & development/virology ; Cluster Analysis ; DNA Viruses/classification/*genetics/*isolation & purification ; *Genome, Viral ; Nematocera/microbiology/*virology ; Phylogeny ; Recombination, Genetic ; Sequence Homology ; Symbiosis ; }, abstract = {Genomoviruses are circular single-stranded DNA viruses (∼2 kb in size) classified into nine genera, they are highly diverse and have been identified in a variety of samples ranging from fungi to animal sera. Here we identify five genomoviruses belonging to the Gemycircularvirus genus and one to the Gemykibivirus genus from mountain pine beetle and western pine beetle sampled in Arizona. Collectively these six viral genomes share <77% genome-wide pairwise identity and hence represent six new species of genomoviruses. Four of the gemycircularviruses from the mountain pine beetles are recombinant, with one having a recombinant region that spans the entire capsid protein. Pine beetles have a symbiotic relationship with certain tree pathogenic fungi. Therefore given that Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1, a gemycircularvirus, induces hypovirulence in the plant pathogenic fungus Sclerotinia sclerotiorum and infects the mycophagous insect Lycoriella ingenua, it is possible that the six genomoviruses identified here may be directly associated with the pine beetle fungal symbionts and/or with the insects themselves.}, } @article {pmid30028247, year = {2018}, author = {Kurečič, M and Rijavec, T and Hribernik, S and Lapanje, A and Kleinschek, KS and Maver, U}, title = {Novel electrospun fibers with incorporated commensal bacteria for potential preventive treatment of the diabetic foot.}, journal = {Nanomedicine (London, England)}, volume = {13}, number = {13}, pages = {1583-1594}, doi = {10.2217/nnm-2018-0014}, pmid = {30028247}, issn = {1748-6963}, mesh = {Biocompatible Materials/administration & dosage/chemistry ; Carboxymethylcellulose Sodium/administration & dosage/chemistry ; Diabetic Foot/*drug therapy/microbiology/pathology ; Humans ; Microbiota/drug effects ; Microscopy, Electron, Scanning ; Nanofibers/*administration & dosage/chemistry/microbiology ; Polyethylene Glycols/chemistry/pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Staphylococcus epidermidis/chemistry/*growth & development/ultrastructure ; *Symbiosis ; }, abstract = {AIM: A novel electrospun biocompatible nanofibrous material loaded with commensal bacteria for potential preventive treatment of the diabetic foot was developed.

MATERIALS & METHODS: Two biocompatible polymers (carboxymethylcellulose and polyethylene oxide) were combined with a bacterium isolate from the skin located between the toes of a healthy adult (identified using a matrix-assisted laser desorption/ionization mass spectrometry-based method as a strain of Staphylococcus epidermidis). Higher bacteria loads in the material were assured through their encapsulation in polyethylenimine. The nanofibrous material was characterized using scanning electron microscopy, zeta-potential measurements and through evaluation of cell growth and viability.

RESULTS & DISCUSSION: nanometer formation was confirmed using scanning electron microscopy, while the zeta-potential measurements revealed successful bacteria encapsulation. Viable and sufficiently growing cells were confirmed prior and after their incorporation.

CONCLUSION: The prepared materials were proven suitable to deliver viable commensal bacteria in a comparable share to the Staphylococcaceae in the foot microbiome making this approach promising for preventive diabetic foot treatment.}, } @article {pmid30017857, year = {2018}, author = {Xu, L and Zhang, Y and Zhang, S and Deng, J and Lu, M and Zhang, L and Zhang, J}, title = {Comparative analysis of the immune system of an invasive bark beetle, Dendroctonus valens, infected by an entomopathogenic fungus.}, journal = {Developmental and comparative immunology}, volume = {88}, number = {}, pages = {65-69}, doi = {10.1016/j.dci.2018.07.002}, pmid = {30017857}, issn = {1879-0089}, mesh = {Animals ; Beauveria/*immunology/pathogenicity ; China ; Coleoptera/*immunology/microbiology ; Forests ; Gene Expression Profiling ; Host-Pathogen Interactions/*immunology ; Introduced Species ; Larva/immunology/microbiology ; Ophiostomatales/*immunology/pathogenicity ; Pest Control, Biological/*methods ; Phylogeny ; Pinus ; Symbiosis/immunology ; Transcriptome/immunology ; }, abstract = {Dendroctonus valens LeConte is one of the most economically important forest pest in China. Leptographium procerum, a mutualistic fungus can assist the host beetle in overcoming the pine's chemical defenses, and Beauveria bassiana, an entomopathogenic fungus has shown high beetle killing efficiency. Considering that the D. valens immune system remains unknown at the genomic level, a mutualistic and antagonistic fungus associated with the beetle provides an ideal model for studying immune interactions between the insect and associated fungi. Here, B. bassiana killed most tested larvae more effectively than L. procerum and Tween. The entomopathogenic fungus provoked stronger responses than the symbiotic fungus at the transcriptome level. We identified 185 immunity-related genes, including pattern recognition receptors, signal modulators, members of immune pathways (Toll, IMD, and JAK/STAT), and immune effectors. Quantitative real-time PCR analysis confirmed that several recognition receptors and effector genes were activated at 1 or 2 days post infection, while the effector genes were suppressed at 4 days post infection by B. bassiana, respectively. In contrast, effector genes were upregulated in response to L. procerum. Together, this study provides a comprehensive sequence resource and insight into the D. valens immune system and lays a basis for understanding the molecular aspects of the interaction between the host and associated fungi.}, } @article {pmid29874266, year = {2018}, author = {Vet, S and de Buyl, S and Faust, K and Danckaert, J and Gonze, D and Gelens, L}, title = {Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0197462}, pmid = {29874266}, issn = {1932-6203}, mesh = {Computer Simulation ; *Microbial Interactions ; *Models, Biological ; Netherlands ; Population Dynamics ; Symbiosis/*physiology ; }, abstract = {We theoretically study the dynamics of two interacting microbial species in the chemostat. These species are competitors for a common resource, as well as mutualists due to cross-feeding. In line with previous studies (Assaneo, et al., 2013; Holland, et al., 2010; Iwata, et al., 2011), we demonstrate that this system has a rich repertoire of dynamical behavior, including bistability. Standard Lotka-Volterra equations are not capable to describe this particular system, as these account for only one type of interaction (mutualistic or competitive). We show here that the different steady state solutions can be well captured by an extended Lotka-Volterra model, which better describe the density-dependent interaction (mutualism at low density and competition at high density). This two-variable model provides a more intuitive description of the dynamical behavior than the chemostat equations.}, } @article {pmid29717331, year = {2018}, author = {Houles, A and Vincent, B and David, M and Ducousso, M and Galiana, A and Juillot, F and Hannibal, L and Carriconde, F and Fritsch, E and Jourand, P}, title = {Ectomycorrhizal Communities Associated with the Legume Acacia spirorbis Growing on Contrasted Edaphic Constraints in New Caledonia.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {964-975}, pmid = {29717331}, issn = {1432-184X}, support = {N° 2013/1434//CIFRE/ ; ANR-12-ADAP-0017 ADASPIR//Agence Nationale pour la Recherche (FR)/ ; }, mesh = {Acacia/growth & development/*microbiology ; Basidiomycota/classification/*physiology ; Mycorrhizae/classification/*physiology ; New Caledonia ; Soil/*chemistry ; *Soil Microbiology ; Symbiosis ; }, abstract = {This study aims to characterize the ectomycorrhizal (ECM) communities associated with Acacia spirorbis, a legume tree widely spread in New Caledonia that spontaneously grows on contrasted edaphic constraints, i.e. calcareous, ferralitic and volcano-sedimentary soils. Soil geochemical parameters and diversity of ECM communities were assessed in 12 sites representative of the three mains categories of soils. The ectomycorrhizal status of Acacia spirorbis was confirmed in all studied soils, with a fungal community dominated at 92% by Basidiomycota, mostly represented by/tomentella-thelephora (27.6%), /boletus (15.8%), /sebacina (10.5%), /russula-lactarius (10.5%) and /pisolithus-scleroderma (7.9%) lineages. The diversity and the proportion of the ECM lineages were similar for the ferralitic and volcano-sedimentary soils but significantly different for the calcareous soils. These differences in the distribution of the ECM communities were statistically correlated with pH, Ca, P and Al in the calcareous soils and with Co in the ferralitic soils. Altogether, these data suggest a high capacity of A. spirorbis to form ECM symbioses with a large spectrum of fungi regardless the soil categories with contrasted edaphic parameters.}, } @article {pmid29675704, year = {2018}, author = {Saucedo-Carabez, JR and Ploetz, RC and Konkol, JL and Carrillo, D and Gazis, R}, title = {Partnerships Between Ambrosia Beetles and Fungi: Lineage-Specific Promiscuity Among Vectors of the Laurel Wilt Pathogen, Raffaelea lauricola.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {925-940}, pmid = {29675704}, issn = {1432-184X}, mesh = {Animals ; Female ; Florida ; Ophiostomatales/*physiology ; Persea/*microbiology ; Plant Diseases/*microbiology ; *Symbiosis ; Weevils/classification/*microbiology ; }, abstract = {Nutritional mutualisms that ambrosia beetles have with fungi are poorly understood. Although these interactions were initially thought to be specific associations with a primary symbiont, there is increasing evidence that some of these fungi are associated with, and move among, multiple beetle partners. We examined culturable fungi recovered from mycangia of ambrosia beetles associated with trees of Persea humilis (silk bay, one site) and P. americana (avocado, six commercial orchards) that were affected by laurel wilt, an invasive disease caused by a symbiont, Raffaelea lauricola, of an Asian ambrosia beetle, Xyleborus glabratus. Fungi were isolated from 20 adult females of X. glabratus from silk bay and 70 each of Xyleborus affinis, Xyleborus bispinatus, Xyleborus volvulus, Xyleborinus saxesenii, and Xylosandrus crassiusculus from avocado. With partial sequences of ribosomal (LSU and SSU) and nuclear (β-tubulin) genes, one to several operational taxonomic units (OTUs) of fungi were identified in assayed individuals. Distinct populations of fungi were recovered from each of the examined beetle species. Raffaelea lauricola was present in all beetles except X. saxesenii and X. crassiusculus, and Raffaelea spp. predominated in Xyleborus spp. Raffaelea arxii, R. subalba, and R. subfusca were present in more than a single species of Xyleborus, and R. arxii was the most abundant symbiont in both X. affinis and X. volvulus. Raffaelea aguacate was detected for the first time in an ambrosia beetle (X. bispinatus). Yeasts (Ascomycota, Saccharomycotina) were found consistently in the mycangia of the examined beetles, and distinct, putatively co-adapted populations of these fungi were associated with each beetle species. Greater understandings are needed for how mycangia in ambrosia beetles interact with fungi, including yeasts which play currently underresearched roles in these insects.}, } @article {pmid29663039, year = {2018}, author = {Birnbaum, C and Bissett, A and Teste, FP and Laliberté, E}, title = {Symbiotic N2-Fixer Community Composition, but Not Diversity, Shifts in Nodules of a Single Host Legume Across a 2-Million-Year Dune Chronosequence.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1009-1020}, pmid = {29663039}, issn = {1432-184X}, support = {DE120100352//Australian Research Council/ ; DP130100016//Australian Research Council/ ; }, mesh = {Acacia/metabolism/*microbiology ; Environment ; Microbiota ; *Nitrogen Fixation ; Oxidoreductases/analysis ; Plant Proteins/analysis ; Root Nodules, Plant/metabolism/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; Symbiosis ; Western Australia ; }, abstract = {Long-term soil age gradients are useful model systems to study how changes in nutrient limitation shape communities of plant root mutualists because they represent strong natural gradients of nutrient availability, particularly of nitrogen (N) and phosphorus (P). Here, we investigated changes in the dinitrogen (N2)-fixing bacterial community composition and diversity in nodules of a single host legume (Acacia rostellifera) across the Jurien Bay chronosequence, a retrogressive 2 million-year-old sequence of coastal dunes representing an exceptionally strong natural soil fertility gradient. We collected nodules from plants grown in soils from five chronosequence stages ranging from very young (10s of years; associated with strong N limitation for plant growth) to very old (> 2,000,000 years; associated with strong P limitation), and sequenced the nifH gene in root nodules to determine the composition and diversity of N2-fixing bacterial symbionts. A total of 335 unique nifH gene operational taxonomic units (OTUs) were identified. Community composition of N2-fixing bacteria within nodules, but not diversity, changed with increasing soil age. These changes were attributed to pedogenesis-driven shifts in edaphic conditions, specifically pH, exchangeable manganese, resin-extractable phosphate, nitrate and nitrification rate. A large number of common N2-fixing bacteria genera (e.g. Bradyrhizobium, Ensifer, Mesorhizobium and Rhizobium) belonging to the Rhizobiaceae family (α-proteobacteria) comprised 70% of all raw sequences and were present in all nodules. However, the oldest soils, which show some of the lowest soil P availability ever recorded, harboured the largest proportion of unclassified OTUs, suggesting a unique set of N2-fixing bacteria adapted to extreme P limitation. Our results show that N2-fixing bacterial composition varies strongly during long-term ecosystem development, even within the same host, and therefore rhizobia show strong edaphic preferences.}, } @article {pmid29516314, year = {2018}, author = {Li, L and Mohamad, OAA and Ma, J and Friel, AD and Su, Y and Wang, Y and Musa, Z and Liu, Y and Hedlund, BP and Li, W}, title = {Synergistic plant-microbe interactions between endophytic bacterial communities and the medicinal plant Glycyrrhiza uralensis F.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {10}, pages = {1735-1748}, doi = {10.1007/s10482-018-1062-4}, pmid = {29516314}, issn = {1572-9699}, support = {31200008//National Natural Science Foundation of China/ ; 31670009//National Natural Science Foundation of China/ ; 201509655013//China Scholarship Council/ ; }, mesh = {Bacteria/*classification/isolation & purification/metabolism ; *Bacterial Physiological Phenomena ; *Endophytes ; Glycyrrhiza uralensis/*microbiology/*physiology ; Lipolysis ; Microbiota ; Molecular Typing ; Nitrogen Fixation ; Phosphates/metabolism ; Plants, Medicinal/microbiology ; Proteolysis ; Quantitative Trait, Heritable ; *Symbiosis ; }, abstract = {Little is known about the composition, diversity, and geographical distribution of bacterial communities associated with medicinal plants in arid lands. To address this, a collection of 116 endophytic bacteria were isolated from wild populations of the herb Glycyrrhiza uralensis Fisch (licorice) in Xinyuan, Gongliu, and Tekesi of Xinjiang Province, China, and identified based on their 16S rRNA gene sequences. The endophytes were highly diverse, including 20 genera and 35 species. The number of distinct bacterial genera obtained from root tissues was higher (n = 14) compared to stem (n = 9) and leaf (n = 6) tissue. Geographically, the diversity of culturable endophytic genera was higher at the Tekesi (n = 14) and Xinyuan (n = 12) sites than the Gongliu site (n = 4), reflecting the extremely low organic carbon content, high salinity, and low nutrient status of Gongliu soils. The endophytic bacteria exhibited a number of plant growth-promoting activities ex situ, including diazotrophy, phosphate and potassium solubilization, siderophore production, auxin synthesis, and production of hydrolytic enzymes. Twelve endophytes were selected based on their ex situ plant growth-promoting activities for growth chamber assays to test for their ability to promote growth of G. uralensis F. and Triticum aestivum (wheat) plants. Several strains belonging to the genera Bacillus (n = 6) and Achromobacter (n = 1) stimulated total biomass production in both G. uralensis and T. aestivum under low-nutrient conditions. This work is the first report on the isolation and characterization of endophytes associated with G. uralensis F. in arid lands. The results demonstrate the broad diversity of endophytes associated with wild licorice and suggest that some Bacillus strains may be promising candidates for biofertilizers to promote enhanced survival and growth of licorice and other valuable crops in arid environments.}, } @article {pmid29501373, year = {2018}, author = {Horká, I and De Grave, S and Fransen, CHJM and Petrusek, A and Ďuriš, Z}, title = {Multiple origins and strong phenotypic convergence in fish-cleaning palaemonid shrimp lineages.}, journal = {Molecular phylogenetics and evolution}, volume = {124}, number = {}, pages = {71-81}, doi = {10.1016/j.ympev.2018.02.006}, pmid = {29501373}, issn = {1095-9513}, mesh = {Acclimatization ; Animals ; Bayes Theorem ; Behavior, Animal ; Likelihood Functions ; Palaemonidae/*physiology ; Perciformes/*physiology ; Phenotype ; *Phylogeny ; Pigmentation ; *Symbiosis ; }, abstract = {Several species of palaemonid shrimps are known to act as fish-cleaning symbionts, with cleaning interactions ranging from dedicated (obligate) to facultative. We confirmed five evolutionarily independent origins of fish cleaning symbioses within the family Palaemonidae based on a phylogenetic analysis and the ancestral state reconstruction of 68 species, including 13 fish-cleaners from the genera Ancylomenes, Brachycarpus, Palaemon, Periclimenes, and Urocaridella. We focus in particular on two distantly related lineages of fish cleaning shrimps with allopatric distributions, the Indo-West Pacific Ancylomenes and the western Atlantic monophyletic Ancylomenes/Periclimenes group, which exhibit striking similarities in morphology, colouration and complex behaviour. Specifically, representatives of both lineages are similar in: (1) the general body shape and colour pattern; (2) the utilization of sea anemones as conspicuous cleaning stations; and (3) the use of sideways body swaying to visually promote their bright colour spots in order to attract fish clients. Such morphological, ecological and ethological convergences are apparently due to adaptations to fish cleaning linked to the establishment of similar modes of communication with fish clients in these species.}, } @article {pmid29426952, year = {2018}, author = {Volland, JM and Schintlmeister, A and Zambalos, H and Reipert, S and Mozetič, P and Espada-Hinojosa, S and Turk, V and Wagner, M and Bright, M}, title = {NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {714-727}, pmid = {29426952}, issn = {1751-7370}, support = {294343//European Research Council/International ; P 24565//Austrian Science Fund FWF/Austria ; }, mesh = {Autoradiography ; Carbon/metabolism ; Carbon Cycle ; Chemoautotrophic Growth ; Gammaproteobacteria/genetics/*physiology ; In Situ Hybridization, Fluorescence ; Mass Spectrometry ; Oligohymenophorea/*microbiology/*physiology ; Oxidation-Reduction ; Sulfides/metabolism ; *Symbiosis ; }, abstract = {The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells fix substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells. Fluorescence in situ hybridization of freshly collected ciliates revealed that the vast majority of ingested microbial cells were ectosymbionts.}, } @article {pmid29410456, year = {2018}, author = {Guidolin, AS and Cataldi, TR and Labate, CA and Francis, F and Cônsoli, FL}, title = {Spiroplasma affects host aphid proteomics feeding on two nutritional resources.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2466}, pmid = {29410456}, issn = {2045-2322}, mesh = {Amino Acids/biosynthesis ; Animals ; Aphids/*genetics/metabolism/microbiology ; Carbohydrate Metabolism/genetics ; Citrus sinensis/*chemistry/parasitology ; Energy Metabolism/genetics ; Gene Expression ; Gene Expression Profiling ; Gene Ontology ; Heat-Shock Proteins/genetics/metabolism ; Insect Proteins/*genetics/metabolism ; Molecular Sequence Annotation ; Proteome/*genetics/metabolism ; Proteomics/methods ; Spiroplasma/*physiology ; Symbiosis/*physiology ; }, abstract = {Bacterial symbionts are broadly distributed among insects, influencing their bioecology to different degrees. Aphids carry a number of secondary symbionts that can influence aphid physiology and fitness attributes. Spiroplasma is seldom reported as an aphid symbiont, but a high level of infection has been observed in one population of the tropical aphid Aphis citricidus. We used sister isolines of Spiroplasma-infected (Ac-BS) and Spiroplasma-free (Ac-B) aphids reared on sweet orange (optimum host) and orange jasmine (suboptimum host) to demonstrate the effects of Spiroplasma infection in the aphid proteome profile. A higher number of proteins were differently abundant in aphids feeding on orange jasmine, indicating an impact of host plant quality. In both host plants, the majority of proteins affected by Spiroplasma infection were heat shock proteins, proteins linked to cell function and structure, and energy metabolism. Spiroplasma also induced changes in proteins involved in antimicrobial activity, carbohydrate processing and metabolism, amino acid synthesis and metabolism in aphids feeding on orange jasmine. We discuss on how the aphid host proteome is differentially affected by Spiroplasma infection when the host is exploiting host plants with different nutritional values.}, } @article {pmid29396559, year = {2018}, author = {Massé, A and Domart-Coulon, I and Golubic, S and Duché, D and Tribollet, A}, title = {Early skeletal colonization of the coral holobiont by the microboring Ulvophyceae Ostreobium sp.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2293}, pmid = {29396559}, issn = {2045-2322}, mesh = {Animal Shells/*microbiology ; Animals ; Anthozoa/*microbiology ; Chlorophyta/classification/genetics/*growth & development ; Genetic Variation ; Metagenome ; Ribulose-Bisphosphate Carboxylase/genetics ; *Symbiosis ; }, abstract = {Ostreobium sp. (Bryopsidales, Ulvophyceae) is a major microboring alga involved in tropical reef dissolution, with a proposed symbiotic lifestyle in living corals. However, its diversity and colonization dynamics in host's early life stages remained unknown. Here, we mapped microborer distribution and abundance in skeletons of the branching coral Pocillopora damicornis from the onset of calcification in primary polyps (7 days) to budding juvenile colonies (1 and 3 months) growing on carbonate and non-carbonate substrates pre-colonized by natural biofilms, and compared them to adult colonies (in aquarium settings). Primary polyps were surprisingly already colonized by microboring filaments and their level of invasion depended on the nature of settlement substrate and the extent of its pre-colonization by microborers. Growth of early coral recruits was unaffected even when microborers were in close vicinity to the polyp tissue. In addition to morphotype observations, chloroplast-encoded rbcL gene sequence analyses revealed nine new Ostreobium clades (OTU99%) in Pocillopora coral. Recruits and adults shared one dominant rbcL clade, undetected in larvae, but also present in aquarium seawater, carbonate and non-carbonate settlement substrates, and in corals from reef settings. Our results show a substratum-dependent colonization by Ostreobium clades, and indicate horizontal transmission of Ostreobium-coral associations.}, } @article {pmid29396397, year = {2018}, author = {Watanabe, S and Yoshimura, J and Hasegawa, E}, title = {Ants improve the reproduction of inferior morphs to maintain a polymorphism in symbiont aphids.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2313}, pmid = {29396397}, issn = {2045-2322}, mesh = {Animals ; Ants/*physiology ; Aphids/*growth & development ; Biodiversity ; Biological Variation, Population ; *Polymorphism, Genetic ; *Sexual Behavior, Animal ; *Symbiosis ; }, abstract = {Identifying stable polymorphisms is essential for understanding biodiversity. Distinctive polymorphisms are rare in nature because a superior morph should dominate a population. In addition to the three known mechanisms for polymorphism persistence, we recently reported a fourth mechanism: protection of the polymorphism by symbionts. Attending ants preferentially protect polymorphic aphid colonies consisting of green and red morphs. Here, we show that attending ants manipulate the reproductive rate of their preferred green morphs to equal that of the red morphs, leading to the persistence of the polymorphism within the colonies. We could not, however, explain how the ants maintained the polymorphism in aphid colonies regardless of inter-morph competition. Manipulation by symbionts may be important for the maintenance of polymorphisms and the resulting biodiversity in certain symbiotic systems.}, } @article {pmid29382931, year = {2018}, author = {Wang, B and Lu, M and Cook, JM and Yang, DR and Dunn, DW and Wang, RW}, title = {Chemical camouflage: a key process in shaping an ant-treehopper and fig-fig wasp mutualistic network.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1833}, pmid = {29382931}, issn = {2045-2322}, mesh = {Animals ; Ants/*physiology ; Biological Evolution ; Biological Mimicry/*physiology ; Ficus/parasitology ; Hemiptera/*physiology ; Host-Parasite Interactions/physiology ; Hydrocarbons/metabolism ; Inflorescence/physiology ; Pollination/physiology ; Predatory Behavior/physiology ; Seeds/parasitology ; Symbiosis/*physiology ; Wasps/*physiology ; }, abstract = {Different types of mutualisms may interact, co-evolve and form complex networks of interdependences, but how species interact in networks of a mutualistic community and maintain its stability remains unclear. In a mutualistic network between treehoppers-weaver ants and fig-pollinating wasps, we found that the cuticular hydrocarbons of the treehoppers are more similar to the surface chemical profiles of fig inflorescence branches (FIB) than the cuticular hydrocarbons of the fig wasps. Behavioral assays showed that the cuticular hydrocarbons from both treehoppers and FIBs reduce the propensity of weaver ants to attack treehoppers even in the absence of honeydew rewards, suggesting that chemical camouflage helps enforce the mutualism between weaver ants and treehoppers. High levels of weaver ant and treehopper abundances help maintain the dominance of pollinating fig wasps in the fig wasp community and also increase fig seed production, as a result of discriminative predation and disturbance by weaver ants of ovipositing non-pollinating fig wasps (NPFWs). Ants therefore help preserve this fig-pollinating wasp mutualism from over exploitation by NPFWs. Our results imply that in this mutualistic network chemical camouflage plays a decisive role in regulating the behavior of a key species and indirectly shaping the architecture of complex arthropod-plant interactions.}, } @article {pmid29321691, year = {2018}, author = {Mohamed, AR and Cumbo, VR and Harii, S and Shinzato, C and Chan, CX and Ragan, MA and Satoh, N and Ball, EE and Miller, DJ}, title = {Deciphering the nature of the coral-Chromera association.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {776-790}, pmid = {29321691}, issn = {1751-7370}, mesh = {Alveolata/genetics/*physiology ; Animals ; Anthozoa/genetics/growth & development/*parasitology/physiology ; Biological Evolution ; Coral Reefs ; Larva/genetics/growth & development/metabolism/parasitology ; Photosynthesis ; *Symbiosis ; Transcriptome ; }, abstract = {Since the discovery of Chromera velia as a novel coral-associated microalga, this organism has attracted interest because of its unique evolutionary position between the photosynthetic dinoflagellates and the parasitic apicomplexans. The nature of the relationship between Chromera and its coral host is controversial. Is it a mutualism, from which both participants benefit, a parasitic relationship, or a chance association? To better understand the interaction, larvae of the common Indo-Pacific reef-building coral Acropora digitifera were experimentally infected with Chromera, and the impact on the host transcriptome was assessed at 4, 12, and 48 h post-infection using Illumina RNA-Seq technology. The transcriptomic response of the coral to Chromera was complex and implies that host immunity is strongly suppressed, and both phagosome maturation and the apoptotic machinery is modified. These responses differ markedly from those described for infection with a competent strain of the coral mutualist Symbiodinium, instead resembling those of vertebrate hosts to parasites and/or pathogens such as Mycobacterium tuberculosis. Consistent with ecological studies suggesting that the association may be accidental, the transcriptional response of A. digitifera larvae leads us to conclude that Chromera could be a coral parasite, commensal, or accidental bystander, but certainly not a beneficial mutualist.}, } @article {pmid29026656, year = {2017}, author = {Harris, HMB and Bourin, MJB and Claesson, MJ and O'Toole, PW}, title = {Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal.}, journal = {Microbial genomics}, volume = {3}, number = {8}, pages = {e000115}, pmid = {29026656}, issn = {2057-5858}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; Genomics ; Lactobacillus salivarius/*genetics ; Mammals ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L. salivarius using bioinformatic techniques. The main aim of the study was to describe intra-species diversity and to determine how this diversity is spread across the replicons. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Additionally, the presence of extra linear and circular megaplasmids is noted in several strains, while small plasmids are not always present. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters and several clustered regularly interspaced short palindromic repeats-associated systems show a lot of variation on the chromosome. Overall, despite its reputation as a mammalian gastrointestinal tract specialist, the intra-specific variation of L. salivarius reveals potential strain-dependant effects on human health.}, } @article {pmid28812548, year = {2018}, author = {Kuhn, KA and Schulz, HM and Regner, EH and Severs, EL and Hendrickson, JD and Mehta, G and Whitney, AK and Ir, D and Ohri, N and Robertson, CE and Frank, DN and Campbell, EL and Colgan, SP}, title = {Bacteroidales recruit IL-6-producing intraepithelial lymphocytes in the colon to promote barrier integrity.}, journal = {Mucosal immunology}, volume = {11}, number = {2}, pages = {357-368}, pmid = {28812548}, issn = {1935-3456}, support = {R37 DK050189/DK/NIDDK NIH HHS/United States ; R29 DK050189/DK/NIDDK NIH HHS/United States ; R01 DK103639/DK/NIDDK NIH HHS/United States ; K08 DK107905/DK/NIDDK NIH HHS/United States ; R01 DK050189/DK/NIDDK NIH HHS/United States ; T32 AR007534/AR/NIAMS NIH HHS/United States ; R01 DK104713/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroidaceae/*physiology ; Cell Membrane Permeability/genetics ; Citrobacter rodentium/*immunology ; Colon/*immunology ; Dysbiosis/*immunology ; Enterobacteriaceae Infections/*immunology ; Gastrointestinal Microbiome/*immunology ; Homeostasis ; Immunity, Innate ; Interleukin-6/genetics/*metabolism ; Intestinal Mucosa/*physiology ; Intraepithelial Lymphocytes/microbiology/*physiology ; Mice, Inbred C57BL ; Mice, Knockout ; Myeloid Differentiation Factor 88/metabolism ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Interactions between the microbiota and distal gut are important for the maintenance of a healthy intestinal barrier; dysbiosis of intestinal microbial communities has emerged as a likely contributor to diseases that arise at the level of the mucosa. Intraepithelial lymphocytes (IELs) are positioned within the epithelial barrier, and in the small intestine they function to maintain epithelial homeostasis. We hypothesized that colon IELs promote epithelial barrier function through the expression of cytokines in response to interactions with commensal bacteria. Profiling of bacterial 16S ribosomal RNA revealed that candidate bacteria in the order Bacteroidales are sufficient to promote IEL presence in the colon that in turn produce interleukin-6 (IL-6) in a MyD88 (myeloid differentiation primary response 88)-dependent manner. IEL-derived IL-6 is functionally important in the maintenance of the epithelial barrier as IL-6-/- mice were noted to have increased paracellular permeability, decreased claudin-1 expression, and a thinner mucus gel layer, all of which were reversed by transfer of IL-6+/+ IELs, leading to protection of mice in response to Citrobacter rodentium infection. Therefore, we conclude that microbiota provide a homeostatic role for epithelial barrier function through regulation of IEL-derived IL-6.}, } @article {pmid28631141, year = {2018}, author = {Lee, KR and Wakeel, A and Chakraborty, P and Foote, CS and Kajiura, L and Barrozo, JC and Chan, AC and Bazarov, AV and Spitler, R and Kutny, PM and Denegre, JM and Taft, RA and Seemann, J and Rice, BW and Contag, CH and Rutt, BK and Bell, CB}, title = {Cell Labeling with Magneto-Endosymbionts and the Dissection of the Subcellular Location, Fate, and Host Cell Interactions.}, journal = {Molecular imaging and biology : MIB : the official publication of the Academy of Molecular Imaging}, volume = {20}, number = {1}, pages = {55-64}, pmid = {28631141}, issn = {1860-2002}, support = {T32 CA009695/CA/NCI NIH HHS/United States ; R43 EB019239/EB/NIBIB NIH HHS/United States ; T32 CA 009695/CA/NCI NIH HHS/United States ; R44 EB019239/EB/NIBIB NIH HHS/United States ; R43EB019239/EB/NIBIB NIH HHS/United States ; R43 TR001202/TR/NCATS NIH HHS/United States ; R01 EB019458/EB/NIBIB NIH HHS/United States ; S10 RR026351/RR/NCRR NIH HHS/United States ; R43TR001202/TR/NCATS NIH HHS/United States ; R01 GM096070/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Autophagy ; *Cell Communication ; Cell Line, Tumor ; *Cell Tracking ; Contrast Media/chemistry ; Ferrozine/metabolism ; Humans ; Iron/metabolism ; Magnetite Nanoparticles/*chemistry/ultrastructure ; Mice, Inbred BALB C ; Rats ; Reproducibility of Results ; *Staining and Labeling ; Subcellular Fractions/metabolism ; *Symbiosis ; }, abstract = {PURPOSE: The purposes of this study are to characterize magneto-endosymbiont (ME) labeling of mammalian cells and to discern the subcellular fate of these living contrast agents. MEs are novel magnetic resonance imaging (MRI) contrast agents that are being used for cell tracking studies. Understanding the fate of MEs in host cells is valuable for designing in vivo cell tracking experiments.

PROCEDURES: The ME's surface epitopes, contrast-producing paramagnetic magnetosomal iron, and genome were studied using immunocytochemistry (ICC), Fe and MRI contrast measurements, and quantitative polymerase chain reaction (qPCR), respectively. These assays, coupled with other common assays, enabled validation of ME cell labeling and dissection of ME subcellular processing.

RESULTS: The assays mentioned above provide qualitative and quantitative assessments of cell labeling, the subcellular localization and the fate of MEs. ICC results, with an ME-specific antibody, qualitatively shows homogenous labeling with MEs. The ferrozine assay shows that MEs have an average of 7 fg Fe/ME, ∼30 % of which contributes to MRI contrast and ME-labeled MDA-MB-231 (MDA-231) cells generally have 2.4 pg Fe/cell, implying ∼350 MEs/cell. Adjusting the concentration of Fe in the ME growth media reduces the concentration of non-MRI contrast-producing Fe. Results from the qPCR assay, which quantifies ME genomes in labeled cells, shows that processing of MEs begins within 24 h in MDA-231 cells. ICC results suggest this intracellular digestion of MEs occurs by the lysosomal degradation pathway. MEs coated with listeriolysin O (LLO) are able to escape the primary phagosome, but subsequently co-localize with LC3, an autophagy-associated molecule, and are processed for digestion. In embryos, where autophagy is transiently suppressed, MEs show an increased capacity for survival and even replication. Finally, transmission electron microscopy (TEM) of ME-labeled MDA-231 cells confirms that the magnetosomes (the MRI contrast-producing particles) remain intact and enable in vivo cell tracking.

CONCLUSIONS: MEs are used to label mammalian cells for the purpose of cell tracking in vivo, with MRI. Various assays described herein (ICC, ferrozine, and qPCR) allow qualitative and quantitative assessments of labeling efficiency and provide a detailed understanding of subcellular processing of MEs. In some cell types, MEs are digested, but the MRI-producing particles remain. Coating with LLO allows MEs to escape the primary phagosome, enhances retention slightly, and confirms that MEs are ultimately processed by autophagy. Numerous intracellular bacteria and all endosymbiotically derived organelles have evolved molecular mechanisms to avoid intracellular clearance, and identification of the specific processes involved in ME clearance provides a framework on which to develop MEs with enhanced retention in mammalian cells.}, } @article {pmid28616842, year = {2018}, author = {Brewer, KD and Spitler, R and Lee, KR and Chan, AC and Barrozo, JC and Wakeel, A and Foote, CS and Machtaler, S and Rioux, J and Willmann, JK and Chakraborty, P and Rice, BW and Contag, CH and Bell, CB and Rutt, BK}, title = {Characterization of Magneto-Endosymbionts as MRI Cell Labeling and Tracking Agents.}, journal = {Molecular imaging and biology : MIB : the official publication of the Academy of Molecular Imaging}, volume = {20}, number = {1}, pages = {65-73}, pmid = {28616842}, issn = {1860-2002}, support = {T32 CA009695/CA/NCI NIH HHS/United States ; T32 CA 009695/CA/NCI NIH HHS/United States ; R43 TR001202/TR/NCATS NIH HHS/United States ; S10 RR026351/RR/NCRR NIH HHS/United States ; RT2-02018//California Institute for Regenerative Medicine/International ; 1R43TR001202-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Cell Line, Tumor ; Cell Survival ; *Cell Tracking ; Female ; Humans ; *Magnetic Resonance Imaging ; Magnetite Nanoparticles/*chemistry ; Mice, Nude ; *Symbiosis ; }, abstract = {PURPOSE: Magneto-endosymbionts (MEs) show promise as living magnetic resonance imaging (MRI) contrast agents for in vivo cell tracking. Here we characterize the biomedical imaging properties of ME contrast agents, in vitro and in vivo.

PROCEDURES: By adapting and engineering magnetotactic bacteria to the intracellular niche, we are creating magneto-endosymbionts (MEs) that offer advantages relative to passive iron-based contrast agents (superparamagnetic iron oxides, SPIOs) for cell tracking. This work presents a biomedical imaging characterization of MEs including: MRI transverse relaxivity (r 2) for MEs and ME-labeled cells (compared to a commercially available iron oxide nanoparticle); microscopic validation of labeling efficiency and subcellular locations; and in vivo imaging of a MDA-MB-231BR (231BR) human breast cancer cells in a mouse brain.

RESULTS: At 7T, r 2 relaxivity of bare MEs was higher (250 s-1 mM-1) than that of conventional SPIO (178 s-1 mM-1). Optimized in vitro loading of MEs into 231BR cells yielded 1-4 pg iron/cell (compared to 5-10 pg iron/cell for conventional SPIO). r 2 relaxivity dropped by a factor of ~3 upon loading into cells, and was on the same order of magnitude for ME-loaded cells compared to SPIO-loaded cells. In vivo, ME-labeled cells exhibited strong MR contrast, allowing as few as 100 cells to be detected in mice using an optimized 3D SPGR gradient-echo sequence.

CONCLUSIONS: Our results demonstrate the potential of magneto-endosymbionts as living MR contrast agents. They have r 2 relaxivity values comparable to traditional iron oxide nanoparticle contrast agents, and provide strong MR contrast when loaded into cells and implanted in tissue.}, } @article {pmid30521551, year = {2018}, author = {Vernocchi, P and Del Chierico, F and Russo, A and Majo, F and Rossitto, M and Valerio, M and Casadei, L and La Storia, A and De Filippis, F and Rizzo, C and Manetti, C and Paci, P and Ercolini, D and Marini, F and Fiscarelli, EV and Dallapiccola, B and Lucidi, V and Miccheli, A and Putignani, L}, title = {Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208171}, doi = {10.1371/journal.pone.0208171}, pmid = {30521551}, issn = {1932-6203}, abstract = {BACKGROUND: Cystic fibrosis (CF) is a disorder affecting the respiratory, digestive, reproductive systems and sweat glands. This lethal hereditary disease has known or suspected links to the dysbiosis gut microbiota. High-throughput meta-omics-based approaches may assist in unveiling this complex network of symbiosis modifications.

OBJECTIVES: The aim of this study was to provide a predictive and functional model of the gut microbiota enterophenotype of pediatric patients affected by CF under clinical stability.

METHODS: Thirty-one fecal samples were collected from CF patients and healthy children (HC) (age range, 1-6 years) and analysed using targeted-metagenomics and metabolomics to characterize the ecology and metabolism of CF-linked gut microbiota. The multidimensional data were low fused and processed by chemometric classification analysis.

RESULTS: The fused metagenomics and metabolomics based gut microbiota profile was characterized by a high abundance of Propionibacterium, Staphylococcus and Clostridiaceae, including Clostridium difficile, and a low abundance of Eggerthella, Eubacterium, Ruminococcus, Dorea, Faecalibacterium prausnitzii, and Lachnospiraceae, associated with overexpression of 4-aminobutyrate (GABA), choline, ethanol, propylbutyrate, and pyridine and low levels of sarcosine, 4-methylphenol, uracil, glucose, acetate, phenol, benzaldehyde, and methylacetate. The CF gut microbiota pattern revealed an enterophenotype intrinsically linked to disease, regardless of age, and with dysbiosis uninduced by reduced pancreatic function and only partially related to oral antibiotic administration or lung colonization/infection.

CONCLUSIONS: All together, the results obtained suggest that the gut microbiota enterophenotypes of CF, together with endogenous and bacterial CF biomarkers, are direct expression of functional alterations at the intestinal level. Hence, it's possible to infer that CFTR impairment causes the gut ecosystem imbalance.This new understanding of CF host-gut microbiota interactions may be helpful to rationalize novel clinical interventions to improve the affected children's nutritional status and intestinal function.}, } @article {pmid30520354, year = {2018}, author = {Yoshikawa, A and Goto, R and Asakura, A}, title = {Morphology and Habitats of the Hermit-Crab-Associated Calyptraeid Gastropod Ergaea walshi.}, journal = {Zoological science}, volume = {35}, number = {6}, pages = {494-504}, doi = {10.2108/zs180046}, pmid = {30520354}, issn = {0289-0003}, abstract = {Ergaea walshi, a gastropod with a markedly flat shell, often lives inside empty snail shells occupied by hermit crabs. We investigated its lifestyle, shell growth pattern, and habitat preference for host hermit crabs and host snail shells. Four hundred sixteen snail shells, including 363 shells with hermit crabs and 53 empty shells, were collected from intertidal zones of sandy and muddy flats around Kii Peninsula, Japan. The specimens comprised seven hermit crab species occupying 24 shell species; E. walshi was harbored in 13.2% of snail shells with hermit crabs and 17.0% of those without hermit crabs. Although no preference was detected for particular species of hermit crab or snail shell, E. walshi preferred to live inside of snail shells with wider apertures used by comparatively bigger hermit crabs. This suggests that the occurrence of E. walshi was influenced by host size rather than host species. When looking at growth patterns, we found that the attached shell portion of E. walshi continued to be enlarged horizontally, while growth in shell height slowed at approximately 5.0 mm. The conspicuously flattened shell of E. walshi is considered as a growth pattern for adapting to the narrow space within the snail shell occupied by hermit crabs. Consistent with this idea, our comparison of shell growth patterns in 23 calyptraeid species showed that shell of E. walshi is the flattest in this family.}, } @article {pmid30519652, year = {2018}, author = {Kountche, BA and Novero, M and Jamil, M and Asami, T and Bonfante, P and Al-Babili, S}, title = {Effect of the strigolactone analogs methyl phenlactonoates on spore germination and root colonization of arbuscular mycorrhizal fungi.}, journal = {Heliyon}, volume = {4}, number = {11}, pages = {e00936}, doi = {10.1016/j.heliyon.2018.e00936}, pmid = {30519652}, issn = {2405-8440}, abstract = {Strigolactones (SLs), a novel class of plant hormones, are key regulator of plant architecture and mediator of biotic interactions in the rhizosphere. Root-released SLs initiate the establishment of arbuscular mycorrhizal (AM) symbiosis by inducing spore germination and hyphal branching in AM fungi (AMF). However, these compounds also trigger the germination of root parasitic weeds, paving the way for deleterious infestation. Availability of SLs is required for investigating of their functions and also for application in agriculture. However, natural SLs are difficult to synthesize due to their complex structure and cannot be isolated at large scale, as they are released at very low concentrations. Therefore, there is a need for synthetic SL analogs. Recently, we reported on the development of simple SL analogs, methyl phenlactonoates (MPs), which show high SL activity in plants. Here, we investigate the effect of MP1, MP3 and the widely used SL-analog GR24 on AMF spore germination and host root colonization. Our results show that MP1 and MP3 inhibit AMF spore germination, but promote the intra-radical root colonization, both more efficiently than GR24. These results indicate that field application of MP1 and MP3 does not have negative impact on mycorrhizal fungi. In conclusion, our data together with the previously reported simple synthesis, high activity in regulating plant architecture and inducing Striga seed germination, demonstrate the utility of MP1 and MP3 as for field application in combating root parasitic weeds by inducing germination in host's absence.}, } @article {pmid30519411, year = {2018}, author = {Bertoloni Meli, S and Bashey, F}, title = {Trade-off between reproductive and anti-competitor abilities in an insect-parasitic nematode-bacteria symbiosis.}, journal = {Ecology and evolution}, volume = {8}, number = {22}, pages = {10847-10856}, doi = {10.1002/ece3.4538}, pmid = {30519411}, issn = {2045-7758}, abstract = {Mutualistic symbionts can provide diverse benefits to their hosts and often supply key trait variation for host adaptation. The bacterial symbionts of entomopathogenic nematodes play a crucial role in successful colonization of and reproduction in the insect host. Additionally, these symbionts can produce a diverse array of antimicrobial compounds to deter within-host competitors. Natural isolates of the symbiont, Xenorhabdus bovienii, show considerable variation in their ability to target sympatric competitors via bacteriocins, which can inhibit the growth of sensitive Xenorhabdus strains. Both the bacteria and its nematode partner have been shown to benefit from bacteriocin production when within-host competition with a sensitive competitor occurs. Despite this benefit, several isolates of Xenorhabdus do not inhibit sympatric strains. To understand how this variation in allelopathy could be maintained, we tested the hypothesis that inhibiting isolates face a reproductive cost in the absence of competition. We tested this hypothesis by examining the reproductive success of inhibiting and non-inhibiting isolates coupled with their natural nematode host in a non-competitive context. We found that nematodes carrying non-inhibitors killed the insect host more rapidly and were more likely to successfully reproduce than nematodes carrying inhibitors. Lower reproductive success of inhibiting isolates was repeatable across nematode generations and across insect host species. However, no difference in insect mortality was observed between inhibiting and non-inhibiting isolates when bacteria were injected into insects without their nematode partners. Our results indicate a trade-off between the competitive and reproductive roles of symbionts, such that inhibiting isolates, which are better in the face of within-host competition, pay a reproductive cost in the absence of competition. Furthermore, our results support the hypothesis that symbiont variation within populations can be maintained through context-dependent fitness benefits conferred to their hosts. As such, our study offers novel insights into the selective forces maintaining variation within a single host-symbiont population and highlights the role of competition in mutualism evolution.}, } @article {pmid30519408, year = {2018}, author = {Burmester, EM and Breef-Pilz, A and Lawrence, NF and Kaufman, L and Finnerty, JR and Rotjan, RD}, title = {The impact of autotrophic versus heterotrophic nutritional pathways on colony health and wound recovery in corals.}, journal = {Ecology and evolution}, volume = {8}, number = {22}, pages = {10805-10816}, doi = {10.1002/ece3.4531}, pmid = {30519408}, issn = {2045-7758}, abstract = {For animals that harbor photosynthetic symbionts within their tissues, such as corals, the different relative contributions of autotrophy versus heterotrophy to organismal energetic requirements have direct impacts on fitness. This is especially true for facultatively symbiotic corals, where the balance between host-caught and symbiont-produced energy can be altered substantially to meet the variable demands of a shifting environment. In this study, we utilized a temperate coral-algal system (the northern star coral, Astrangia poculata, and its photosynthetic endosymbiont, Symbiodinium psygmophilum) to explore the impacts of nutritional sourcing on the host's health and ability to regenerate experimentally excised polyps. For fed and starved colonies, wound healing and total colony tissue cover were differentially impacted by heterotrophy versus autotrophy. There was an additive impact of positive nutritional and symbiotic states on a coral's ability to initiate healing, but a greater influence of symbiont state on the recovery of lost tissue at the lesion site and complete polyp regeneration. On the other hand, regardless of symbiont state, fed corals maintained a higher overall colony tissue cover, which also enabled more active host behavior (polyp extension) and endosymbiont behavior (photosynthetic ability of Symbiondinium). Overall, we determined that the impact of nutritional state and symbiotic state varied between biological functions, suggesting a diversity in energetic sourcing for each of these processes.}, } @article {pmid30519403, year = {2018}, author = {Bolin, LG and Benning, JW and Moeller, DA}, title = {Mycorrhizal interactions do not influence plant-herbivore interactions in populations of Clarkia xantiana ssp. xantiana spanning from center to margin of the geographic range.}, journal = {Ecology and evolution}, volume = {8}, number = {22}, pages = {10743-10753}, doi = {10.1002/ece3.4523}, pmid = {30519403}, issn = {2045-7758}, abstract = {Multispecies interactions can be important to the expression of phenotypes and in determining patterns of individual fitness in nature. Many plants engage in symbiosis with arbuscular mycorrhizal fungi (AMF), but the extent to which AMF modulate other species interactions remains poorly understood. We examined multispecies interactions among plants, AMF, and insect herbivores under drought stress using a greenhouse experiment and herbivore choice assays. The experiment included six populations of Clarkia xantiana (Onagraceae), which span a complex environmental gradient in the Southern Sierra Nevada of California. Clarkia xantiana's developing fruits are commonly attacked by grasshoppers at the end of the growing season, and the frequency of attack is more common in populations from the range center than range margin. We found that AMF negatively influenced all metrics of plant growth and reproduction across all populations, presumably because plants supplied carbon to AMF but did not benefit substantially from resources potentially supplied by the AMF. The fruits of plants infected with AMF did not differ from those without AMF in their resistance to grasshoppers. There was significant variation among populations in damage from herbivores but did not reflect the center-to-margin pattern of herbivory observed in the field. In sum, our results do not support the view that AMF interactions modulate plant-herbivore interactions in this system.}, } @article {pmid30519234, year = {2018}, author = {Temprano-Vera, F and Rodríguez-Navarro, DN and Acosta-Jurado, S and Perret, X and Fossou, RK and Navarro-Gómez, P and Zhen, T and Yu, D and An, Q and Buendía-Clavería, AM and Moreno, J and López-Baena, FJ and Ruiz-Sainz, JE and Vinardell, JM}, title = {Sinorhizobium fredii Strains HH103 and NGR234 Form Nitrogen Fixing Nodules With Diverse Wild Soybeans (Glycine soja) From Central China but Are Ineffective on Northern China Accessions.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2843}, doi = {10.3389/fmicb.2018.02843}, pmid = {30519234}, issn = {1664-302X}, abstract = {Sinorhizobium fredii indigenous populations are prevalent in provinces of Central China whereas Bradyrhizobium species (Bradyrhizobium japonicum, B. diazoefficiens, B. elkanii, and others) are more abundant in northern and southern provinces. The symbiotic properties of different soybean rhizobia have been investigated with 40 different wild soybean (Glycine soja) accessions from China, Japan, Russia, and South Korea. Bradyrhizobial strains nodulated all the wild soybeans tested, albeit efficiency of nitrogen fixation varied considerably among accessions. The symbiotic capacity of S. fredii HH103 with wild soybeans from Central China was clearly better than with the accessions found elsewhere. S. fredii NGR234, the rhizobial strain showing the broadest host range ever described, also formed nitrogen-fixing nodules with different G. soja accessions from Central China. To our knowledge, this is the first report describing an effective symbiosis between S. fredii NGR234 and G. soja. Mobilization of the S. fredii HH103 symbiotic plasmid to a NGR234 pSym-cured derivative (strain NGR234C) yielded transconjugants that formed ineffective nodules with G. max cv. Williams 82 and G. soja accession CH4. By contrast, transfer of the symbiotic plasmid pNGR234a to a pSym-cured derivative of S. fredii USDA193 generated transconjugants that effectively nodulated G. soja accession CH4 but failed to nodulate with G. max cv. Williams 82. These results indicate that intra-specific transference of the S. fredii symbiotic plasmids generates new strains with unpredictable symbiotic properties, probably due to the occurrence of new combinations of symbiotic signals.}, } @article {pmid30518840, year = {2018}, author = {Tena, G}, title = {Symbiosis gatekeeper.}, journal = {Nature plants}, volume = {4}, number = {12}, pages = {982}, doi = {10.1038/s41477-018-0333-4}, pmid = {30518840}, issn = {2055-0278}, } @article {pmid30518342, year = {2018}, author = {Brottier, L and Chaintreuil, C and Simion, P and Scornavacca, C and Rivallan, R and Mournet, P and Moulin, L and Lewis, GP and Fardoux, J and Brown, SC and Gomez-Pacheco, M and Bourges, M and Hervouet, C and Gueye, M and Duponnois, R and Ramanankierana, H and Randriambanona, H and Vandrot, H and Zabaleta, M and DasGupta, M and D'Hont, A and Giraud, E and Arrighi, JF}, title = {A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses.}, journal = {BMC plant biology}, volume = {18}, number = {1}, pages = {333}, doi = {10.1186/s12870-018-1567-z}, pmid = {30518342}, issn = {1471-2229}, support = {ANR-AeschyNod-14-CE19-0005-01//ANR/ ; }, abstract = {BACKGROUND: Among semi-aquatic species of the legume genus Aeschynomene, some have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the synthesis of Nod factors. Knowledge of the specificities underlying this Nod-independent symbiosis has been gained from the model legume Aeschynomene evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod factor-dependent process. To fill this gap, we combined different approaches to perform a thorough comparative analysis in the genus Aeschynomene.

RESULTS: This study significantly broadened previous taxon sampling, including in allied genera, in order to construct a comprehensive phylogeny. In the phylogenetic tree, five main lineages were delineated, including a novel lineage, the Nod-independent clade and another one containing a polytomy that comprised several Aeschynomene groups and all the allied genera. This phylogeny was matched with data on chromosome number, genome size and low-copy nuclear gene sequences to reveal the diploid species and a polytomy containing mostly polyploid taxa. For these taxa, a single allopolyploid origin was inferred and the putative parental lineages were identified. Finally, nodulation tests with different Bradyrhizobium strains revealed new nodulation behaviours and the diploid species outside of the Nod-independent clade were compared for their experimental tractability and genetic diversity.

CONCLUSIONS: The extended knowledge of the genetics and biology of the different lineages sheds new light of the evolutionary history of the genus Aeschynomene and they provide a solid framework to exploit efficiently the diversity encountered in Aeschynomene legumes. Notably, our backbone tree contains all the species that are diploid and it clarifies the genetic relationships between the Nod-independent clade and the Nod-dependent lineages. This study enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses.}, } @article {pmid30508325, year = {2018}, author = {Hsiao, CC and Sieber, S and Georgiou, A and Bailly, A and Emmanouilidou, D and Carlier, A and Eberl, L and Gademann, K}, title = {Synthesis and Biological Evaluation of the Novel Growth Inhibitor Streptol Glucoside, Isolated from an Obligate Plant Symbiont.}, journal = {Chemistry (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {}, doi = {10.1002/chem.201805693}, pmid = {30508325}, issn = {1521-3765}, abstract = {The plant Psychotria kirkii hosts an obligatory bacterial symbiont, Candidatus Burkholderia kirkii, in nodules on their leaves. Recently, a glucosylated derivative of (+)-streptol, (+)-streptol glucoside, was isolated from the nodulated leaves and was found to possess a plant growth inhibitory activity. To establish a structure activity relationship study, a convergent strategy was developed to obtain several pseudosugars from a single synthetic precursor. Furthermore, the glucosylation of streptol was investigated in detail and conditions affording specifically the alpha or beta glucosidic anomer were identified. Although (+)-streptol was the most active compound, its concentration in P. kirkii plant leaves extract was approximately 10 fold lower than that of (+)-streptol glucoside. These results provide compelling evidence that the glucosylation of (+)-streptol protects the plant host against the growth inhibitory effect of the compound, which might constitute a molecular cornerstone for this successful plant-bacteria symbiosis.}, } @article {pmid30506600, year = {2018}, author = {Wasilko, NP and Larios-Valencia, J and Steingard, CH and Nunez, BM and Verma, SC and Miyashiro, T}, title = {Sulfur availability for Vibrio fischeri growth during symbiosis establishment depends on biogeography within the squid light organ.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.14177}, pmid = {30506600}, issn = {1365-2958}, abstract = {The fitness of host-associated microbes depends on their ability to access nutrients in vivo. Identifying these mechanisms is significant for understanding how microbes have evolved to fill specific ecological niches within a host. Vibrio fischeri is a bioluminescent bacterium that colonizes and proliferates within the light organ of the Hawaiian bobtail squid, which provides an opportunity to study how bacteria grow in vivo. Here, the transcription factor CysB is shown to be necessary for V. fischeri both to grow on several sulfur sources in vitro and to establish symbiosis with juvenile squid. CysB is also found to regulate several genes involved in sulfate assimilation and to contribute to the growth of V. fischeri on cystine, which is the oxidized form of cysteine. A mutant that grows on cystine but not sulfate could establish symbiosis, suggesting that V. fischeri acquires nutrients related to this compound within the host. Finally, CysB-regulated genes are shown to be differentially expressed among the V. fischeri populations occupying the various colonization sites found within the light organ. Together, these results suggest the biogeography of V. fischeri populations within the squid light organ impacts the physiology of this symbiotic bacterium in vivo through CysB-dependent gene regulation. This article is protected by copyright. All rights reserved.}, } @article {pmid30505297, year = {2018}, author = {Pardo-De la Hoz, CJ and Magain, N and Lutzoni, F and Goward, T and Restrepo, S and Miadlikowska, J}, title = {Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2770}, doi = {10.3389/fmicb.2018.02770}, pmid = {30505297}, issn = {1664-302X}, abstract = {Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus Peltigera, section Chloropeltigera. We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries. Single locus phylogenies were used to establish the identity of both photobionts, Nostoc (cyanobacterium) and Coccomyxa (green alga). Distribution and specificity patterns were compared to the closely related clade, section Peltidea, which includes mainly Peltigera species with trimembered thalli. For section Chloropeltigera, eight fungal species (including five newly delimited putative species) were found in association with nine Nostoc phylogroups and two Coccomyxa species. In contrast, eight fungal species (including three newly delimited putative species) in section Peltidea were found in association with only four Nostoc phylogroups and the same two Coccomyxa species as for section Chloropeltigera. This difference in cyanobiont biodiversity between these two sections can potentially be explained by a significantly higher frequency of sexual reproductive structures in species from section Chloropeltigera compared to section Peltidea. Therefore, horizontal transmission of the cyanobiont might be more prevalent in Chloropeltigera species, while vertical transmission might be more common in Peltidea species. All Peltigera species in section Chloropeltigera are generalists in their association with Nostoc compared to more specialized Peltigera species in section Peltidea. Constrained distributions of Peltigera species that associate strictly with one species of green algae (Coccomyxa subellipsoidea) indicate that the availability of the green alga and the specificity of the interaction might be important factors limiting geographic ranges of trimembered Peltigera, in addition to constraints imposed by their interaction with Nostoc partners and by climatic factors.}, } @article {pmid30504321, year = {2018}, author = {Nazha, A}, title = {The MDS genomics-prognosis symbiosis.}, journal = {Hematology. American Society of Hematology. Education Program}, volume = {2018}, number = {1}, pages = {270-276}, doi = {10.1182/asheducation-2018.1.270}, pmid = {30504321}, issn = {1520-4383}, abstract = {Myelodysplastic syndromes (MDS) are clonal disorders characterized by the accumulation of complex genomic abnormalities that define disease phenotype, prognosis, and the risk of transformation to acute myeloid leukemia. The clinical manifestations and overall outcomes of MDS are very heterogeneous with an overall survival that can be measured in years for some patients to a few months for others. Prognostic scoring systems are important staging tools that aid physicians in their treatment recommendations and decision-making and can help patients understand their disease trajectory and expectations. Several scoring systems have been developed in MDS with the International Prognostic Scoring System and its revised version, the most widely used systems in clinical practice and trial eligibility. These models and others use mainly clinical variables that are obtained from bone marrow biopsy and peripheral blood measurements. Adding molecular data to current models may improve its predictive power but the ultimate method to incorporate this information remains a work in progress. Novel methods to develop a personalized prediction model that provides outcomes that are specific for a patient are currently under way and may change how we think about risk stratification in MDS patients in the future.}, } @article {pmid30504145, year = {2018}, author = {Tokuda, G and Mikaelyan, A and Fukui, C and Matsuura, Y and Watanabe, H and Fujishima, M and Brune, A}, title = {Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1810550115}, pmid = {30504145}, issn = {1091-6490}, abstract = {Symbiotic digestion of lignocellulose in wood-feeding higher termites (family Termitidae) is a two-step process that involves endogenous host cellulases secreted in the midgut and a dense bacterial community in the hindgut compartment. The genomes of the bacterial gut microbiota encode diverse cellulolytic and hemicellulolytic enzymes, but the contributions of host and bacterial symbionts to lignocellulose degradation remain ambiguous. Our previous studies of Nasutitermes spp. documented that the wood fibers in the hindgut paunch are consistently colonized not only by uncultured members of Fibrobacteres, which have been implicated in cellulose degradation, but also by unique lineages of Spirochaetes. Here, we demonstrate that the degradation of xylan, the major component of hemicellulose, is restricted to the hindgut compartment, where it is preferentially hydrolyzed over cellulose. Metatranscriptomic analysis documented that the majority of glycoside hydrolase (GH) transcripts expressed by the fiber-associated bacterial community belong to family GH11, which consists exclusively of xylanases. The substrate specificity was further confirmed by heterologous expression of the gene encoding the predominant homolog. Although the most abundant transcripts of GH11 in Nasutitermes takasagoensis were phylogenetically placed among their homologs of Firmicutes, immunofluorescence microscopy, compositional binning of metagenomics contigs, and the genomic context of the homologs indicated that they are encoded by Spirochaetes and were most likely obtained by horizontal gene transfer among the intestinal microbiota. The major role of spirochetes in xylan degradation is unprecedented and assigns the fiber-associated Treponema clades in the hindgut of wood-feeding higher termites a prominent part in the breakdown of hemicelluloses.}, } @article {pmid30503958, year = {2018}, author = {Shaaban, M and Elgaml, A and Habib, EE}, title = {Biotechnological applications of quorum sensing inhibition as novel therapeutic strategies for multidrug resistant pathogens.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.micpath.2018.11.043}, pmid = {30503958}, issn = {1096-1208}, abstract = {High incidence of antibiotic resistance among bacterial clinical isolates necessitates the discovery of new targets for inhibition of microbial pathogenicity without stimulation of microbial resistance. This could be achieved by targeting virulence determinants which cause host damage and disease. Many pathogenic bacteria elaborate signaling molecules for cellular communication. This signaling system is named quorum sensing system (QS), and it is contingent on the bacterial population density and mediated by signal molecules called pheromones or autoinducers (AIs). Bacteria utilize QS to regulate activities and behaviors including competence, conjugation, symbiosis, virulence, motility, sporulation, antibiotic production, and biofilm formation. Hence, targeting bacterial communicating signals and suppression of QS exhibit a fundamental approach for competing microbial communication. In this review, we illustrate the common up to date approaches to utilize QS circuits in pathogenic bacteria, including Vibrio fischeri, Pseudomonas aeruginosa, Escherichia coli and Acinetobacter baumannii, as novel therapeutic targets.}, } @article {pmid30502748, year = {2019}, author = {Dargahi, N and Johnson, J and Donkor, O and Vasiljevic, T and Apostolopoulos, V}, title = {Immunomodulatory effects of probiotics: Can they be used to treat allergies and autoimmune diseases?.}, journal = {Maturitas}, volume = {119}, number = {}, pages = {25-38}, doi = {10.1016/j.maturitas.2018.11.002}, pmid = {30502748}, issn = {1873-4111}, abstract = {As a person ages, physiological, immunological and gut microbiome changes collectively result in an array of chronic conditions. According to the 'hygiene hypothesis' the increasing prevalence of immune-mediated disorders may be related to intestinal dysbiosis, leading to immune dysfunction and associated conditions such as eczema, asthma, allergies and autoimmune diseases. Beneficial probiotic bacteria can be utilized by increasing their abundance within the gastrointestinal lumen, which in turn will modulate immune cells, such as, T helper (Th)-1, Th2, Th17, regulatory T (Treg) cells and B cells, which have direct relevance to human health and the pathogenesis of immune disorders. Here, we describe the cross-talk between probiotics and the gastrointestinal immune system, and their effects in relation to inflammatory bowel disease, multiple sclerosis, allergies and atopic dermatitis.}, } @article {pmid30502467, year = {2018}, author = {Wang, H and Tang, W and Zhang, R and Ding, S}, title = {Analysis of enzyme activity, antibacterial activity, antiparasitic activity and physico-chemical stability of skin mucus derived from Amphiprion clarkii.}, journal = {Fish & shellfish immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fsi.2018.11.066}, pmid = {30502467}, issn = {1095-9947}, abstract = {Recently, mucosal surfaces, especially fish skin and its secreted mucus, have attracted significant interest from immunologists. Amphiprion clarkii, a member of the family Pomacentridae, lives symbiosis with sea anemones and has a good resistance to common seawater bacterial diseases and parasites owing to the protection from its abundant skin mucus. In the present work, the activity of immune-related enzymes (lysozyme, protease, antiprotease, cathepsin B, alkaline phosphatase and peroxidase), the antibacterial activity against two Gram-positive bacteria and five Gram-negative bacteria, the antiparasitic activity against the pathogen of marine white spot disease (Cryptocaryon irritans theronts) and the physico-chemical stability (to pH and heat) of the skin mucus of A. clarkii were analysed. The results showed that the levels of lysozyme and peroxidase were very similar (from 2 to 4 U mg-1 protein). However, cathepsin B was detected of 63.32 U mg-1 protein and alkaline phosphatase was only 0.12 U mg-1 protein. Moreover, protease showed a higher percentage of activity than antiprotease. A. clarkii skin mucus showed a strong antibacterial activity against Gram-negative bacteria, particularly against Aeromonas hydrophila and Vibrio parahaemolyticus but showed no effect on Gram-positive bacteria at the tested concentrations. The bactericidal activity functioned within a short time in a distinct time- and dose-dependent manner. SEM showed that after treated with A. clarkii skin mucus, the V. parahaemolyticus cells distorted and piled together, and the filaments appeared and became into cotton-shaped or quasi-honeycomb texture to adhere cells. Meanwhile, A. clarkii skin mucus showed an apparent antiparasitic activity against C. irritans theronts with a distinct dose- and time-dependent relationship. LM and SEM observation showed that after treated with skin mucus, the theronts quickly stopped their swimming and cilia movement, cells beacme rounded, cilia shed, small bubbles formed on the surface, cell nucleolus enlarged, cytoskeleton deformed, cell membranes ruptured and cell content leaked out. Antibacterial activity was not affected by 30-90 °C heat treatment but was slightly suppressed by 100 °C. In the pH treatment groups, antibacterial activity was not affected by the moderate pH treatment of 5.0-8.0, and slightly suppressed by weak acid and weak base. Therefore, we speculated that the skin mucus of A. clarkii might be a potential source of novel antibacterial and antiparasitic components for fish or human health-related applications. This study broadened our understanding of the role of skin mucus in the innate immune system and provided a basis for the further isolation and purification of active substances.}, } @article {pmid30517276, year = {2018}, author = {Fuente, AL and Urcuyo, RJ and Vega, GH}, title = {Protists and other organisms on a minute snail periostracum.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {}, number = {}, pages = {}, doi = {10.1590/1519-6984.186837}, pmid = {30517276}, issn = {1678-4375}, abstract = {Since the foundation of the Malacological Center in 1980, Universidad Centro Americana (UCA), Managua-Nicaragua, has been monitoring and collecting the marine, terrestrial, fluvial and lake mollusk population of the country. Many specimens have been photographed by Scanning Electronic Microscope (SEM), and in one of these, observation of the hairy periostracum reveals a seemingly thriving population of minute protists in possible symbiosis with their host. Adequate magnification and comparison with previous studies allowed the determination of these hosts as diatoms, testaceous amoebae, yeast, phacus, spores and other undetermined organisms which occur in tropical forests on rocks, trees and leaves. Here illustrated are diatoms and other organisms detected for the first time on the periostracum of a tropical rainforest mollusk.}, } @article {pmid30515182, year = {2018}, author = {Gil-Martínez, M and López-García, Á and Domínguez, MT and Navarro-Fernández, CM and Kjøller, R and Tibbett, M and Marañón, T}, title = {Ectomycorrhizal Fungal Communities and Their Functional Traits Mediate Plant-Soil Interactions in Trace Element Contaminated Soils.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1682}, doi = {10.3389/fpls.2018.01682}, pmid = {30515182}, issn = {1664-462X}, abstract = {There is an increasing consensus that microbial communities have an important role in mediating ecosystem processes. Trait-based ecology predicts that the impact of the microbial communities on ecosystem functions will be mediated by the expression of their traits at community level. The link between the response of microbial community traits to environmental conditions and its effect on plant functioning is a gap in most current microbial ecology studies. In this study, we analyzed functional traits of ectomycorrhizal fungal species in order to understand the importance of their community assembly for the soil-plant relationships in holm oak trees (Quercus ilex subsp. ballota) growing in a gradient of exposure to anthropogenic trace element (TE) contamination after a metalliferous tailings spill. Particularly, we addressed how the ectomycorrhizal composition and morphological traits at community level mediate plant response to TE contamination and its capacity for phytoremediation. Ectomycorrhizal fungal taxonomy and functional diversity explained a high proportion of variance of tree functional traits, both in roots and leaves. Trees where ectomycorrhizal fungal communities were dominated by the abundant taxa Hebeloma cavipes and Thelephora terrestris showed a conservative root economics spectrum, while trees colonized by rare taxa presented a resource acquisition strategy. Conservative roots presented ectomycorrhizal functional traits characterized by high rhizomorphs formation and low melanization which may be driven by resource limitation. Soil-to-root transfer of TEs was explained substantially by the ectomycorrhizal fungal species composition, with the highest transfer found in trees whose roots were colonized by Hebeloma cavipes. Leaf phosphorus was related to ectomycorrhizal species composition, specifically higher leaf phosphorus was related to the root colonization by Thelephora terrestris. These findings support that ectomycorrhizal fungal community composition and their functional traits mediate plant performance in metal-contaminated soils, and have a high influence on plant capacity for phytoremediation of contaminants. The study also corroborates the overall effects of ectomycorrhizal fungi on ecosystem functioning through their mediation over the plant economics spectrum.}, } @article {pmid30513975, year = {2018}, author = {Nath, A and Molnár, MA and Csighy, A and Kőszegi, K and Galambos, I and Huszár, KP and Koris, A and Vatai, G}, title = {Biological Activities of Lactose-Based Prebiotics and Symbiosis with Probiotics on Controlling Osteoporosis, Blood-Lipid and Glucose Levels.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {54}, number = {6}, pages = {}, doi = {10.3390/medicina54060098}, pmid = {30513975}, issn = {1648-9144}, abstract = {Lactose-based prebiotics are synthesized by enzymatic- or microbial- biotransformation of lactose and have unique functional values. In this comprehensive review article, the biochemical mechanisms of controlling osteoporosis, blood-lipid, and glucose levels by lactose-based prebiotics and symbiosis with probiotics are reported along with the results of clinical investigations. Interaction between lactose-based prebiotics and probiotics reduces osteoporosis by (a) transforming insoluble inorganic salts to soluble and increasing their absorption to gut wall; (b) maintaining and protecting mineral absorption surface in the intestine; (c) increasing the expression of calcium-binding proteins in the gut wall; (d) remodeling osteoclasts and osteoblasts formation; (e) releasing bone modulating factors; and (f) degrading mineral complexing phytic acid. Lactose-based prebiotics with probiotics control lipid level in the bloodstream and tissue by (a) suppressing the expressions of lipogenic- genes and enzymes; (b) oxidizing fatty acids in muscle, liver, and adipose tissue; (c) binding cholesterol with cell membrane of probiotics and subsequent assimilation by probiotics; (d) enzymatic-transformations of bile acids; and (e) converting cholesterol to coprostanol and its defecation. Symbiosis of lactose-based prebiotics with probiotics affect plasma glucose level by (a) increasing the synthesis of gut hormones plasma peptide-YY, glucagon-like peptide-1 and glucagon-like peptide-2 from entero-endocrine L-cells; (b) altering glucose assimilation and metabolism; (c) suppressing systematic inflammation; (d) reducing oxidative stress; and (e) producing amino acids. Clinical investigations show that lactose-based prebiotic galacto-oligosaccharide improves mineral absorption and reduces hyperlipidemia. Another lactose-based prebiotic, lactulose, improves mineral absorption, and reduces hyperlipidemia and hyperglycemia. It is expected that this review article will be of benefit to food technologists and medical practitioners.}, } @article {pmid30511528, year = {2018}, author = {Chen, S and Shao, G and Shao, F and Zhang, M}, title = {[Diffusion-weighted imaging texture features in differentiation of malignant from benign nonpalpable breast lesions for patients with microcalcifications-only in mammography].}, journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences}, volume = {47}, number = {4}, pages = {400-404}, pmid = {30511528}, issn = {1008-9292}, abstract = {OBJECTIVE: To evaluate the application of MR diffusion-weighted imaging(DWI) texture features in differentiation of malignant from benign nonpalpable breast lesion for patients with microcalcifications-only in mammography.

METHODS: The clinical and MR-DWI data of 61 patients with microcalcifications, who underwent three-dimensional positioning of breast X-ray wire from October 2012 to December 2015 in Zhejiang Cancer Hospital, were retrospectively analyzed, including 38 patients with malignant lesions and 23 patients with benign lesions. Two radiologists independently drew the regions of interest (ROI) on DWI for image segmentation, and 6 histogram features and 16 grayscale symbiosis matrix (GLCM) texture features were extracted on each ROI. The random forest algorithm was applied to select the features and built the classification model. The leave-one-out cross-validation (LOOCV) was used to validate the classifier, and the performance of the classifier was evaluated by ROC curve.

RESULTS: Six features were selected, including histogram features of mean, variance, skewness, entropy, as well as contrast (0°) and correlation (45°) in GLCM. The histogram features of mean, variance, skewness and entropy were significantly different between the benign and malignant breast lesions (all P<0.05). The AUC of the model was 0.76, and the diagnostic accuracy, sensitivity and specificity were 77.05%, 84.21% and 65.21%, respectively.

CONCLUSIONS: The texture feature analysis of DWI can improve the diagnostic accuracy of differentiating benign and malignant breast nonpalpable lesions with microcalcifications-only in mammography. Histogram features of mean, variance, skewness, entropy of DWI may be used as important imaging markers.}, } @article {pmid30510528, year = {2018}, author = {Hernandez, AE and Claussenius-Kalman, HL and Ronderos, J and Vaughn, KA}, title = {Symbiosis, Parasitism and Bilingual Cognitive Control: A Neuroemergentist Perspective.}, journal = {Frontiers in psychology}, volume = {9}, number = {}, pages = {2171}, doi = {10.3389/fpsyg.2018.02171}, pmid = {30510528}, issn = {1664-1078}, abstract = {Interest in the intersection between bilingualism and cognitive control and accessibility to neuroimaging methods has resulted in numerous studies with a variety of interpretations of the bilingual cognitive advantage. Neurocomputational Emergentism (or Neuroemergentism for short) is a new framework for understanding this relationship between bilingualism and cognitive control. This framework considers Emergence, in which two small elements are recombined in an interactive manner, yielding a non-linear effect. Added to this is the notion that Emergence can be captured in neural systems using computationally inspired models. This review poses that bilingualism and cognitive control, as examined through the Neuroemergentist framework, are interwoven through development and involve the non-linear growth of cognitive processing encompassing brain areas that combine and recombine, in symbiotic and parasitic ways, in order to handle more complex types of processing. The models that have sought to explain the neural substrates of bilingual cognitive differences will be discussed with a reinterpretation of the entire bilingual cognitive advantage within a Neuroemergentist framework incorporating its neural bases. It will conclude by discussing how this new Neuroemergentist approach alters our view of the effects of language experience on cognitive control. Avenues to move beyond the simple notion of a bilingual advantage or lack thereof will be proposed.}, } @article {pmid30500814, year = {2018}, author = {Lopes, LE and Waldis, SJ and Terrell, SM and Lindgren, KA and Charkoudian, LK}, title = {Vibrant symbiosis: Achieving reciprocal science outreach through biological art.}, journal = {PLoS biology}, volume = {16}, number = {11}, pages = {e3000061}, doi = {10.1371/journal.pbio.3000061}, pmid = {30500814}, issn = {1545-7885}, abstract = {Scientific outreach efforts traditionally involve formally trained scientists teaching the general public about the methods, significance, and excitement of science. We recently experimented with an alternative "symbiotic outreach" model that prioritizes building a reciprocal relationship between formally trained and "outsider" scientists to facilitate active two-way communication. Herein, we present the results of our outreach effort involving college students and adults with intellectual and developmental disabilities working together to make biological and multimedia art. By discussing the steps others can take to cultivate reciprocal outreach within their local communities, we hope to lower the barrier for widespread adoption of similar approaches and ultimately to decrease the gap between formally trained scientists and the general public.}, } @article {pmid30497879, year = {2018}, author = {Tsaftaris, SA and Scharr, H}, title = {Sharing the Right Data Right: A Symbiosis with Machine Learning.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2018.10.016}, pmid = {30497879}, issn = {1878-4372}, abstract = {In 2014 plant phenotyping research was not benefiting from the machine learning (ML) revolution because appropriate data were lacking. We report the success of the first open-access dataset suitable for ML in image-based plant phenotyping suitable for machine learning, fuelling a true interdisciplinary symbiosis, increased awareness, and steep performance improvements on key phenotyping tasks.}, } @article {pmid30489239, year = {2018}, author = {Khasa, R and Vaidya, A and Vrati, S and Kalia, M}, title = {Membrane trafficking RNA interference screen identifies a crucial role of the clathrin endocytic pathway and ARP2/3 complex for Japanese encephalitis virus infection in HeLa cells.}, journal = {The Journal of general virology}, volume = {}, number = {}, pages = {}, doi = {10.1099/jgv.0.001182}, pmid = {30489239}, issn = {1465-2099}, abstract = {Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, is one of the leading global causes of virus-induced encephalitis. The infectious life-cycle of viruses is heavily dependent on the host membrane trafficking network. Here, we have performed a RNA-interference-based screen using a siRNA panel targeting 136 membrane trafficking proteins to identify the key regulators of JEV infection in HeLa cells. We identified 35 proteins whose siRNA depletion restricts JEV replication by over twofold. We observe that JEV infection in HeLa cells is largely dependent on components of the clathrin-mediated endocytic (CME) pathway. Proteins involved in actin-filament-based processes, specifically CDC42 and members of the ARP2/3 complex are crucial for establishment of infection. Pharmacological pertubations of actin polymerization, a small molecule inhibitor of actin nucleation by the ARP2/3 complex - CK-548 - and the inhibitor of neural Wiskott-Aldrich syndrome proteins- Wiskostatin- inhibited JEV replication, highlighting the important role of the dynamic actin network. Other proteins involved in cargo-recognition for CME and endomembrane system organization were also validated as essential host factors for virus replication.}, } @article {pmid30488371, year = {2018}, author = {Paulitsch, F and Klepa, MS and da Silva, AR and do Carmo, MRB and Dall'Agnol, RF and Delamuta, JRM and Hungria, M and da Silva Batista, JS}, title = {Phylogenetic diversity of rhizobia nodulating native Mimosa gymnas grown in a South Brazilian ecotone.}, journal = {Molecular biology reports}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11033-018-4506-z}, pmid = {30488371}, issn = {1573-4978}, support = {465133/2014-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; UEPG 09/2016//Fundação Araucária/ ; N/A//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Floristic surveys performed in "Campos Gerais" (Paraná, Brazil), an ecotone of Mata Atlântica and Cerrado biomes, highlights the richness and relative abundance of the family Fabaceae and point out the diversity and endemism of Mimosa spp. Our study reports the genetic diversity of rhizobia isolated from root nodules of native/endemic Mimosa gymnas Barneby in three areas of Guartelá State Park, an important conservation unit of "Campos Gerais". Soils of the sample areas were characterized as sandy, acid, poor in nutrients and organic matter. The genetic variability among the isolates was revealed by BOX-PCR genomic fingerprinting. Phylogeny based on 16S rRNA gene grouped the strains in a large cluster including Paraburkholderia nodosa and P. bannensis, while recA-gyrB phylogeny separated the strains in two groups: one including P. nodosa and the other without any described Paraburkholderia species. MLSA confirmed the separate position of this second group of strains within the genus Paraburkholderia and the nucleotide identity of the five concatened housekeeping genes was 95.9% in relation to P. nodosa BR 3437T. Phylogram based on symbiosis-essential nodC gene was in agreement with 16S rRNA analysis. Our molecular phylogenetic analysis support that Paraburkholderia are the main symbionts of native Mimosa in specific edaphic conditions found in South America and reveal the importance of endemic/native leguminous plants as reservoirs of novel rhizobial species.}, } @article {pmid30487315, year = {2018}, author = {Matthews, JL and Oakley, CA and Lutz, A and Hillyer, KE and Roessner, U and Grossman, AR and Weis, VM and Davy, SK}, title = {Partner switching and metabolic flux in a model cnidarian-dinoflagellate symbiosis.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1892}, pages = {}, doi = {10.1098/rspb.2018.2336}, pmid = {30487315}, issn = {1471-2954}, abstract = {Metabolite exchange is fundamental to the viability of the cnidarian-Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using 13C stable-isotope labelling coupled to gas chromatography-mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian Exaiptasia pallida (Aiptasia) when experimentally colonized with either native Breviolum minutum or non-native Durusdinium trenchii Relative to anemones containing B. minutum, D. trenchii-colonized hosts exhibited a 4.5-fold reduction in 13C-labelled glucose and reduced abundance and diversity of 13C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular, D. trenchii-colonized hosts exhibited a 40-fold reduction in 13C-labelled scyllo-inositol, a potential interpartner signalling molecule in symbiosis specificity. 13C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses to different symbiont species. Such differences in symbiont metabolite contribution and host utilization may limit the proliferation of stress-driven symbioses; this contributes valuable information towards future scenarios that select in favour of less-competent symbionts in response to environmental change.}, } @article {pmid30483906, year = {2018}, author = {Chan, CK and Rosic, N and Lorenc, MT and Visendi, P and Lin, M and Kaniewska, P and Ferguson, BJ and Gresshoff, PM and Batley, J and Edwards, D}, title = {A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference.}, journal = {Functional & integrative genomics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10142-018-0647-3}, pmid = {30483906}, issn = {1438-7948}, abstract = {Next-generation DNA sequencing technologies, such as RNA-Seq, currently dominate genome-wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies, a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the high cost of generating high-coverage data for de novo assembly hinders this approach and more importantly the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences. As an alternative to the standard reference mapping approach, we have developed a k-mer-based analysis pipeline (DiffKAP) to identify differentially expressed reads between RNA-Seq datasets without the requirement for a reference. We compared the DiffKAP approach with the traditional Tophat/Cuffdiff method using RNA-Seq data from soybean, which has a suitable reference genome. We subsequently examined differential gene expression for a coral meta-transcriptome where no reference is available, and validated the results using qRT-PCR. We conclude that DiffKAP is an accurate method to study differential gene expression in complex meta-transcriptomes without the requirement of a reference genome.}, } @article {pmid30483280, year = {2018}, author = {Gagic, M and Faville, MJ and Zhang, W and Forester, NT and Rolston, MP and Johnson, RD and Ganesh, S and Koolaard, JP and Easton, HS and Hudson, D and Johnson, LJ and Moon, CD and Voisey, CR}, title = {Seed Transmission of Epichloë Endophytes in Lolium perenne Is Heavily Influenced by Host Genetics.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1580}, doi = {10.3389/fpls.2018.01580}, pmid = {30483280}, issn = {1664-462X}, abstract = {Vertical transmission of symbiotic Epichloë endophytes from host grasses into progeny seed is the primary mechanism by which the next generation of plants is colonized. This process is often imperfect, resulting in endophyte-free seedlings which may have poor ecological fitness if the endophyte confers protective benefits to its host. In this study, we investigated the influence of host genetics and environment on the vertical transmission of Epichloë festucae var. lolii strain AR37 in the temperate forage grass Lolium perenne. The efficiency of AR37 transmission into the seed of over 500 plant genotypes from five genetically diverse breeding populations was determined. In Populations I-III, which had undergone previous selection for high seed infection by AR37, mean transmission was 88, 93, and 92%, respectively. However, in Populations IV and V, which had not undergone previous selection, mean transmission was 69 and 70%, respectively. The transmission values, together with single-nucleotide polymorphism data obtained using genotyping-by-sequencing for each host, was used to develop a genomic prediction model for AR37 seed transmission. The predictive ability of the model was estimated at r = 0.54. While host genotype contributed greatly to differences in AR37 seed transmission, undefined environmental variables also contributed significantly to seed transmission across different years and geographic locations. There was evidence for a small host genotype-by-environment effect; however this was less pronounced than genotype or environment alone. Analysis of endophyte infection levels in parent plants within Populations I and IV revealed a loss of endophyte infection over time in Population IV only. This population also had lower average tiller infection frequencies than Population I, suggesting that AR37 failed to colonize all the daughter tillers and therefore seeds. However, we also observed that infection of seed by AR37 may fail during or after initiation of floral development from plants where all tillers remained endophyte-infected over time. While the effects of environment and host genotype on fungal endophyte transmission have been evaluated previously, this is the first study that quantifies the relative impacts of host genetics and environment on endophyte vertical transmission.}, } @article {pmid30483277, year = {2018}, author = {Mohammadi-Dehcheshmeh, M and Niazi, A and Ebrahimi, M and Tahsili, M and Nurollah, Z and Ebrahimi Khaksefid, R and Ebrahimi, M and Ebrahimie, E}, title = {Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1550}, doi = {10.3389/fpls.2018.01550}, pmid = {30483277}, issn = {1664-462X}, abstract = {Plant root symbiosis with Arbuscular mycorrhizal (AM) fungi improves uptake of water and mineral nutrients, improving plant development under stressful conditions. Unraveling the unified transcriptomic signature of a successful colonization provides a better understanding of symbiosis. We developed a framework for finding the transcriptomic signature of Arbuscular mycorrhiza colonization and its regulating transcription factors in roots of Medicago truncatula. Expression profiles of roots in response to AM species were collected from four separate studies and were combined by direct merging meta-analysis. Batch effect, the major concern in expression meta-analysis, was reduced by three normalization steps: Robust Multi-array Average algorithm, Z-standardization, and quartiling normalization. Then, expression profile of 33685 genes in 18 root samples of Medicago as numerical features, as well as study ID and Arbuscular mycorrhiza type as categorical features, were mined by seven models: RELIEF, UNCERTAINTY, GINI INDEX, Chi Squared, RULE, INFO GAIN, and INFO GAIN RATIO. In total, 73 genes selected by machine learning models were up-regulated in response to AM (Z-value difference > 0.5). Feature weighting models also documented that this signature is independent from study (batch) effect. The AM inoculation signature obtained was able to differentiate efficiently between AM inoculated and non-inoculated samples. The AP2 domain class transcription factor, GRAS family transcription factors, and cyclin-dependent kinase were among the highly expressed meta-genes identified in the signature. We found high correspondence between the AM colonization signature obtained in this study and independent RNA-seq experiments on AM colonization, validating the repeatability of the colonization signature. Promoter analysis of upregulated genes in the transcriptomic signature led to the key regulators of AM colonization, including the essential transcription factors for endosymbiosis establishment and development such as NF-YA factors. The approach developed in this study offers three distinct novel features: (I) it improves direct merging meta-analysis by integrating supervised machine learning models and normalization steps to reduce study-specific batch effects; (II) seven attribute weighting models assessed the suitability of each gene for the transcriptomic signature which contributes to robustness of the signature (III) the approach is justifiable, easy to apply, and useful in practice. Our integrative framework of meta-analysis, promoter analysis, and machine learning provides a foundation to reveal the transcriptomic signature and regulatory circuits governing Arbuscular mycorrhizal symbiosis and is transferable to the other biological settings.}, } @article {pmid30479610, year = {2018}, author = {Bauça, JM}, title = {Reflections on the Mentor-Mentee Relationship: A Symbiosis.}, journal = {EJIFCC}, volume = {29}, number = {3}, pages = {230-233}, pmid = {30479610}, issn = {1650-3414}, } @article {pmid30478939, year = {2018}, author = {Seró, R and Núñez, N and Núñez, O and Camprubí, A and Grases, JM and Saurina, J and Moyano, E and Calvet, C}, title = {Modified distribution in the polyphenolic profile of rosemary leaves induced by plant inoculation with an arbuscular mycorrhizal fungus.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.9510}, pmid = {30478939}, issn = {1097-0010}, abstract = {BACKGROUND: Rosemary forms an arbuscular mycorrhizal (AM) symbiosis with a group of soilborne fungi belonging to the phylum Glomeromycota, which can modify the plant metabolome responsible for the antioxidant capacity and other health beneficial properties of Rosemary.

RESULTS: The effect of inoculating rosemary plants with an AM fungus on their growth via their polyphenolic fingerprinting was evaluated after analyzing leaf extracts from non-inoculated and inoculated rosemary plants by ultra-high performance liquid chromatography-high resolution mass spectrometry. . Plant growth parameters indicated that mycorrhizal inoculation significantly increased plant height and biomass. Chemical modifications in the plant polyphenolic profile distribution were found after a principal components analysis (PCA) loading plots study. Four compounds hosting strong antioxidant properties: ferulic acid, asiatic acid, carnosol, and vanillin were related to mycorrhizal rosemary plants while caffeic and chlorogenic acids had a higher influence in non-mycorrhizal plants.

CONCLUSION: Mycorrhization was found to stimulate growth in order to obtain a higher biomass of plant leaves in short time and avoiding chemical fertilization, while analytical results demonstrate that there is an alteration in the distribution of polyphenols in plants colonized by the symbiotic fungus, which can be related to an improvement in nutritional properties with future industrial significance. This article is protected by copyright. All rights reserved.}, } @article {pmid30477837, year = {2018}, author = {Anheyer, D and Kern, C and Dobos, G and Cramer, H}, title = {"I think you can achieve quite a lot if all of the staff stands behind it"-A qualitative study about the experience, knowledge and application of complementary therapies and integrative medicine in pediatrics.}, journal = {Complementary therapies in medicine}, volume = {41}, number = {}, pages = {186-191}, doi = {10.1016/j.ctim.2018.09.025}, pmid = {30477837}, issn = {1873-6963}, abstract = {BACKGROUND: In the United States there is an increasing use of complementary and alternative medicine (CAM) as well as integrative medicine (IM) in pediatrics. This study investigates the extent of knowledge and practical application of and attitudes towards the use and integration of CAM/IM therapies in two German pediatric clinics.

METHODS: A semi-standardized qualitative interview study was conducted in a rural children's hospital in Bavaria and in a children's clinic in the metropolitan area of Ruhr. Sixteen employees (7 nurses, 9 medical doctors, 68.8% female), who had volunteered through a local contact, were questioned during their shift on CAM/IM therapies. The data collected were analyzed with MAXQDA 12 using a qualitative technique for content analysis (by Mayring).

RESULTS: On average all respondents had little to superficial knowledge about the possibilities or evidence base of the therapies concerned, but did believe that CAM/IM could be an enhancement. In addition, many took interest in learning more about CAM/IM medical options. Nurses desired more practical and theoretical knowledge; while medical doctors focused on standardization and evidence base. All of them agreed that self-care strategies could enhance parental independence when treating symptoms of minor illnesses. They further agreed, that a symbiosis of conventional medicine and CAM/IM has great potential for patients and employees. It was stated that training of staff would be indispensable in order to implement standardized procedures.

CONCLUSIONS: There is great potential and interest in CAM/IM among pediatric care employees. Regardless of the challenges, this investigation did find that implementing CAM/IM might be a promising extension to the daily care routine.}, } @article {pmid30477264, year = {2018}, author = {Almendras, K and García, J and Carú, M and Orlando, J}, title = {Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {12}, pages = {}, doi = {10.3390/molecules23123077}, pmid = {30477264}, issn = {1420-3049}, support = {11100381 and 1181510//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.}, } @article {pmid30476329, year = {2018}, author = {Valdés-López, O and Jayaraman, D and Maeda, J and Delaux, PM and Venkateshwaran, M and Isidra-Arellano, MC and Del Rocío Reyero-Saavedra, M and Del Socorro Sánchez-Correa, M and Verastegui-Vidal, MA and Delgado-Buenrostro, N and Van Ness, L and Mysore, KS and Wen, J and Sussman, MR and Ané, JM}, title = {A Novel Positive Regulator of the Early Stages of the Root Nodule Symbiosis Identified by Phosphoproteomics.}, journal = {Plant & cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcy228}, pmid = {30476329}, issn = {1471-9053}, abstract = {Signals and signaling pathways underlying the symbiosis between legumes and rhizobia have been studied extensively over the past decades. In a previous phosphoproteomic study on the Medicago truncatula - Sinorhizobium meliloti symbiosis, we identified plant proteins that are differentially phosphorylated upon the perception of rhizobial signals, called Nod factors. In this study, we provide experimental evidence that one of these proteins, Early Phosphorylated Protein 1 (EPP1), is required for the initiation of this symbiosis. Upon inoculation with rhizobia, MtEPP1 expression was induced in curled root hairs. Down-regulation of MtEPP1 in M. truncatula roots almost abolished calcium spiking, reduced the expression of essential symbiosis-related genes (MtNIN, MtNF-YB1, MtERN1, and MtENOD40), and strongly decreased nodule development. Phylogenetic analyses revealed that orthologs of MtEPP1 are present in legumes and specifically in plant species able to host arbuscular mycorrhizal fungi, suggesting a possible role in this association too. Short chitin oligomers induced the phosphorylation of MtEPP1 like Nod factors. However, the down-regulation of MtEPP1 affected the colonization of M. truncatula roots by arbuscular mycorrhizal fungi only moderately. Altogether, these findings indicate that MtEPP1 is essential for the establishment of the legume-rhizobia symbiosis but might plays a limited role in the arbuscular mycorrhizal symbiosis.}, } @article {pmid30476071, year = {2018}, author = {Alonso, D and Mancini, MV and Damiani, C and Cappelli, A and Ricci, I and Niz Alvarez, MV and Bandi, C and Ribolla, P and Favia, G}, title = {Genome reduction in the mosquito symbiont Asaia.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evy255}, pmid = {30476071}, issn = {1759-6653}, abstract = {Symbiosis is now recognized as a driving force in evolution, a role that finds its ultimate expression in the variety of associations bonding insects with microbial symbionts. These associations have contributed to the evolutionary success of insects, with the hosts acquiring the capacity to exploit novel ecological niches, and the symbionts passing from facultative associations to obligate, mutualistic symbioses. In bacterial symbiont of insects, the transition from the free-living life style to mutualistic symbiosis often resulted in a reduction in the genome size, with the generation of the smallest bacterial genomes thus far described. Here we show that the process of genome reduction is still occurring in Asaia, a group of bacterial symbionts associated with a variety of insects. Indeed, comparative genomics of Asaia isolated from different mosquito species revealed a substantial genome size and gene content reduction in Asaia from Anopheles darlingi, a South-American malaria vector. We thus propose Asaia as a novel model to study genome reduction dynamics, within a single bacterial taxon, evolving in a common biological niche.}, } @article {pmid30471496, year = {2018}, author = {Yang, T and Cheng, H and Wang, H and Drews, M and Li, S and Huang, W and Zhou, H and Chen, CM and Diao, X}, title = {Comparative study of polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) in corals, surrounding sediments and surface water at the Dazhou Island, China.}, journal = {Chemosphere}, volume = {218}, number = {}, pages = {157-168}, doi = {10.1016/j.chemosphere.2018.11.063}, pmid = {30471496}, issn = {1879-1298}, abstract = {This study investigated polycyclic aromatic hydrocarbons (PAHs) content in corals (Acropora sp.), surficial sediments, and surface seawater, and heavy metals (HMs) contents in corals and sediments from Dazhou Island, Hainan, China. Concentrations of PAHs in seawater and sediment seasonally ranged from 191.5 ng L-1 to 587.7 ng L-1, and from 37.9 ng g-1 to 233 ng g-1, while levels in corals were higher (185.2-545.0 ng g-1) compared to those found in sediments, demonstrating bioaccumulation of PAHs by corals. A similar seasonally variation of PAHs was observed in water/sediments and corals, and the proportions of low molecular weight PAHs (LPAHs) in seawater and corals were higher. Pyrolytic and petrogenic contaminations were identified to be the main sources of PAHs. Lower HMs concentrations were detected in corals (9.8-39.4 μg g-1) than in sediments (65.0-83.3 μg g-1), but HMs bioaccumulation still occurs in corals. Higher concentrations of HMs in sediment and corals were detected in March and December, especially Mn and Zn. Application of an enrichment factor showed that Cu in corals was delivered from non-crustal materials, and anthropogenic inputs were possibly the main sources. According to Biota Sediment Accumulation Factor, corals could strongly bioaccumulate LPAHs and Cd, and PAHs at a higher (p < 0.05) rate than HMs. There was a lack of correlation between the accumulation of PAHs and HMs in corals based on the cluster analysis. Dual hierarchical clustering analysis result revealed that feeding, instead of symbiosis, might be the main process responsible for the bioaccumulation of PAHs and HMs.}, } @article {pmid30470196, year = {2018}, author = {Doudoumis, V and Augustinos, A and Saridaki, A and Parker, A and Abd-Alla, AMM and Bourtzis, K and Tsiamis, G}, title = {Different laboratory populations similar bacterial profile? The case of Glossina palpalis gambiensis.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {148}, doi = {10.1186/s12866-018-1290-9}, pmid = {30470196}, issn = {1471-2180}, abstract = {BACKGROUND: Microbiota plays an important role in the biology, ecology and evolution of insects including tsetse flies. The bacterial profile of 3 Glossina palpalis gambiensis laboratory colonies was examined using 16S rRNA gene amplicon sequencing to evaluate the dynamics of the bacterial diversity within and between each G. p. gambiensis colony.

RESULTS: The three G. p. gambiensis laboratory colonies displayed similar bacterial diversity indices and OTU distribution. Larval guts displayed a higher diversity when compared with the gastrointestinal tract of adults while no statistically significant differences were observed between testes and ovaries. Wigglesworthia and Sodalis were the most dominant taxa. In more detail, the gastrointestinal tract of adults was more enriched by Wigglesworthia while Sodalis were prominent in gonads. Interestingly, in larval guts a balanced co-existence between Wigglesworthia and Sodalis was observed. Sequences assigned to Wolbachia, Propionibacterium, and Providencia were also detected but to a much lesser degree. Clustering analysis indicated that the bacterial profile in G. p. gambiensis exhibits tissue tropism, hence distinguishing the gut bacterial profile from that present in reproductive organs.

CONCLUSIONS: Our results indicated that age, gender and the origin of the laboratory colonies did not significantly influence the formation of the bacterial profile, once these populations were kept under the same rearing conditions. Within the laboratory populations a tissue tropism was observed between the gut and gonadal bacterial profile.}, } @article {pmid30470190, year = {2018}, author = {Augustinos, AA and Meki, IK and Demirbas-Uzel, G and Ouédraogo, GMS and Saridaki, A and Tsiamis, G and Parker, AG and Abd-Alla, AMM and Bourtzis, K}, title = {Nuclear and Wolbachia-based multimarker approach for the rapid and accurate identification of tsetse species.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {147}, doi = {10.1186/s12866-018-1295-4}, pmid = {30470190}, issn = {1471-2180}, abstract = {BACKGROUND: Tsetse flies (Diptera: Glossinidae) are solely responsible for the transmission of African trypanosomes, causative agents of sleeping sickness in humans and nagana in livestock. Due to the lack of efficient vaccines and the emergence of drug resistance, vector control approaches such as the sterile insect technique (SIT), remain the most effective way to control disease. SIT is a species-specific approach and therefore requires accurate identification of natural pest populations at the species level. However, the presence of morphologically similar species (species complexes and sub-species) in tsetse flies challenges the successful implementation of SIT-based population control.

RESULTS: In this study, we evaluate different molecular tools that can be applied for the delimitation of different Glossina species using tsetse samples derived from laboratory colonies, natural populations and museum specimens. The use of mitochondrial markers, nuclear markers (including internal transcribed spacer 1 (ITS1) and different microsatellites), and bacterial symbiotic markers (Wolbachia infection status) in combination with relatively inexpensive techniques such as PCR, agarose gel electrophoresis, and to some extent sequencing provided a rapid, cost effective, and accurate identification of several tsetse species.

CONCLUSIONS: The effectiveness of SIT benefits from the fine resolution of species limits in nature. The present study supports the quick identification of large samples using simple and cost effective universalized protocols, which can be easily applied by countries/laboratories with limited resources and expertise.}, } @article {pmid30470188, year = {2018}, author = {Engl, T and Michalkova, V and Weiss, BL and Uzel, GD and Takac, P and Miller, WJ and Abd-Alla, AMM and Aksoy, S and Kaltenpoth, M}, title = {Effect of antibiotic treatment and gamma-irradiation on cuticular hydrocarbon profiles and mate choice in tsetse flies (Glossina m. morsitans).}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {145}, doi = {10.1186/s12866-018-1292-7}, pmid = {30470188}, issn = {1471-2180}, abstract = {BACKGROUND: Symbiotic microbes represent a driving force of evolutionary innovation by conferring novel ecological traits to their hosts. Many insects are associated with microbial symbionts that contribute to their host's nutrition, digestion, detoxification, reproduction, immune homeostasis, and defense. In addition, recent studies suggest a microbial involvement in chemical communication and mating behavior, which can ultimately impact reproductive isolation and, hence, speciation. Here we investigated whether a disruption of the microbiota through antibiotic treatment or irradiation affects cuticular hydrocarbon profiles, and possibly mate choice behavior in the tsetse fly, Glossina morsitans morsitans. Four independent experiments that differentially knock down the multiple bacterial symbionts of tsetse flies were conducted by subjecting tsetse flies to ampicillin, tetracycline, or gamma-irradiation and analyzing their cuticular hydrocarbon profiles in comparison to untreated controls by gas chromatography - mass spectrometry. In two of the antibiotic experiments, flies were mass-reared, while individual rearing was done for the third experiment to avoid possible chemical cross-contamination between individual flies.

RESULTS: All three antibiotic experiments yielded significant effects of antibiotic treatment (particularly tetracycline) on cuticular hydrocarbon profiles in both female and male G. m. morsitans, while irradiation itself had no effect on the CHC profiles. Importantly, tetracycline treatment reduced relative amounts of 15,19,23-trimethyl-heptatriacontane, a known compound of the female contact sex pheromone, in two of the three experiments, suggesting a possible implication of microbiota disturbance on mate choice decisions. Concordantly, both female and male flies preferred non-treated over tetracycline-treated flies in direct choice assays.

CONCLUSIONS: While we cannot exclude the possibility that antibiotic treatment had a directly detrimental effect on fly vigor as we are unable to recolonize antibiotic treated flies with individual symbiont taxa, our results are consistent with an effect of the microbiota, particularly the obligate nutritional endosymbiont Wigglesworthia, on CHC profiles and mate choice behavior. These findings highlight the importance of considering host-microbiota interactions when studying chemical communication and mate choice in insects.}, } @article {pmid30470176, year = {2018}, author = {Zaidman-Rémy, A and Vigneron, A and Weiss, BL and Heddi, A}, title = {What can a weevil teach a fly, and reciprocally? Interaction of host immune systems with endosymbionts in Glossina and Sitophilus.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {150}, doi = {10.1186/s12866-018-1278-5}, pmid = {30470176}, issn = {1471-2180}, support = {R01 AI051584/AI/NIAID NIH HHS/United States ; }, abstract = {The tsetse fly (Glossina genus) is the main vector of African trypanosomes, which are protozoan parasites that cause human and animal African trypanosomiases in Sub-Saharan Africa. In the frame of the IAEA/FAO program 'Enhancing Vector Refractoriness to Trypanosome Infection', in addition to the tsetse, the cereal weevil Sitophilus has been introduced as a comparative system with regards to immune interactions with endosymbionts. The cereal weevil is an agricultural pest that destroys a significant proportion of cereal stocks worldwide. Tsetse flies are associated with three symbiotic bacteria, the multifunctional obligate Wigglesworthia glossinidia, the facultative commensal Sodalis glossinidius and the parasitic Wolbachia. Cereal weevils house an obligatory nutritional symbiosis with the bacterium Sodalis pierantonius, and occasionally Wolbachia. Studying insect host-symbiont interactions is highly relevant both for understanding the evolution of symbiosis and for envisioning novel pest control strategies. In both insects, the long co-evolution between host and endosymbiont has led to a stringent integration of the host-bacteria partnership. These associations were facilitated by the development of specialized host traits, including symbiont-housing cells called bacteriocytes and specific immune features that enable both tolerance and control of the bacteria. In this review, we compare the tsetse and weevil model systems and compile the latest research findings regarding their biological and ecological similarities, how the immune system controls endosymbiont load and location, and how host-symbiont interactions impact developmental features including cuticle synthesis and immune system maturation. We focus mainly on the interactions between the obligate symbionts and their host's immune systems, a central theme in both model systems. Finally, we highlight how parallel studies on cereal weevils and tsetse flies led to mutual discoveries and stimulated research on each model, creating a pivotal example of scientific improvement through comparison between relatively distant models.}, } @article {pmid30467509, year = {2018}, author = {Libault, M}, title = {Transcriptional Reprogramming of Legume Genomes: Perspective and Challenges Associated With Single-Cell and Single Cell-Type Approaches During Nodule Development.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1600}, doi = {10.3389/fpls.2018.01600}, pmid = {30467509}, issn = {1664-462X}, abstract = {Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate picture of the transcriptome, epigenome, proteome, and metabolome of the cells infected by rhizobia and cells composing the nodule, there is a need to implement plant single-cell and single cell-types strategies and methods. Accessing such information would allow a better understanding of the infection of plant cells by rhizobia and will help understanding the complex interactions existing between rhizobia and the plant cells. In this mini-review, we are reporting the current knowledge on legume nodulation gained by plant scientists at the level of single cell-types, and provide perspectives on single cell/single cell-type approaches when applied to legume nodulation.}, } @article {pmid30467310, year = {2018}, author = {Pollock, FJ and McMinds, R and Smith, S and Bourne, DG and Willis, BL and Medina, M and Thurber, RV and Zaneveld, JR}, title = {Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4921}, doi = {10.1038/s41467-018-07275-x}, pmid = {30467310}, issn = {2041-1723}, abstract = {Scleractinian corals' microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbiomes are anatomically compartmentalized in both modern microbial ecology and evolutionary assembly. Coral mucus, tissue, and skeleton microbiomes differ in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflect coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Interactions between bacterial and coral phylogeny significantly influence the abundance of four groups of bacteria-including Endozoicomonas-like bacteria, which divide into host-generalist and host-specific subclades. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage.}, } @article {pmid30466096, year = {2018}, author = {Antonopoulos, CN and Liapis, CD}, title = {Aneurysms and Diabetes Mellitus: A Strange Symbiosis?.}, journal = {Cardiology}, volume = {141}, number = {2}, pages = {123-124}, doi = {10.1159/000490925}, pmid = {30466096}, issn = {1421-9751}, } @article {pmid30465068, year = {2018}, author = {Hubert, J and Nesvorna, M and Kopecky, J and Erban, T and Klimov, P}, title = {Population and Culture Age Influence the Microbiome Profiles of House Dust Mites.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1294-x}, pmid = {30465068}, issn = {1432-184X}, support = {17-12068S//Grantová Agentura České Republiky/ ; (No. 6.1933.2014/K Project Code 1933//Ministry of Education and Science of the Russian Federation/ ; No. 15-04-0s5185-a//the Russian Foundation for Basic Research/ ; }, abstract = {Interactions with microorganisms might enable house dust mites (HDMs) to derive nutrients from difficult-to-digest structural proteins and to flourish in human houses. We tested this hypothesis by investigating the effects of changes in the mite culture growth and population of two HDM species on HDM microbiome composition and fitness. Growing cultures of laboratory and industrial allergen-producing populations of Dermatophagoides farinae (DFL and DFT, respectively) and Dermatophagoides pteronyssinus (DPL and DPT, respectively) were sampled at four time points. The symbiotic microorganisms of the mites were characterized by DNA barcode sequencing and quantified by qPCR using universal/specific primers. The population growth of mites and nutrient contents of mite bodies were measured and correlated with the changes in bacteria in the HDM microbiome. The results showed that both the population and culture age significantly influenced the microbiome profiles. Cardinium formed 93% and 32% of the total sequences of the DFL and DFT bacterial microbiomes, respectively, but this bacterial species was less abundant in the DPL and DPT microbiomes. Staphylococcus abundance was positively correlated with increased glycogen contents in the bodies of mites, and increased abundances of Aspergillus, Candida, and Kocuria were correlated with increased lipid contents in the bodies of mites. The xerophilic fungus Wallemia accounted for 39% of the fungal sequences in the DPL microbiome, but its abundance was low in the DPT, DFL, and DFT microbiomes. With respect to the mite culture age, we made three important observations: the mite population growth from young cultures was 5-8-fold higher than that from old cultures; specimens from old cultures had greater abundances of fungi and bacteria in their bodies; and yeasts predominated in the gut contents of specimens from young cultures, whereas filamentous mycelium prevailed in specimens from old cultures. Our results are consistent with the hypothesis that mites derive nutrients through associations with microorganisms.}, } @article {pmid30463949, year = {2018}, author = {Mao, M and Yang, X and Bennett, GM}, title = {Evolution of host support for two ancient bacterial symbionts with differentially degraded genomes in a leafhopper host.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1811932115}, pmid = {30463949}, issn = {1091-6490}, abstract = {Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system.}, } @article {pmid30463525, year = {2018}, author = {Toju, H and Sato, H and Yamamoto, S and Tanabe, AS}, title = {Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks.}, journal = {BMC plant biology}, volume = {18}, number = {1}, pages = {292}, doi = {10.1186/s12870-018-1500-5}, pmid = {30463525}, issn = {1471-2229}, support = {26711026//Japan Society for the Promotion of Science/ ; JPMJPR16Q6//Precursory Research for Embryonic Science and Technology/ ; GS014//Cabinet Office, Government of Japan/ ; }, abstract = {BACKGROUND: Below-ground linkage between plant and fungal communities is one of the major drivers of terrestrial ecosystem dynamics. However, we still have limited knowledge of how such plant-fungus associations vary in their community-scale properties depending on fungal functional groups and geographic locations.

METHODS: By compiling a high-throughput sequencing dataset of root-associated fungi in eight forests along the Japanese Archipelago, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions.

RESULTS: In most of the plant-fungus networks analyzed, host-symbiont associations were significantly specialized but lacked "nested" architecture, which has been commonly reported in plant-pollinator and plant-seed disperser networks. In particular, the entire networks involving all functional groups of plants and fungi and partial networks consisting of ectomycorrhizal plant and fungal species/taxa displayed "anti-nested" architecture (i.e., negative nestedness scores) in many of the forests examined. Our data also suggested that geographic factors affected the organization of plant-fungus network structure. For example, the southernmost subtropical site analyzed in this study displayed lower network-level specificity of host-symbiont associations and higher (but still low) nestedness than northern localities.

CONCLUSIONS: Our comparative analyses suggest that arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic plant-fungus associations often lack nested network architecture, while those associations can vary, to some extent, in their community-scale properties along a latitudinal gradient. Overall, this study provides a basis for future studies that will examine how different types of plant-fungus associations collectively structure terrestrial ecosystems.}, } @article {pmid30462254, year = {2018}, author = {Hernández-López, A and Díaz, M and Rodríguez-López, J and Guillén, G and Sánchez, F and Díaz-Camino, C}, title = {The overexpression of Bax inhibitor-1 in common bean roots highlights its dual role in the legume-rhizobia symbiosis.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/ery417}, pmid = {30462254}, issn = {1460-2431}, abstract = {Bax-inhibitor 1 (BI-1) is a cell death suppressor conserved in all eukaryotes that modulates cell death in response to abiotic stress and pathogen attack in plants. Thus far nothing is known about its role in the establishment of symbiotic interactions. Here, we demonstrate the functional relevance of an Arabidopsisthaliana BI-1 homolog (PvBI-1a) to symbiosis between the common bean (Phaseolus vulgaris) and Rhizobium tropici. We show that the PvBI-1a expression changes observed during early symbiosis resemble those of some defence-response related proteins. By using gain- and loss-of-function approaches, we demonstrate that the overexpression of PvBI-1a in the roots of common bean increases the number of rhizobial infection events (and therefore the final number of nodules per root), but induces the premature death of nodule cells, thus affecting their nitrogen fixation efficiency. Nodule morphological alterations are known to be associated with changes in the expression of genes tied to defence, autophagy, and vesicular trafficking. Results obtained in the present work suggest that BI-1 has a dual role in the regulation of programmed cell death during symbiosis, thus extending our understanding about its critical function in the modulation of host immunity while responding to by beneficial microbes.}, } @article {pmid30460828, year = {2018}, author = {Song, YY and Xia, M and Lin, YB and Lin, XH and Ding, CH and Wang, J and Hu, L and Zeng, RS}, title = {[Colonization with arbuscular mycorrhizal fungus Funneliformis mosseae enhanced the responses of tomato plants to mechanical wounding].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {29}, number = {11}, pages = {3811-3818}, doi = {10.13287/j.1001-9332.201811.035}, pmid = {30460828}, issn = {1001-9332}, abstract = {Insect herbivore feeding causes mechanical damage to plants, which can activate plant defense responses. Whether symbiosis with beneficial microorganisms can enhance the responses of plants to mechanical damage is of importance for plant anti-herbivore resistance. In this study, defense responses of tomato (Lycopersicon esculentum) plants to mechanical wounding was investigated after the tomato roots being infected by arbuscular mycorrhizal fungus (AMF) Funneliformis mosseae. The results showed that in response to leaf mechanical wounding, the activities of phenylalanine ammonia-lyase (PAL), superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO) and catalase (CAT) in the leaves of tomato pre-inoculated with AMF (FD), as well as transcript levels of genes encoding phenylalanine ammonia lyase (PAL) and β-1,3-glucanase (PR2) in the leaves and roots were significantly higher in relative to sole mechanical wounding (D), sole mycorrhizal inoculation (F), and control without mechanical wounding and mycorrhizal inoculation (CK). Although the activities of protective enzyme and transcript levels of the two defense-related genes were induced in the plants of sole mechanical wounding (D) and sole mycorrhizal inoculation (F), the induction was faster and stronger in the plants with leaf mechanical wounding and mycorrhizal pre-inoculation (FD). Our findings indicated that arbuscular mycorrhizal colonization could prime quicker and stronger defense responses of tomato plants to mechanical damage.}, } @article {pmid30460206, year = {2018}, author = {Arora, G and Chaudhary, D and Kidwai, S and Sharma, D and Singh, R}, title = {CitE Enzymes Are Essential for Mycobacterium tuberculosis to Establish Infection in Macrophages and Guinea Pigs.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {385}, doi = {10.3389/fcimb.2018.00385}, pmid = {30460206}, issn = {2235-2988}, abstract = {Bacterial citrate lyase activity has been demonstrated in various eukaryotes, bacteria and archaea, underscoring their importance in energy metabolism of the cell. While the bacterial citrate lyase comprises of three different subunits, M. tuberculosis genome lacks CitD and CitF subunits of citrate lyase complex but encodes for 2 homologs of CitE subunits, Rv2498c and Rv3075c. Using temperature sensitive mycobacteriophages, we were able to generate both single and double citE mutant strains of M. tuberculosis. The survival experiments revealed increased susceptibility of the double mutant strain to oxidative stress in comparison to the parental strain. Also, simultaneous deletion of both citE1 and citE2 in M. tuberculosis genome resulted in impairment of intracellular replication in macrophages. The double mutant strain displayed reduced growth in lungs and spleens of guinea pigs. This is the first study demonstrating that M. tuberculosis critically requires CitE subunits of citrate lyase for pathogenesis. Taken together, these findings position these enzymes as potential targets for development of anti-tubercular small molecules.}, } @article {pmid30459800, year = {2018}, author = {Grosche, C and Genau, AC and Rensing, SA}, title = {Evolution of the Symbiosis-Specific GRAS Regulatory Network in Bryophytes.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1621}, doi = {10.3389/fpls.2018.01621}, pmid = {30459800}, issn = {1664-462X}, abstract = {Arbuscular mycorrhiza is one of the most common plant symbiotic interactions observed today. Due to their nearly ubiquitous occurrence and their beneficial impact on both partners it was suggested that this mutualistic interaction was crucial for plants to colonize the terrestrial habitat approximately 500 Ma ago. On the plant side the association is established via the common symbiotic pathway (CSP). This pathway allows the recognition of the fungal symbiotic partner, subsequent signaling to the nucleus, and initiation of the symbiotic program with respect to specific gene expression and cellular re-organization. The downstream part of the CSP is a regulatory network that coordinates the transcription of genes necessary to establish the symbiosis, comprising multiple GRAS transcription factors (TFs). These regulate their own expression as an intricate transcriptional network. Deduced from non-host genome data the loss of genes encoding CSP components coincides with the loss of the interaction itself. Here, we analyzed bryophyte species with special emphasis on the moss Physcomitrella patens, supposed to be a non-host, for the composition of the GRAS regulatory network components. We show lineage specific losses and expansions of several of these factors in bryophytes, potentially coinciding with the proposed host/non-host status of the lineages. We evaluate losses and expansions and infer clade-specific evolution of GRAS TFs.}, } @article {pmid30459731, year = {2018}, author = {Chun, SC and Paramasivan, M and Chandrasekaran, M}, title = {Proline Accumulation Influenced by Osmotic Stress in Arbuscular Mycorrhizal Symbiotic Plants.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2525}, doi = {10.3389/fmicb.2018.02525}, pmid = {30459731}, issn = {1664-302X}, abstract = {Salinity and drought are the major osmotic stress limitations that affect plant growth and crop yield in agriculture worldwide. The alternative response mediated by plants in response to salinity and drought are principally proline accumulation which regulates stress combat strategies owing to sustainable production in the realm of agricultural production even under severe stress. Symbiotic and soil associated arbuscular mycorrhizal fungi (AMF) are regarded as efficient biofertilizers in several crops under these stresses. Summarily AMF is renowned for effective scavengers of free radicals in soil thereby increasing soil parameters optimal for plant growth. AMF contribute to augment host plant tolerance to stress specifically salinity and drought. Mycorrhizal colonization positively regulates root uptake of available nutrients and enhance growth even when bestowed by water constraints which has contributory roles due to proline accumulation providing several intriguing researches on AMF symbiosis pertaining to plant productivity and yield. Mycorrhizal plants and their non-mycorrhizal counterparts show varied expression pattern regarding proline amass. Hence, the precise role of proline with respect to stress tolerance and equivocal mechanisms involved in evasion of osmotic stress has not been extensively reviewed earlier. Further molecular forecasting in this arena is still an underexploited research field. This review comprehensively addresses the observable facts pertaining to proline accumulation upon AMF association and adherence relevant to stress tolerance and host plant efficiency and efficacy.}, } @article {pmid30459726, year = {2018}, author = {Brown, AMV and Wasala, SK and Howe, DK and Peetz, AB and Zasada, IA and Denver, DR}, title = {Comparative Genomics of Wolbachia-Cardinium Dual Endosymbiosis in a Plant-Parasitic Nematode.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2482}, doi = {10.3389/fmicb.2018.02482}, pmid = {30459726}, issn = {1664-302X}, abstract = {Wolbachia and Cardinium are among the most important and widespread of all endosymbionts, occurring in nematodes and more than half of insect and arachnid species, sometimes as coinfections. These symbionts are of significant interest as potential biocontrol agents due to their abilities to cause major effects on host biology and reproduction through cytoplasmic incompatibility, sex ratio distortion, or obligate mutualism. The ecological and metabolic effects of coinfections are not well understood. This study examined a Wolbachia-Cardinium coinfection in the plant-parasitic nematode (PPN), Pratylenchus penetrans, producing the first detailed study of such a coinfection using fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), and comparative genomic analysis. Results from FISH and single-nematode PCR showed 123/127 individuals in a focal population carried Cardinium (denoted strain cPpe), and 48% were coinfected with Wolbachia strain wPpe. Both endosymbionts showed dispersed tissue distribution with highest densities in the anterior intestinal walls and gonads. Phylogenomic analyses confirmed an early place of cPpe and long distance from a sister strain in another PPN, Heterodera glycines, supporting a long history of both Cardinium and Wolbachia in PPNs. The genome of cPpe was 1.36 Mbp with 35.8% GC content, 1,131 predicted genes, 41% having no known function, and missing biotin and lipoate synthetic capacity and a plasmid present in other strains, despite having a slightly larger genome compared to other sequenced Cardinium. The larger genome revealed expansions of gene families likely involved in host-cellular interactions. More than 2% of the genes of cPpe and wPpe were identified as candidate horizontally transferred genes, with some of these from eukaryotes, including nematodes. A model of the possible Wolbachia-Cardinium interaction is proposed with possible complementation in function for pathways such as methionine and fatty acid biosynthesis and biotin transport.}, } @article {pmid30459295, year = {2018}, author = {Rubio, AO and Kupferberg, SJ and Vargas García, V and Ttito, A and Shepack, A and Catenazzi, A}, title = {Widespread occurrence of the antifungal cutaneous bacterium Janthinobacterium lividum on Andean water frogs threatened by fungal disease.}, journal = {Diseases of aquatic organisms}, volume = {131}, number = {3}, pages = {233-238}, doi = {10.3354/dao03298}, pmid = {30459295}, issn = {0177-5103}, abstract = {Amphibian diversity has declined due to the infectious disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Coexistence between amphibian hosts and this pathogen in some locations is attributed to the presence of the cutaneous bacterium Janthinobacterium lividum (Jliv). This microbe inhibits the growth of Bd on the host, reduces morbidity, and improves survival. Andean water frogs in the genus Telmatobius seem to be particularly vulnerable to the disease yet populations of T. intermedius and T. marmoratus persist in southern and central Peru. We investigated the presence of Jliv on these 2 frog species and assessed the relationship of Jliv presence with prevalence and intensity of Bd infection. By sampling 125 frogs from 7 streams (3323-3950 m a.s.l.) and 27 from a city market, we found spatial variation in the mutualism among populations (range 0-40% proportion of Jliv-positives). Overall, 57% of frogs were infected with Bd, 12.5% of frogs hosted both Jliv and Bd, while 7.2% hosted just Jliv. We found that the probability of an individual being infected with Bd was independent of the presence of Jliv; however, we did detect a protective effect of Jliv with respect to intensity of infection. The extent of Jliv distribution in the high Andes stands in stark contrast to the rarity of Jliv on frogs in lower elevation cloud forest biomes.}, } @article {pmid30458424, year = {2018}, author = {Salducci, MD and Folzer, H and Issartel, J and Rabier, J and Masotti, V and Prudent, P and Affre, L and Hardion, L and Tatoni, T and Laffont-Schwob, I}, title = {How can a rare protected plant cope with the metal and metalloid soil pollution resulting from past industrial activities? Phytometabolites, antioxidant activities and root symbiosis involved in the metal tolerance of Astragalus tragacantha.}, journal = {Chemosphere}, volume = {217}, number = {}, pages = {887-896}, doi = {10.1016/j.chemosphere.2018.11.078}, pmid = {30458424}, issn = {1879-1298}, abstract = {Astragalus tragacantha is a protected plant species in France that grows even in the trace metal and metalloid (TMM) polluted soils of the Calanques National Park (PNCal). Soils are mainly contaminated by lead, copper, zinc and arsenic. An ex situ experiment was conducted, firstly to determine the molecular responses and root traits involved in the TMM tolerance of this plant species by growing individuals in a soil from the surroundings of one of the brownfields of the PNCal, known as l'Escalette, where this plant species grows spontaneously. Secondly, in order to determine the plasticity of these responses, seeds were collected from three different populations, 1 at l'Escalette (polluted site), one from the Frioul archipelago (non-polluted, insular site) and one from La Seyne (non-polluted, littoral site). The results of this study confirmed the capacity of A. tragacantha to germinate and grow in TMM contaminated soils. Only moderate significant variations in chlorophyll and flavonol indices, proline content and antioxidant activities were detected between polluted and control soil conditions for all populations. The main driver for A. tragacantha TMM tolerance seemed to be its ability to be associated with root symbionts i.e. arbuscular mycorrhizal fungi and dark septate endophytes, corresponding to a nutrient-uptake strategy trait. This work provides support for the challenge of A. tragacantha conservation along the littoral of the PNCal, because increasing the number of A. tragacantha individuals would both increase vegetation cover of the polluted soils to reduce the pollution transfer and reinforce the populations of this species.}, } @article {pmid30458368, year = {2018}, author = {Tinkov, AA and Ajsuvakova, OP and Skalnaya, MG and Skalny, AV and Aschner, M and Suliburska, J and Aaseth, J}, title = {Organotins in obesity and associated metabolic disturbances.}, journal = {Journal of inorganic biochemistry}, volume = {191}, number = {}, pages = {49-59}, doi = {10.1016/j.jinorgbio.2018.11.002}, pmid = {30458368}, issn = {1873-3344}, abstract = {The objective of the present study was to review the mechanisms of organotin-induced adipogenesis, obesity, and associated metabolic disturbances. Peroxisome proliferator-activated receptor γ (PPARγ) and retinoid X receptor α (RXRα) activation is considered as the key mechanism of organotin-induced adipogenesis. Particularly, organotin exposure results in increased adipogenesis both in cell and animal models. Moreover, transgenerational inheritance of organotin-induced obese phenotype was demonstrated in vivo. At the same time, the existing data demonstrate that organotin compounds (OTCs) induces aberrant expression of PPARγ-targeted genes, resulting in altered of adipokine, glucose transporter, proinflammatory cytokines levels, and lipid and carbohydrate metabolism. The latter is generally characterized by hyperglycemia and insulin resistance. Other mechanisms involved in organotin-induced obesity may include estrogen receptor and corticosteroid signaling, altered DNA methylation, and gut dysfunction. In addition to cellular effects, organotin exposure may also affect neural circuits of appetite regulation, being characterized by neuropeptide Y (NPY) up-regulation in parallel with of pro-opiomelanocortin (POMC), Agouti-related protein (AgRP), and cocaine and amphetamine regulated transcript (CART) down-regulation in the arcuate nucleus. These changes result in increased orexigenic and reduced anorexigenic signaling, leading to increased food intake. The existing data demonstrate that organotins are potent adipogenic agents, however, no epidemiologic studies have been performed to reveal the association between organotin exposure and obesity and the existing indirect human data are contradictory.}, } @article {pmid30458311, year = {2018}, author = {Yu, J and Wang, M and Liu, B and Yue, X and Li, C}, title = {Gill symbionts of the cold-seep mussel Bathymodiolus platifrons: Composition, environmental dependency and immune control.}, journal = {Fish & shellfish immunology}, volume = {86}, number = {}, pages = {246-252}, doi = {10.1016/j.fsi.2018.11.041}, pmid = {30458311}, issn = {1095-9947}, abstract = {Deep-sea Bathymodiolus mussels depend on the organic carbon supplied by symbionts inside their gills. In this study, optimized methods of quantitative real-time PCR and fluorescence in situ hybridization targeted to both mRNA and 16S rRNA were used to investigate the gill symbionts of the cold-seep mussel Bathymodiolus platifrons, including species composition, environmental dependency and immune control by the host. Our results showed that methanotrophs were the major symbiotic bacteria in the gills of B. platifrons, while thiotrophs were scarce. In the mussels freshly collected from the deep sea, methanotrophs were housed in bacteriocytes in a unique circular pattern, and a lysosome-related gene (VAMP) encoding a vesicle-associated membrane protein was expressed at a high level and presented exactly where the methanotrophs occurred. After the mussels were reared for three months in aquaria without methane supply, the abundance of methanotrophs decreased significantly and their circle-shaped distribution pattern disappeared; in addition, the expression of VAMP decreased significantly. These results suggest that the symbiosis between B. platifrons and methanotrophs is influenced by the environment and that the lysosomal system plays an important immune role in controlling the abundance of endosymbionts in host. This study provides a reliable method for investigating symbionts in deep-sea mussels and enriches the knowledge about symbionts in B. platifrons.}, } @article {pmid30450723, year = {2018}, author = {Prazeres, M and Renema, W}, title = {Evolutionary significance of the microbial assemblages of large benthic Foraminifera.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.12482}, pmid = {30450723}, issn = {1469-185X}, support = {//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, abstract = {Large benthic Foraminifera (LBF) are major carbonate producers on coral reefs, and are hosts to a diverse symbiotic microbial community. During warm episodes in the geological past, these reef-building organisms expanded their geographical ranges as subtropical and tropical belts moved into higher latitudes. During these range-expansion periods, LBF were the most prolific carbonate producers on reefs, dominating shallow carbonate platforms over reef-building corals. Even though the fossil and modern distributions of groups of species that harbour different types of symbionts are known, the nature, mechanisms, and factors that influence their occurrence remain elusive. Furthermore, the presence of a diverse and persistent bacterial community has only recently gained attention. We examined recent advances in molecular identification of prokaryotic (i.e. bacteria) and eukaryotic (i.e. microalgae) associates, and palaeoecology, and place the partnership with bacteria and algae in the context of climate change. In critically reviewing the available fossil and modern data on symbiosis, we reveal a crucial role of microalgae in the response of LBF to ocean warming, and their capacity to colonise a variety of habitats, across both latitudes and broad depth ranges. Symbiont identity is a key factor enabling LBF to expand their geographic ranges when the sea-surface temperature increases. Our analyses showed that over the past 66 million years (My), diatom-bearing species were dominant in reef environments. The modern record shows that these species display a stable, persistent eukaryotic assemblage across their geographic distribution range, and are less dependent on symbiotic photosynthesis for survival. By contrast, dinoflagellate and chlorophytic species, which show a provincial distribution, tend to have a more flexible eukaryotic community throughout their range. This group is more dependent on their symbionts, and flexibility in their symbiosis is likely to be the driving force behind their evolutionary history, as they form a monophyletic group originating from a rhodophyte-bearing ancestor. The study of bacterial assemblages, while still in its infancy, is a promising field of study. Bacterial communities are likely to be shaped by the local environment, although a core bacterial microbiome is found in species with global distributions. Cryptic speciation is also an important factor that must be taken into consideration. As global warming intensifies, genetic divergence in hosts in addition to the range of flexibility/specificity within host-symbiont associations will be important elements in the continued evolutionary success of LBF species in a wide range of environments. Based on fossil and modern data, we conclude that the microbiome, which includes both algal and bacterial partners, is a key factor influencing the evolution of LBF. As a result, the microbiome assists LBF in colonising a wide range of habitats, and allowed them to become the most important calcifiers on shallow platforms worldwide during periods of ocean warming in the geologic past. Since LBF are crucial ecosystem engineers and prolific carbonate producers, the microbiome is a critical component that will play a central role in the responses of LBF to a changing ocean, and ultimately in shaping the future of coral reefs.}, } @article {pmid30450139, year = {2018}, author = {Najafi, A and Moradinasab, M and Seyedabadi, M and Haghighi, MA and Nabipour, I}, title = {First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran.}, journal = {The open microbiology journal}, volume = {12}, number = {}, pages = {323-332}, doi = {10.2174/1874285801812010323}, pmid = {30450139}, issn = {1874-2858}, abstract = {Background: Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran.

Methods: Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning.

Results: In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group.

Conclusion: The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.}, } @article {pmid30450084, year = {2018}, author = {Gong, S and Chai, G and Xiao, Y and Xu, L and Yu, K and Li, J and Liu, F and Cheng, H and Zhang, F and Liao, B and Li, Z}, title = {Flexible Symbiotic Associations of Symbiodinium With Five Typical Coral Species in Tropical and Subtropical Reef Regions of the Northern South China Sea.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2485}, doi = {10.3389/fmicb.2018.02485}, pmid = {30450084}, issn = {1664-302X}, abstract = {The coral symbiont Symbiodinium plays important roles in the adaptation of coral to environmental changes. However, coral-Symbiodinium symbiotic associations are not well-understood in the South China Sea (SCS) whilst considering environmental factors and host taxa. In this study, next-generation sequencing of the internal transcribed spacer region 2 (ITS2) marker gene was used to explore the symbiotic associations between Symbiodinium and five typical coral species across tropical and subtropical reef regions of the SCS. The results showed that Acropora sp., Galaxea fascicularis, Platygyra lamellina, and Sarcophyton glaucum exhibited distinct Symbiodinium compositions between tropical and subtropical reef regions, whereas Porites lutea had stable Symbiodinium compositions. More heterogeneous Symbiodinium compositions among different coral species were observed in the tropical region, but there were no statistically significant differences in Symbiodinium compositions among different coral species in subtropical reef regions. There was a correlation between the Symbiodinium compositions and environmental factors, except for the composition of P. lutea. Symbiodinium subclades D1, D2, C71, C71a, C21, C3b, and C161 were primarily explained by the seawater temperature, nitrate, ammonia, and phosphate. Several host-specific Symbiodinium subclades (e.g., C15, C15.6, and C91) were observed in P. lutea as well. The findings of this study demonstrate the relationship of Symbiodinium diversity with coral hosts and the environment are helpful for elucidating the adaptation of corals to global climate change and anthropogenic disturbance.}, } @article {pmid30449358, year = {2018}, author = {Aylward, J and Wingfield, BD and Dreyer, LL and Roets, F and Wingfield, MJ and Steenkamp, ET}, title = {Genomic overview of closely related fungi with different Protea host ranges.}, journal = {Fungal biology}, volume = {122}, number = {12}, pages = {1201-1214}, doi = {10.1016/j.funbio.2018.10.001}, pmid = {30449358}, issn = {1878-6146}, abstract = {Genome comparisons of species with distinctive ecological traits can elucidate genetic divergence that influenced their differentiation. The interaction of a microorganism with its biotic environment is largely regulated by secreted compounds, and these can be predicted from genome sequences. In this study, we considered Knoxdaviesia capensis and Knoxdaviesia proteae, two closely related saprotrophic fungi found exclusively in Protea plants. We investigated their genome structure to compare their potential inter-specific interactions based on gene content. Their genomes displayed macrosynteny and were approximately 10 % repetitive. Both species had fewer secreted proteins than pathogens and other saprotrophs, reflecting their specialized habitat. The bulk of the predicted species-specific and secreted proteins coded for carbohydrate metabolism, with a slightly higher number of unique carbohydrate-degrading proteins in the broad host-range K. capensis. These fungi have few secondary metabolite gene clusters, suggesting minimal competition with other microbes and symbiosis with antibiotic-producing bacteria common in this niche. Secreted proteins associated with detoxification and iron sequestration likely enable these Knoxdaviesia species to tolerate antifungal compounds and compete for resources, facilitating their unusual dominance. This study confirms the genetic cohesion between Protea-associated Knoxdaviesia species and reveals aspects of their ecology that have likely evolved in response to their specialist niche.}, } @article {pmid30449353, year = {2018}, author = {Poinar, GO and Vega, FE}, title = {A mid-Cretaceous ambrosia fungus, Paleoambrosia entomophila gen. nov. et sp. nov. (Ascomycota: Ophiostomatales) in Burmese (Myanmar) amber, and evidence for a femoral mycangium.}, journal = {Fungal biology}, volume = {122}, number = {12}, pages = {1159-1162}, doi = {10.1016/j.funbio.2018.08.002}, pmid = {30449353}, issn = {1878-6146}, abstract = {An ambrosia fungus is described from filamentous sporodochia adjacent to a wood-boring ambrosia beetle (Coleoptera: Curculionidae: Platypodinae) in mid-Cretaceous Burmese amber. Yeast-like propagules and hyphal fragments of Paleoambrosia entomophila gen. nov. et sp. nov. occur in glandular sac mycangia located inside the femur of the beetle. This is the first record of a fossil ambrosia fungus, showing that symbiotic associations between wood-boring insects and ectosymbiotic fungi date back some 100 million years ago. The present finding moves the origin of fungus-growing by insects from the Oligocene to the mid-Cretaceous and suggests a Gondwanan origin.}, } @article {pmid30448757, year = {2018}, author = {Ren, CG and Kong, CC and Wang, SX and Xie, ZH}, title = {Enhanced phytoremediation of uranium-contaminated soils by arbuscular mycorrhiza and rhizobium.}, journal = {Chemosphere}, volume = {217}, number = {}, pages = {773-779}, doi = {10.1016/j.chemosphere.2018.11.085}, pmid = {30448757}, issn = {1879-1298}, abstract = {Uranium phytoextraction is a promising technology, however, facing difficult that limited plant biomass due to nutrient deficiency in the contaminated sites. The aim of this study is to evaluate the potential of a symbiotic associations of a legume Sesbania rostrata, rhizobia and arbuscular mycorrhiza fungi (AMF) for reclamation of uranium contaminated soils. Results showed AMF and rhizobia had a mutual beneficial relations in the triple symbiosis, which significantly increased plant biomass and uranium accumulation in S. rostrata plant. The highest uranium removal rates was observed in plant-AMF-rhizobia treated soils, in which 50.5-73.2% had been extracted, whereas 7.2-23.3% had been extracted in plant-treated soil. Also, the S. rostrata phytochelatin synthase (PCS) genes expression were increased in AMF and rhizobia plants compared with the plants. Meantime, content of malic acid, succinic acid and citric acid were elevated in S. rostrata root exudates of AMF and rhizobia inoculated plants. The facts suggest that the mutual interactions in the triple symbiosis help to improve phytoremediation efficiency of uranium by S. rostrata.}, } @article {pmid30447602, year = {2018}, author = {Ma, J and Zhu, D and Chen, QL and Ding, J and Zhu, YG and Sheng, GD and Qiu, YP}, title = {Exposure to tetracycline perturbs the microbiome of soil oligochaete Enchytraeus crypticus.}, journal = {The Science of the total environment}, volume = {654}, number = {}, pages = {643-650}, doi = {10.1016/j.scitotenv.2018.11.154}, pmid = {30447602}, issn = {1879-1026}, abstract = {Microbial symbiosis is essential for the normal development and growth of hosts. Past attention has mostly been paid to its effects on plants and vertebrates. The effects of environmental pressures such as antibiotics on the microbiome of soil fauna remain largely elusive. We used bacterial 16S rRNA gene high-throughput sequencing to examine the response of microbiome of soil invertebrate Enchytraeus crypticus to oral tetracycline exposure. After two-week exposure, tetracycline-free oat was used as food to monitor the restoration of E. crypticus microbiome. The results showed that Proteobacteria, Actinobacteria and Planctomycetes were the three dominant phyla in all samples, Rhizobiaceae and Kaistia were the most abundant family and genus in all samples, respectively. After 14 days tetracycline exposure, Planctomycetes declined dramatically from 33.05% to 3.28% (P = 0.016), but Actinobacteria elevated substantially from 2.47% to 23.65% (P = 0.004). The alpha-diversity of microbial community increased significantly after tetracycline exposure compared to the control (P = 0.014). Terminating tetracycline exposure led to the recovery of E. crypticus microbiome back to the background level within 14 days. Our results suggest that while tetracycline can disturb the microbiome in E. crypticus significantly, the effects of the antibiotic on E. crypticus microbiome may not be permanent but reversibly diminish after stopping exposure for a period of time. The results may contribute to extending our understanding of the effect of antibiotics on microbiome of soil invertebrates. CAPSULE: The microbiome of E. crypticus exposed to tetracycline is perturbed and reversibly restored after terminating the exposure.}, } @article {pmid30447333, year = {2018}, author = {Limpens, E and Geurts, R}, title = {Transcriptional Regulation of Nutrient Exchange in Arbuscular Mycorrhizal Symbiosis.}, journal = {Molecular plant}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molp.2018.11.003}, pmid = {30447333}, issn = {1752-9867}, } @article {pmid30443991, year = {2018}, author = {Schneider, S and Schintlmeister, A and Becana, M and Wagner, M and Woebken, D and Wienkoop, S}, title = {Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13481}, pmid = {30443991}, issn = {1365-3040}, abstract = {Legume-rhizobia symbioses play a major role in food production for an ever growing human population. In this symbiosis, dinitrogen is reduced ('fixed') to ammonia by the rhizobial nitrogenase enzyme complex and is secreted to the plant host cells, while dicarboxylic acids derived from photosynthetically-produced sucrose are transported into the symbiosomes and serve as respiratory substrates for the bacteroids. The symbiosome membrane contains high levels of SST1 protein, a sulfate transporter. Sulfate is an essential nutrient for all living organisms, but its importance for symbiotic nitrogen fixation and nodule metabolism has long been underestimated. Using chemical imaging, we demonstrate that the bacteroids take up 20-fold more sulfate than the nodule host cells. Furthermore, we show that nitrogenase biosynthesis relies on high levels of imported sulfate, making sulfur as essential as carbon for the regulation and functioning of symbiotic nitrogen fixation. Our findings thus establish the importance of sulfate and its active transport for the plant-microbe interaction that is most relevant for agriculture and soil fertility. This article provides a comprehensive explanation for the importance of the nodule specific sulfate transporter (SST1) and the role of sulfate by dissecting the sulfur distribution across the nodule tissue and directly linking sulfate incorporation to nitrogenase biosynthesis.}, } @article {pmid30442721, year = {2018}, author = {Shrestha, M and Compton, KK and Mancl, J and Webb, B and Brown, A and Scharf, B and Schubot, FD}, title = {Structure of the sensory domain of McpX from Sinorhizobium meliloti the first known bacterial chemotactic sensor for quaternary ammonium compounds.}, journal = {The Biochemical journal}, volume = {}, number = {}, pages = {}, doi = {10.1042/BCJ20180769}, pmid = {30442721}, issn = {1470-8728}, abstract = {The alpha-proteobacterium Sinorhizobium meliloti can live freely in the soil or engage in a symbiosis with its legume host. S. meliloti facilitates nitrogen-fixation in root nodules, thus providing pivotal, utilizable nitrogen to the host. The organism has eight chemoreceptors, namely McpT to McpZ and IcpA that facilitate chemotaxis. McpX is the first known bacterial sensor of quaternary amine compounds (QACs) such as choline and betaines. Because QACs are exuded at chemotaxis-relevant concentrations by germinating alfalfa seeds, McpX has been proposed to contribute to host-specific chemotaxis. We have determined the crystal structure of the McpX periplasmic region (McpXPR) in complex with the proline betaine at 2.7 Å resolution. In the crystal the protein forms a symmetric dimer with one proline betaine molecule bound to each monomer of McpXPR within membrane distal CACHE module. The ligand is bound through cation- interactions with four aromatic amino acid residues. Mutational analysis in conjunction with binding studies revealed that a conserved aspartate residue is pivotal for ligand binding. We discovered that, in a striking example of convergent evolution, the ligand binding site of McpXPR resembles that of a group of structurally unrelated betaine binding proteins including ProX and OpuAC. Through this comparison and docking studies we rationalized the specificity of McpXPR for this specific group of ligands. Collectively, our structural, biochemical, and molecular docking data have revealed the molecular determinants in McpX that are crucial for its rare ligand specificity for QACs.}, } @article {pmid30439953, year = {2018}, author = {Dixit, KK and Verma, S and Singh, OP and Singh, D and Singh, AP and Gupta, R and Negi, NS and Das, P and Sundar, S and Singh, R and Salotra, P}, title = {Validation of SYBR green I based closed tube loop mediated isothermal amplification (LAMP) assay and simplified direct-blood-lysis (DBL)-LAMP assay for diagnosis of visceral leishmaniasis (VL).}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {11}, pages = {e0006922}, doi = {10.1371/journal.pntd.0006922}, pmid = {30439953}, issn = {1935-2735}, abstract = {BACKGROUND: The World Health Organization has targeted elimination of visceral leishmaniasis (VL) in the Indian subcontinent (ISC) by 2020. Despite distinctive decline seen in the number of VL cases in ISC, there is still a quest for development of a diagnostic test which has the utility for detection of active infection and relapse cases and as a test of cure. The present study validated the sensitivity and specificity of SYBR Green I based closed tube LAMP assay reported by us for diagnosis of VL.

METHODOLOGY: The validation study was carried out at two endemic sites in India, located at Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna and Institute of Medical Sciences (IMS), Banaras Hindu University (BHU), Varanasi. Standard operating protocols were provided at the two sites for applying LAMP assay on confirmed VL cases. The diagnostic accuracy of LAMP assay was evaluated by Receiver operator curve (ROC) analysis. Furthermore, a simplified LAMP assay based on direct blood lysis, DBL-LAMP, was developed and verified for its diagnostic accuracy.

PRINCIPAL FINDINGS: A total of 267 eligible participants were included in the study which comprised of 179 VL cases and 88 controls. Sensitivity and specificity of the LAMP assay were 98.32% (95% C.I- 95.2-99.7%) and 96.59% (95% C.I.-90.4-99.3%), respectively. ROC curve analysis depicted no significant difference between area under curve (AUCROC) for LAMP assay and rK39 RDT, indicative of LAMP as an excellent diagnostic test. DBL-LAMP assay, performed on 67 VL and 100 control samples, yielded a sensitivity of 93.05% (95% C.I- 84.75-97%) and specificity of 100% (95% C.I.- 96.30-100%).

CONCLUSIONS/SIGNIFICANCE: The validated closed tube LAMP for diagnosis of VL will provide impetus to the ongoing VL elimination programme in ISC. The assay based on direct blood lysis promotes its scope for application in field settings by further reducing time and cost.}, } @article {pmid30429501, year = {2018}, author = {Yuyama, I and Ishikawa, M and Nozawa, M and Yoshida, MA and Ikeo, K}, title = {Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16802}, doi = {10.1038/s41598-018-34575-5}, pmid = {30429501}, issn = {2045-2322}, support = {14J40135//Japan Society for the Promotion of Science (JSPS)/ ; 15K18744//Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {To clarify the establishment process of coral-algal symbiotic relationships, coral transcriptome changes during increasing algal symbiont densities were examined in juvenile corals following inoculation with the algae Symbiodinium goreaui (clade C) and S. trenchii (clade D), and comparison of their transcriptomes with aposymbiotic corals by RNA-sequencing. Since Symbiodinium clades C and D showed very different rates of density increase, comparisons were made of early onsets of both symbionts, revealing that the host behaved differently for each. RNA-sequencing showed that the number of differentially-expressed genes in corals colonized by clade D increased ca. two-fold from 10 to 20 days, whereas corals with clade C showed unremarkable changes consistent with a slow rate of density increase. The data revealed dynamic metabolic changes in symbiotic corals. In addition, the endocytosis pathway was also upregulated, while lysosomal digestive enzymes and the immune system tended to be downregulated as the density of clade D algae increased. The present dataset provides an enormous number of candidate symbiosis-related molecules that exhibit the detailed process by which coral-algal endosymbiosis is established.}, } @article {pmid30429307, year = {2018}, author = {Georgieva, MN and Little, CTS and Bailey, RJ and Ball, AD and Glover, AG}, title = {Microbial-tubeworm associations in a 440 million year old hydrothermal vent community.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1891}, pages = {}, doi = {10.1098/rspb.2018.2004}, pmid = {30429307}, issn = {1471-2954}, abstract = {Microorganisms are the chief primary producers within present-day deep-sea hydrothermal vent ecosystems, and play a fundamental role in shaping the ecology of these environments. However, very little is known about the microbes that occurred within, and structured, ancient vent communities. The evolutionary history, diversity and the nature of interactions between ancient vent microorganisms and hydrothermal vent animals are largely undetermined. The oldest known hydrothermal vent community that includes metazoans is preserved within the Ordovician to early Silurian Yaman Kasy massive sulfide deposit, Ural Mountains, Russia. This deposit contains two types of tube fossil attributed to annelid worms. A re-examination of these fossils using a range of microscopy, chemical analysis and nano-tomography techniques reveals the preservation of filamentous microorganisms intimately associated with the tubes. The microfossils bear a strong resemblance to modern hydrothermal vent microbial filaments, including those preserved within the mineralized tubes of the extant vent polychaete genus Alvinella The Yaman Kasy fossil filaments represent the oldest animal-microbial associations preserved within an ancient hydrothermal vent environment. They allude to a diverse microbial community, and also demonstrate that remarkable fine-scale microbial preservation can also be observed in ancient vent deposits, suggesting the possible existence of similar exceptionally preserved microfossils in even older vent environments.}, } @article {pmid30427559, year = {2018}, author = {Stabb, EV}, title = {Should they stay or should they go? Nitric oxide and the clash of regulators governing Vibrio fischeri biofilm formation.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.14163}, pmid = {30427559}, issn = {1365-2958}, abstract = {A key regulatory decision for many bacteria is the switch between biofilm formation and motile dispersal, and this dynamic is well illustrated in the light-organ symbiosis between the bioluminescent bacterium Vibrio fischeri and the Hawaiian bobtail squid. Biofilm formation mediated by the syp gene cluster helps V. fischeri transition from a dispersed planktonic lifestyle to a robust aggregate on the surface of the nascent symbiotic organ. However, the bacteria must then swim to pores and down into the deeper crypt tissues that they ultimately colonize. A number of positive and negative regulators control syp expression and biofilm formation, but until recently the environmental inputs controlling this clash between opposing regulatory mechanisms have been unclear. Thompson et al. have now shown that Syp-mediated biofilms can be repressed by a well known host-derived molecule: nitric oxide. This regulation is accomplished by the NO sensor HnoX exerting control over the biofilm regulator HahK. The discoveries reported here by Thompson et al. cast new light on a critical early stage of symbiotic initiation in the V. fischeri-squid model symbiosis, and more broadly it adds to a growing understanding of the role(s) that NO and HnoX play in biofilm regulation by many bacteria. This article is protected by copyright. All rights reserved.}, } @article {pmid30425705, year = {2018}, author = {Farkas, A and Pap, B and Kondorosi, É and Maróti, G}, title = {Antimicrobial Activity of NCR Plant Peptides Strongly Depends on the Test Assays.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2600}, doi = {10.3389/fmicb.2018.02600}, pmid = {30425705}, issn = {1664-302X}, abstract = {The symbiosis specific NCR247 and NCR335 cationic plant peptides of Medicago truncatula have been shown to exert antimicrobial activity against a wide range of microbes. However, their antimicrobial efficiency is clearly limited by divalent cations. Here, the antibacterial and antifungal activities of NCR247 and NCR335 peptides were compared to those of the well-characterized peptide antibiotics polymyxin B and the aminoglycoside streptomycin on three model microbes, Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae as representatives of Gram-negative and Gram-positive bacteria as well as eukaryotic fungi. The aim of the study was to assess how the killing efficiency of these peptides depends on various, widely used antimicrobial susceptibility assays. Validated resazurin microdilution assay was used to determine minimal growth inhibitory concentrations in three general test media (MHB, MHBII and low-salt medium LSM). Bactericidal/fungicidal activities were determined by the commonly used drop plate assay. The natural plant peptides showed distinct characteristics, NCR247 had a generally high sensitivity for Ca2+ and Mg2+ in the medium, while NCR335 proved to be a robust and strong antimicrobial agent with comparable efficiency values to polymyxin B. Activity data were confirmed visually, both NCR247 and NCR335 treatments at minimal bactericidal concentrations induced complete disruption of the membranes and provoked cell lysis on all tested microorganisms as observed by scanning electron microscopy.}, } @article {pmid30423115, year = {2018}, author = {Romano, S and Ansorge, R}, title = {Scientific communication strategies of microbiologists in the era of social media.}, journal = {FEMS microbiology letters}, volume = {365}, number = {23}, pages = {}, doi = {10.1093/femsle/fny264}, pmid = {30423115}, issn = {1574-6968}, abstract = {Over the last decades, the world of communication underwent drastic changes, and internet and social media emerged as essential vehicles for exchanging information. Following these trends, it is important that scientists adapt to changes and adopt optimal strategies to communicate with colleagues, lay people and institutions. We conducted an online survey to investigate the communication strategies of microbiologists and their colleagues from other disciplines. We collected data from 527 scholars from 57 countries, with ∼42% of them being microbiologists. We focused particularly on social media and found that >80% of participants used them for work, and that ∼50% of interviewed actively shared and gathered scientific contents from social media. Compared to colleagues from other fields, microbiologists were less averse to use social media for work and were also less accustomed to use pre-prints as a source and vehicle of information. However, a large proportion of microbiologists declared to have planned pre-print publications in the future. Surprisingly, our data revealed that age is a poor predictor of social media usage, but it is strongly associated with the type of social media used, the activity undertaken on them and the attitude towards pre-print publications. Considering the kaleidoscopic variety of scientific communication tools, our data might help to optimize the scientific promotion strategies among microbiologists.}, } @article {pmid30421109, year = {2018}, author = {La, A and Perré, P and Taidi, B}, title = {Process for symbiotic culture of Saccharomyces cerevisiae and Chlorella vulgaris for in situ CO2 mitigation.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-9506-3}, pmid = {30421109}, issn = {1432-0614}, abstract = {Industrial biotechnology relies heavily on fermentation processes that release considerable amounts of CO2. Apart from the fact that this CO2 represents a considerable part of the organic substrate, it has a negative impact on the environment. Microalgae cultures have been suggested as potential means of capturing the CO2 with further applications in high-value compounds production or directly for feed applications. We developed a sustainable process based on a mixed co-dominant culture of Saccharomyces cerevisiae and Chlorella vulgaris where the CO2 production and utilization controlled the microbial ecology of the culture. By mixing yeast and microalga in the same culture, the CO2 is produced in dissolved form and is available to the microalga avoiding degassing and dissolution phenomena. With this process, the CO2 production and utilization rates were balanced and a mutual symbiosis between the yeast and the microalga was set up in the culture. In this study, the reutilization of CO2 and growth of C. vulgaris was demonstrated. The two organism populations were balanced at approximately 20 × 106 cells ml-1 and almost all the CO2 produced by yeast was reutilized by microalga within 168 h of culture. The C. vulgaris inoculum preparation played a key role in establishing co-dominance of the two organisms. Other key factors in establishing symbiosis were the inoculum ratio of the two organisms and the growth medium design. A new method allowed the independent enumeration of each organism in a mixed culture. This study could provide a basis for the development of green processes of low environmental impact.}, } @article {pmid30417315, year = {2018}, author = {Kalita, M and Małek, W}, title = {The ftsA gene as a molecular marker for phylogenetic studies in Bradyrhizobium and identification of Bradyrhizobium japonicum.}, journal = {Journal of applied genetics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s13353-018-0479-9}, pmid = {30417315}, issn = {2190-3883}, support = {IP2011 021571//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; }, abstract = {The use of ftsA gene sequences for taxonomic studies of the genus Bradyrhizobium bacteria was assessed. The ftsA gene codes for an actin-like protein involved in prokaryotic cell division. Up to now, this gene has not been used as a phylogenetic marker for analysis of bacteria establishing root nodule symbiosis with Fabaceae plants. In this study, the ftsA gene sequences obtained for bradyrhizobia forming N2 fixing symbiosis with four Genisteae tribe plants growing in Poland and most of the type strains of the genus Bradyrhizobium species were analyzed and evaluated as molecular markers for phylogenetic studies of these bacteria for the first time. The ftsA gene sequences of all bradyrhizobial strains with completely or partially sequenced genomes, available in the GenBank database, were also included into the analysis. The phylogeny of the ftsA gene was compared to the phylogenies of other chromosomal genes commonly used in the studies of Bradyrhizobium bacteria. The results showed that the phylogenies of ftsA and the core genes recA and glnII were congruent, making the ftsA gene useful as a phylogenetic marker. Analysis of the ftsA gene sequences revealed a single-nucleotide polymorphism unique to Bradyrhizobium japonicum strains, and the potential use of this SNP for identification of this species was discussed.}, } @article {pmid30416203, year = {2018}, author = {Treanor, D and Pamminger, T and Hughes, WOH}, title = {The evolution of caste-biasing symbionts in the social hymenoptera.}, journal = {Insectes sociaux}, volume = {65}, number = {4}, pages = {513-519}, doi = {10.1007/s00040-018-0638-3}, pmid = {30416203}, issn = {0020-1812}, abstract = {The separation of individuals into reproductive and worker castes is the defining feature of insect societies. However, caste determination is itself a complex phenomenon, dependent on interacting genetic and environmental factors. It has been suggested by some authors that widespread maternally transmitted symbionts such as Wolbachia may be selected to interfere with caste determination, whilst others have discounted this possibility on theoretical grounds. We argue that there are in fact three distinct evolutionary scenarios in which maternally transmitted symbionts might be selected to influence the process of caste determination in a social hymenopteran host. Each of these scenarios generate testable predictions which we outline here. Given the increasing recognition of the complexity and multi-faceted nature of caste determination in social insects, we argue that maternally transmitted symbionts should also be considered as possible factors influencing the development of social hymenopterans.}, } @article {pmid30416059, year = {2018}, author = {Gaudioso-Pedraza, R and Beck, M and Frances, L and Kirk, P and Ripodas, C and Niebel, A and Oldroyd, GED and Benitez-Alfonso, Y and de Carvalho-Niebel, F}, title = {Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development.}, journal = {Current biology : CB}, volume = {28}, number = {22}, pages = {3562-3577.e6}, doi = {10.1016/j.cub.2018.09.031}, pmid = {30416059}, issn = {1879-0445}, abstract = {The formation of nitrogen-fixing nodules in legumes involves the initiation of synchronized programs in the root epidermis and cortex to allow rhizobial infection and nodule development. In this study, we provide evidence that symplastic communication, regulated by callose turnover at plasmodesmata (PD), is important for coordinating nodule development and infection in Medicago truncatula. Here, we show that rhizobia promote a reduction in callose levels in inner tissues where nodules initiate. This downregulation coincides with the localized expression of M. truncatula β-1,3-glucanase 2 (MtBG2), encoding a novel PD-associated callose-degrading enzyme. Spatiotemporal analyses revealed that MtBG2 expression expands from dividing nodule initials to rhizobia-colonized cortical and epidermal tissues. As shown by the transport of fluorescent molecules in vivo, symplastic-connected domains are created in rhizobia-colonized tissues and enhanced in roots constitutively expressing MtBG2. MtBG2-overexpressing roots additionally displayed reduced levels of PD-associated callose. Together, these findings suggest an active role for MtBG2 in callose degradation and in the formation of symplastic domains during sequential nodule developmental stages. Interfering with symplastic connectivity led to drastic nodulation phenotypes. Roots ectopically expressing β-1,3-glucanases (including MtBG2) exhibited increased nodule number, and those expressing MtBG2 RNAi constructs or a hyperactive callose synthase (under symbiotic promoters) showed defective nodulation phenotypes. Obstructing symplastic connectivity appears to block a signaling pathway required for the expression of NODULE INCEPTION (NIN) and its target NUCLEAR FACTOR-YA1 (NF-YA1) in the cortex. We conclude that symplastic intercellular communication is proactively enhanced by rhizobia, and this is necessary for appropriate coordination of bacterial infection and nodule development.}, } @article {pmid30416058, year = {2018}, author = {Decelle, J and Carradec, Q and Pochon, X and Henry, N and Romac, S and Mahé, F and Dunthorn, M and Kourlaiev, A and Voolstra, CR and Wincker, P and de Vargas, C}, title = {Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean.}, journal = {Current biology : CB}, volume = {28}, number = {22}, pages = {3625-3633.e3}, doi = {10.1016/j.cub.2018.09.024}, pmid = {30416058}, issn = {1879-0445}, abstract = {The dinoflagellate microalga Symbiodinium sustains coral reefs, one of the most diverse ecosystems of the biosphere, through mutualistic endosymbioses with a wide diversity of benthic hosts [1]. Despite its ecological and economic importance, the presence of Symbiodinium in open oceanic waters remains unknown, which represents a significant knowledge gap to fully understand the eco-evolutionary trajectory and resilience of endangered Symbiodinium-based symbioses. Here, we document the existence of Symbiodinium (i.e., now the family Symbiodiniaceae [2]) in tropical- and temperate-surface oceans using DNA and RNA metabarcoding of size-fractionated plankton samples collected at 109 stations across the globe. Symbiodinium from clades A and C were, by far, the most prevalent and widely distributed lineages (representing 0.1% of phytoplankton reads), while other lineages (clades B, D, E, F, and G) were present but rare. Concurrent metatranscriptomics analyses using the Tara Oceans gene catalog [3] revealed that Symbiodinium clades A and C were transcriptionally active in the open ocean and expressed core metabolic pathways (e.g., photosynthesis, carbon fixation, glycolysis, and ammonium uptake). Metabarcodes and expressed genes of clades A and C were detected in small and large plankton size fractions, suggesting the existence of a free-living population and a symbiotic lifestyle within planktonic hosts, respectively. However, high-resolution genetic markers and microscopy are required to confirm the life history of oceanic Symbiodinium. Overall, the previously unknown, metabolically active presence of Symbiodinium in oceanic waters opens up new avenues for investigating the potential of this oceanic reservoir to repopulate coral reefs following stress-induced bleaching.}, } @article {pmid30415881, year = {2018}, author = {Flores-Félix, JD and Sánchez-Juanes, F and García-Fraile, P and Valverde, A and Mateos, PF and Gónzalez-Buitrago, JM and Velázquez, E and Rivas, R}, title = {Phaseolus vulgaris is nodulated by the symbiovar viciae of several genospecies of Rhizobium laguerreae complex in a Spanish region where Lens culinaris is the traditionally cultivated legume.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2018.10.009}, pmid = {30415881}, issn = {1618-0984}, abstract = {Phaseolus vulgaris and Lens culinaris are two legumes with different distribution centers that were introduced in Spain at different times, but in some regions L. culinaris has been traditionally cultivated and P. vulgaris did not. Here we analysed the rhizobia isolated from nodules of these two legumes in one of these regions. MALDI-TOF MS analysis showed that all isolated strains matched with Rhizobium laguerreae and the phylogenetic analysis of rrs, atpD and recA genes confirmed these results. The phylogenetic analysis of these core genes allowed the differentiation of several groups within R. laguerreae and unexpectedly, strains with housekeeping genes identical to that of the type strain of R. laguerreae presented some differences in the rrs gene. In some strains this gene contains an intervening sequence (IVS) identical to that found in Rhizobium strains nodulating several legumes in different geographical locations. The atpD, recA and nodC genes of all isolated strains clustered with those of strains nodulating L. culinaris in its distribution centers, but not with those nodulating P. vulgaris in theirs. Therefore, all these strains belong to the symbiovar viciae, including those isolated from P. vulgaris, which in the studied region established effective symbiosis with the common endosymbiont of L. culinaris, instead to with its common endosymbiont, the symbiovar phaseoli. These results are particularly interesting for biogeography studies, because they showed that, due its high promiscuity degree, P. vulgaris is able to establish symbiosis with local symbiovars well established in the soil after centuries of cultivation with other legumes.}, } @article {pmid30413093, year = {2018}, author = {Fagorzi, C and Checcucci, A and diCenzo, GC and Debiec-Andrzejewska, K and Dziewit, L and Pini, F and Mengoni, A}, title = {Harnessing Rhizobia to Improve Heavy-Metal Phytoremediation by Legumes.}, journal = {Genes}, volume = {9}, number = {11}, pages = {}, doi = {10.3390/genes9110542}, pmid = {30413093}, issn = {2073-4425}, support = {2017-0719//Fondazione Cassa di Risparmio di Firenze/ ; Dinamiche dell'evoluzione dei genomi batterici: l'evoluzione del genoma multipartito e la suddivisione in moduli funzionali//Università degli Studi di Firenze/ ; PDF to GDC//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 7376//EMBO Short-Term Fellowship program/ ; 2016/23/N/NZ9/01655//National Science Center (Poland)/ ; }, abstract = {Rhizobia are bacteria that can form symbiotic associations with plants of the Fabaceae family, during which they reduce atmospheric di-nitrogen to ammonia. The symbiosis between rhizobia and leguminous plants is a fundamental contributor to nitrogen cycling in natural and agricultural ecosystems. Rhizobial microsymbionts are a major reason why legumes can colonize marginal lands and nitrogen-deficient soils. Several leguminous species have been found in metal-contaminated areas, and they often harbor metal-tolerant rhizobia. In recent years, there have been numerous efforts and discoveries related to the genetic determinants of metal resistance by rhizobia, and on the effectiveness of such rhizobia to increase the metal tolerance of host plants. Here, we review the main findings on the metal resistance of rhizobia: the physiological role, evolution, and genetic determinants, and the potential to use native and genetically-manipulated rhizobia as inoculants for legumes in phytoremediation practices.}, } @article {pmid30411190, year = {2018}, author = {Rossi, A and Bellone, A and Fokin, SI and Boscaro, V and Vannini, C}, title = {Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1279-9}, pmid = {30411190}, issn = {1432-184X}, support = {565-60%2016//University of Pisa/ ; 565-60%2017//University of Pisa/ ; 565-FFABR 2017//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, abstract = {Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.}, } @article {pmid30410727, year = {2018}, author = {Morris, JJ}, title = {What is the hologenome concept of evolution?.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {}, doi = {10.12688/f1000research.14385.1}, pmid = {30410727}, issn = {2046-1402}, abstract = {All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host-microbiome ecosystem as a "holobiont". Because natural selection acts on an organism's realized phenotype, and the phenotype of a holobiont is the result of the integrated activities of both the host and all of its microbiome inhabitants, it is reasonable to think that evolution can act at the level of the holobiont and cause changes in the "hologenome", or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.}, } @article {pmid30410449, year = {2018}, author = {Colella, S and Parisot, N and Simonet, P and Gaget, K and Duport, G and Baa-Puyoulet, P and Rahbé, Y and Charles, H and Febvay, G and Callaerts, P and Calevro, F}, title = {Bacteriocyte Reprogramming to Cope With Nutritional Stress in a Phloem Sap Feeding Hemipteran, the Pea Aphid Acyrthosiphon pisum.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {1498}, doi = {10.3389/fphys.2018.01498}, pmid = {30410449}, issn = {1664-042X}, abstract = {Nutritional symbioses play a central role in the ability of insects to thrive on unbalanced diets and in ensuring their evolutionary success. A genomic model for nutritional symbiosis comprises the hemipteran Acyrthosiphon pisum, and the gamma-3-proteobacterium, Buchnera aphidicola, with genomes encoding highly integrated metabolic pathways. A. pisum feeds exclusively on plant phloem sap, a nutritionally unbalanced diet highly variable in composition, thus raising the question of how this symbiotic system responds to nutritional stress. We addressed this by combining transcriptomic, phenotypic and life history trait analyses to determine the organismal impact of deprivation of tyrosine and phenylalanine. These two aromatic amino acids are essential for aphid development, are synthesized in a metabolic pathway for which the aphid host and the endosymbiont are interdependent, and their concentration can be highly variable in plant phloem sap. We found that this nutritional challenge does not have major phenotypic effects on the pea aphid, except for a limited weight reduction and a 2-day delay in onset of nymph laying. Transcriptomic analyses through aphid development showed a prominent response in bacteriocytes (the core symbiotic tissue which houses the symbionts), but not in gut, thus highlighting the role of bacteriocytes as major modulators of this homeostasis. This response does not involve a direct regulation of tyrosine and phenylalanine biosynthetic pathway and transporter genes. Instead, we observed an extensive transcriptional reprogramming of the bacteriocyte with a rapid down-regulation of genes encoding sugar transporters and genes required for sugar metabolism. Consistently, we observed continued overexpression of the A. pisum homolog of RRAD, a small GTPase implicated in repressing aerobic glycolysis. In addition, we found increased transcription of genes involved in proliferation, cell size control and signaling. We experimentally confirmed the significance of these gene expression changes detecting an increase in bacteriocyte number and cell size in vivo under tyrosine and phenylalanine depletion. Our results support a central role of bacteriocytes in the aphid response to amino acid deprivation: their transcriptional and cellular responses fine-tune host physiology providing the host insect with an effective way to cope with the challenges posed by the variability in composition of phloem sap.}, } @article {pmid30410018, year = {2018}, author = {Roth, R and Chiapello, M and Montero, H and Gehrig, P and Grossmann, J and O'Holleran, K and Hartken, D and Walters, F and Yang, SY and Hillmer, S and Schumacher, K and Bowden, S and Craze, M and Wallington, EJ and Miyao, A and Sawers, R and Martinoia, E and Paszkowski, U}, title = {A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4677}, doi = {10.1038/s41467-018-06865-z}, pmid = {30410018}, issn = {2041-1723}, abstract = {In terrestrial ecosystems most plant species live in mutualistic symbioses with nutrient-delivering arbuscular mycorrhizal (AM) fungi. Establishment of AM symbioses includes transient, intracellular formation of fungal feeding structures, the arbuscules. A plant-derived peri-arbuscular membrane (PAM) surrounds the arbuscules, mediating reciprocal nutrient exchange. Signaling at the PAM must be well coordinated to achieve this dynamic cellular intimacy. Here, we identify the PAM-specific Arbuscular Receptor-like Kinase 1 (ARK1) from maize and rice to condition sustained AM symbiosis. Mutation of rice ARK1 causes a significant reduction in vesicles, the fungal storage structures, and a concomitant reduction in overall root colonization by the AM fungus Rhizophagus irregularis. Arbuscules, although less frequent in the ark1 mutant, are morphologically normal. Co-cultivation with wild-type plants restores vesicle and spore formation, suggesting ARK1 function is required for the completion of the fungal life-cycle, thereby defining a functional stage, post arbuscule development.}, } @article {pmid30408885, year = {2019}, author = {Parakh, SK and Praveen, P and Loh, KC and Tong, YW}, title = {Wastewater treatment and microbial community dynamics in a sequencing batch reactor operating under photosynthetic aeration.}, journal = {Chemosphere}, volume = {215}, number = {}, pages = {893-903}, doi = {10.1016/j.chemosphere.2018.10.085}, pmid = {30408885}, issn = {1879-1298}, abstract = {A sequencing batch bioreactor (SBR) treating municipal wastewater was photosynthetically aerated using microalgae cultivated in a photobioreactor (PBR). Symbiotic interactions and CO2/O2 exchange were established between activated sludge in the SBR and microalgae in the PBR through hydrophobic hollow fiber membranes. Photosynthetic aeration enhanced COD removal in the SBR from 52.2% (without external aeration) to 90.3%, whereas N-NH4+ and P-PO43- removal increased by 63.5% and 90.4%, respectively. The SBR performance under photosynthetic aeration was comparable to that under mechanical aeration. However, no nitrification was observed in the SBR, indicating oxygen limitation and poor growth condition for nitrifiers. In the PBR, there was a rapid increase in biomass concentration and it stabilized at 3.0 g/L after 22 days of operation. High nitrogen demand in the PBR indicated the steady flow of inorganic carbon from the SBR through the membranes. Prolonged oxygen limitation and massive sludge attachment on the membranes resulted in low suspended sludge concentration in the SBR. Microbial community analysis indicated gradual enrichment of facultative and strictly anaerobic microorganisms in the SBR. These results highlight the potential of microalgae in lowering the cost of wastewater aeration and underline the challenges in sustaining symbiotic gas exchange during long-term.}, } @article {pmid30405668, year = {2018}, author = {Buendia, L and Girardin, A and Wang, T and Cottret, L and Lefebvre, B}, title = {LysM Receptor-Like Kinase and LysM Receptor-Like Protein Families: An Update on Phylogeny and Functional Characterization.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1531}, doi = {10.3389/fpls.2018.01531}, pmid = {30405668}, issn = {1664-462X}, abstract = {Members of plant specific families of receptor-like kinases (RLKs) and receptor-like proteins (RLPs), containing 3 extracellular LysMs have been shown to directly bind and/or to be involved in perception of lipo-chitooligosaccharides (LCO), chitooligosaccharides (CO), and peptidoglycan (PGN), three types of GlcNAc-containing molecules produced by microorganisms. These receptors are involved in microorganism perception by plants and can activate different plant responses leading either to symbiosis establishment or to defense responses against pathogens. LysM-RLK/Ps belong to multigenic families. Here, we provide a phylogeny of these families in eight plant species, including dicotyledons and monocotyledons, and we discuss known or putative biological roles of the members in each of the identified phylogenetic groups. We also report and discuss known biochemical properties of the LysM-RLK/Ps.}, } @article {pmid30404651, year = {2018}, author = {Hujber, Z and Horváth, G and Petővári, G and Krencz, I and Dankó, T and Mészáros, K and Rajnai, H and Szoboszlai, N and Leenders, WPJ and Jeney, A and Tretter, L and Sebestyén, A}, title = {GABA, glutamine, glutamate oxidation and succinic semialdehyde dehydrogenase expression in human gliomas.}, journal = {Journal of experimental & clinical cancer research : CR}, volume = {37}, number = {1}, pages = {271}, doi = {10.1186/s13046-018-0946-5}, pmid = {30404651}, issn = {1756-9966}, support = {Bolyai Fellowship Program//Hungarian Academy of Sciences/ ; Scientific and Innovative Research Found of Semmelweis University//Semmelweis University/ ; New National Excellence Program ÚNKP-17/2//Ministry of Human Capacities - Hungary/ ; New National Excellence Program ÚNKP-17/3 and ÚNKP-18/3//Ministry of Human Capacities - Hungary/ ; New National Excellence Program - ÚNKP-17/3 and ÚNKP-18/3//Ministry of Human Capacities - Hungary/ ; Richter Centenarium Foundation Fellowship-2016//Richter Centenarium Foundation/ ; NVKP_16-1-2016-0004 grant//Hungarian National Research, Development and Innovation Office (NKFIH)/ ; }, abstract = {BACKGROUND: Bioenergetic characterisation of malignant tissues revealed that different tumour cells can catabolise multiple substrates as salvage pathways, in response to metabolic stress. Altered metabolism in gliomas has received a lot of attention, especially in relation to IDH mutations, and the associated oncometabolite D-2-hydroxyglutarate (2-HG) that impact on metabolism, epigenetics and redox status. Astrocytomas and oligodendrogliomas, collectively called diffuse gliomas, are derived from astrocytes and oligodendrocytes that are in metabolic symbiosis with neurons; astrocytes can catabolise neuron-derived glutamate and gamma-aminobutyric acid (GABA) for supporting and regulating neuronal functions.

METHODS: Metabolic characteristics of human glioma cell models - including mitochondrial function, glycolytic pathway and energy substrate oxidation - in relation to IDH mutation status and after 2-HG incubation were studied to understand the Janus-faced role of IDH1 mutations in the progression of gliomas/astrocytomas. The metabolic and bioenergetic features were identified in glioma cells using wild-type and genetically engineered IDH1-mutant glioblastoma cell lines by metabolic analyses with Seahorse, protein expression studies and liquid chromatography-mass spectrometry.

RESULTS: U251 glioma cells were characterised by high levels of glutamine, glutamate and GABA oxidation. Succinic semialdehyde dehydrogenase (SSADH) expression was correlated to GABA oxidation. GABA addition to glioma cells increased proliferation rates. Expression of mutated IDH1 and treatment with 2-HG reduced glutamine and GABA oxidation, diminished the pro-proliferative effect of GABA in SSADH expressing cells. SSADH protein overexpression was found in almost all studied human cases with no significant association between SSADH expression and clinicopathological parameters (e.g. IDH mutation).

CONCLUSIONS: Our findings demonstrate that SSADH expression may participate in the oxidation and/or consumption of GABA in gliomas, furthermore, GABA oxidation capacity may contribute to proliferation and worse prognosis of gliomas. Moreover, IDH mutation and 2-HG production inhibit GABA oxidation in glioma cells. Based on these data, GABA oxidation and SSADH activity could be additional therapeutic targets in gliomas/glioblastomas.}, } @article {pmid30404159, year = {2018}, author = {Wang, T and Song, Z and Wang, X and Xu, L and Sun, Q and Li, L}, title = {Functional Insights into the Roles of Hormones in the Dendrobium officinale-Tulasnella sp. Germinated Seed Symbiotic Association.}, journal = {International journal of molecular sciences}, volume = {19}, number = {11}, pages = {}, doi = {10.3390/ijms19113484}, pmid = {30404159}, issn = {1422-0067}, support = {Z171100001417006//Beijing Science and Technology Projects of China/ ; }, abstract = {Dendrobium is one of the largest genera in the Orchidaceae, and D. officinale is used in traditional medicine, particularly in China. D. officinale seeds are minute and contain limited energy reserves, and colonization by a compatible fungus is essential for germination under natural conditions. When the orchid mycorrhizal fungi (OMF) initiates symbiotic interactions with germination-driven orchid seeds, phytohormones from the orchid or the fungus play key roles, but the details of the possible biochemical pathways are still poorly understood. In the present study, we established a symbiotic system between D. officinale and Tulasnella sp. for seed germination. RNA-Seq was used to construct libraries of symbiotic-germinated seeds (DoTc), asymbiotic-germinated seeds (Do), and free-living OMF (Tc) to investigate the expression profiles of biosynthesis and metabolism pathway genes for three classes of endogenous hormones: JA (jasmonic acid), ABA (abscisic acid) and SLs (strigolactones), in D. officinale seeds and OMF under symbiotic and asymbiotic conditions. Low concentrations of endogenous JA, ABA, or SLs were detected in the D. officinale-Tulasnella symbiont compared with the asymbiotic tissues. Gene annotation results suggest that the expression of DEGs (differentially expressed genes) related to JA and ABA biosynthesis from D. officinale were down-regulated, while most of the key DEGs related to SL biosynthesis from D. officinale were up-regulated in the symbiotic germinated seeds compared with the asymbiotic germinated seeds. Moreover, in the OMF, we found a significantly up-regulated differential expression of the JA and ABA biosynthesis-related genes in the symbiotic interaction, with the opposite expression trends to those found in Dendrobium. This indicates that Dendrobium seed symbiotic germination may be stimulated by the apparent involvement of the OMF in the production of hormones, and relatively low concentrations of endogenous JA, ABA, or SLs might be maintained to promote the growth of the D. officinale-Tulasnella symbiotic protocorm-like body. These results will increase our understanding of the possible roles played by endogenous hormones in the regulation of the orchid-fungus symbiosis.}, } @article {pmid30403490, year = {2018}, author = {Somporn, P and Walters, L and Ash, J}, title = {Expectations of rural community-based medical education: a case study from Thailand.}, journal = {Rural and remote health}, volume = {18}, number = {4}, pages = {4709}, doi = {10.22605/RRH4709}, pmid = {30403490}, issn = {1445-6354}, abstract = {INTRODUCTION: Thailand has recognised and sought to remedy rural medical workforce shortages. The Collaborative Project to Increase Production of Rural Doctors (CPIRD) has improved rural workforce recruitment through publicly funding medical school places for students with rural backgrounds. However, challenges in rural retention continue. CPIRD is seeking to develop a Thai rural community-based medical education (RCBME) program in the southern region of Thailand to improve preparation for rural practice and rural medical retention rates. Prospective stakeholder consultations will allow the understanding of expectations and concerns of stakeholders required for successful RCBME implementation. This study aims to explore stakeholders' expectations of the Southern Thai RCBME initiative.

METHODS: A qualitative case study comprised a purposive sample of students, clinical educators, policymakers, rural health professionals and local community stakeholders, all likely to be involved in a new RCBME program in Songkhla Province, Thailand. Individual semi-structured interviews were audiotaped, transcribed in Thai and coded using Worley's symbiosis framework. Following this, text and quotes used in the initial analysis were translated into English, discussed and reanalysed for emergent themes across the framework.

RESULTS: A total of 21 participants contributed RCBME stakeholder perspectives. They demonstrated expectations and concerns in each of the relationship axes of the symbiosis model including the clinical, institutional, social and personal axes. Three major themes emerged from the data that integrated stakeholder perspectives on the implication of RCBME in Thailand. These themes were a dramatic shift in Thai medical education paradigm, seeing rural practice as a future career, and collaboration to improve education and health in rural services.

CONCLUSION: This study comprehensively describes Thai stakeholder expectations of RCBME and demonstrates that, although some principles of RCBME are universal, context does influence the expectations and capacity of stakeholders to contribute to RCBME. Prospective formal stakeholder engagement is recommended to ensure successful implementation of new educational innovations.}, } @article {pmid30403423, year = {2018}, author = {Sepp, SK and Davison, J and Jairus, T and Vasar, M and Moora, M and Zobel, M and Öpik, M}, title = {Non-random association patterns in a plant-mycorrhizal fungal network reveal host-symbiont specificity.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.14924}, pmid = {30403423}, issn = {1365-294X}, abstract = {Arbuscular mycorrhizal (AM) fungi are obligate plant symbionts that have important functions in most terrestrial ecosystems, but there remains an incomplete understanding of host-fungus specificity and the relationships between species or functional groups of plants and AM fungi. Here, we aimed to provide a comprehensive description of plant-AM fungal interactions in a biodiverse semi-natural grassland. We sampled all plant species in a 1000 m2 homogeneous plot of dry calcareous grassland in two seasons (summer and autumn) and identified root-colonizing AM fungi by SSU rDNA sequencing. In the network of 33 plant and 100 AM fungal species, we found a significant effect of both host plant species and host plant functional group on AM fungal richness and community composition. Comparison with network null models revealed a larger-than-random degree of partner selectivity among plants. Grasses harbored a larger number of AM fungal partners and were more generalist in partner selection, compared with forbs. More generalist partner association and lower specialization were apparent among obligately, compared with facultatively, mycorrhizal plant species and among locally more abundant plant species. This study provides the most complete dataset of co-occurring plant and AM fungal taxa to date, showing that at this particular site, the interaction network is assembled non-randomly, with moderate selectivity in associations between plant species and functional groups and their fungal symbionts. This article is protected by copyright. All rights reserved.}, } @article {pmid30403141, year = {2018}, author = {Joshi, S and Cook, E and Mannoor, MS}, title = {Bacterial Nanobionics via 3D Printing.}, journal = {Nano letters}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.nanolett.8b02642}, pmid = {30403141}, issn = {1530-6992}, abstract = {Investigating the multidimensional integration between different microbiological kingdoms possesses potential toward engineering next-generation bionic architectures. Bacterial and fungal kingdom exhibits mutual symbiosis that can offer advanced functionalities to these bionic architectures. Moreover, functional nanomaterials can serve as probing agents for accessing newer information from microbial organisms due to their dimensional similarities. In this article, a bionic mushroom was created by intertwining cyanobacterial cells with graphene nanoribbons (GNRs) onto the umbrella-shaped pileus of mushroom for photosynthetic bioelectricity generation. These seamlessly merged GNRs function as agents for mediating extracellular electron transport from cyanobacteria resulting in photocurrent generation. Additionally, three-dimensional (3D) printing technique was used to assemble cyanobacterial cells in anisotropic, densely packed geometry resulting in adequate cell-population density for efficient collective behavior. These 3D printed cyanobacterial colonies resulted in comparatively higher photocurrent (almost 8-fold increase) than isotropically casted cyanobacteria of similar seeding density. An insight of the proposed integration between cyanobacteria and mushroom derives remarkable advantage that arises from symbiotic relationship, termed here as engineered bionic symbiosis. Existence of this engineered bionic symbiosis was confirmed by UV-visible spectroscopy and standard plate counting method. Taken together, the present study augments scientific understanding of multidimensional integration between the living biological microworld and functional abiotic nanomaterials to establish newer dimensionalities toward advancement of bacterial nanobionics.}, } @article {pmid30402759, year = {2018}, author = {Chashchina, OE and Chibilev, AA and Veselkin, DV and Kuyantseva, NB and Mumber, AG}, title = {The Natural Abundance of Heavy Nitrogen Isotope (15N) in Plants Increases near a Large Copper Smelter.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {482}, number = {1}, pages = {198-201}, doi = {10.1134/S0012496618050083}, pmid = {30402759}, issn = {1608-3105}, abstract = {The ratio of stable isotopes of nitrogen (15N and 14N) has been assessed in leaves of the forest plants from different functional groups (with ectomycorrhiza, ericoid, and arbuscular mycorrhiza; in a nitrogen-fixing symbiosis) under the conditions of strong transformation of ecosystems by the Karabashsky Copper-Smelting Plant effluents in the Southern Urals. The abundance of 15N in the plants generally increases in polluted habitats. The abundance of the heavy isotope 15N increases significantly with pollution in ericaceous dwarf shrubs (by 3.3‰) and herbs with arbuscular mycorrhizae (by 2.8‰). This indicates a strong alteration in conditions or modes of plant mineral nutrition under the influence of heavy metal pollution of forest ecosystems.}, } @article {pmid30402695, year = {2018}, author = {Alvarado-López, CJ and Dasgupta-Schubert, N and Ambriz, JE and Arteaga-Velazquez, JC and Villegas, JA}, title = {Lead uptake by the symbiotic Daucus carota L.-Glomus intraradices system and its effect on the morphology of extra- and intraradical fungal microstructures.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-018-3569-7}, pmid = {30402695}, issn = {1614-7499}, support = {168355//CONACyT/ ; }, abstract = {This work examines the strategies adopted by an arbuscular mycorrhizal symbiotic system to ameliorate environmental Pb stress by examining the concentrations of P, Fe, and Pb in the fungal microstructures and the host's root. In vitro cultures of Ri-T DNA-transformed carrot (Daucus carota L.) roots were inoculated with Glomus intraradices and treated with Pb(NO3)2 solution and the extraradical spores and mycelia (S/M) and the root with the vesicles, mycelia, and root cells were subsequently analyzed by polarized energy dispersive x-ray fluorescence (PEDXRF) spectrometry. Upon Pb treatment, within the root, the percentages of mycorrhizal colonization, the vesicles, and mycelia increased as well as the areas of the vesicles and the (extraradical) spores, although the number of spores and arbuscules decreased. The S/M and the mycorrhizal root showed enhanced concentrations of Pb, Fe, and P. These were particularly marked for Fe in the Pb-treated cultures. This indicates a synergistic relationship between the arbuscular mycorrhizal fungus and the host that confers a higher Pb tolerance to the latter by the induction of higher Fe absorption in the host. The intraradical vesicle, mycelia, and arbuscule numbers are interpreted as a "tactic to divert" the intraradical Pb traffic away from the root cells to the higher affinity cell walls of the arbuscular mycorrhizal fungi (AMF) microstructures in the apoplast. The results of this work show that the symbiosis between the AMF G. intraradices and the host plant D. carota distinctly improves the latter's Pb tolerance, and imply that the appropriate metal tolerant host-AMF combinations could be employed in process designs for the phytoremediation of Pb.}, } @article {pmid30401930, year = {2018}, author = {Jones, VAS and Bucher, M and Hambleton, EA and Guse, A}, title = {Microinjection to deliver protein, mRNA, and DNA into zygotes of the cnidarian endosymbiosis model Aiptasia sp.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16437}, doi = {10.1038/s41598-018-34773-1}, pmid = {30401930}, issn = {2045-2322}, support = {LTF//European Molecular Biology Organization (EMBO)/ ; GU 1128/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 724715//EC | European Research Council (ERC)/ ; }, abstract = {Reef-building corals depend on an intracellular symbiosis with photosynthetic dinoflagellates for their survival in nutrient-poor oceans. Symbionts are phagocytosed by coral larvae from the environment and transfer essential nutrients to their hosts. Aiptasia, a small tropical marine sea anemone, is emerging as a tractable model system for coral symbiosis; however, to date functional tools and genetic transformation are lacking. Here we have established an efficient workflow to collect Aiptasia eggs for in vitro fertilization and microinjection as the basis for experimental manipulations in the developing embryo and larvae. We demonstrate that protein, mRNA, and DNA can successfully be injected into live Aiptasia zygotes to label actin with recombinant Lifeact-eGFP protein; to label nuclei and cell membranes with NLS-eGFP and farnesylated mCherry translated from injected mRNA; and to transiently drive transgene expression from an Aiptasia-specific promoter, respectively, in embryos and larvae. These proof-of-concept approaches pave the way for future functional studies of development and symbiosis establishment in Aiptasia, a powerful model to unravel the molecular mechanisms underlying intracellular coral-algal symbiosis.}, } @article {pmid30400148, year = {2018}, author = {Wang, J and Wang, J and Liu, C and Ma, C and Li, C and Zhang, Y and Qi, Z and Zhu, R and Shi, Y and Zou, J and Li, Q and Zhu, J and Wen, Y and Sun, Z and Liu, H and Jiang, H and Yin, Z and Hu, Z and Chen, Q and Wu, X and Xin, D}, title = {Identification of Soybean Genes Whose Expression is Affected by the Ensifer fredii HH103 Effector Protein NopP.}, journal = {International journal of molecular sciences}, volume = {19}, number = {11}, pages = {}, doi = {10.3390/ijms19113438}, pmid = {30400148}, issn = {1422-0067}, support = {2017YFE0111000//The Ministry of Science and Technology of People's Republic of China/ ; 31400074//The National Natural Science Foundation/ ; 31471516//the National Natural Science Foundation of China/ ; 31271747//the National Natural Science Foundation of China/ ; 30971809//the National Natural Science Foundation of China/ ; ZD201213//the Natural Science Foundation of Heilongjiang Province of China/ ; LBH-Q16014//the Heilongjiang Postdoctoral Science Foundation/ ; 2013RFQXJ005//Harbin Science Technology Project/ ; 2014RFXXJ012//Harbin Science Technology Project/ ; 2016YFD0100500//the National Key R&D Program of China/ ; 2016YFD0100300//the National Key R&D Program of China/ ; 2016YFD0100201-21//the National Key R&D Program of China/ ; 1254G011//Foundation for University Key Teachers from the education department of Heilongjiang Province in China/ ; }, abstract = {In some legume⁻rhizobium symbioses, host specificity is influenced by rhizobial nodulation outer proteins (Nops). However, the genes encoding host proteins that interact with Nops remain unknown. We generated an Ensifer fredii HH103 NopP mutant (HH103ΩNopP), and analyzed the nodule number (NN) and nodule dry weight (NDW) of 10 soybean germplasms inoculated with the wild-type E. fredii HH103 or the mutant strain. An analysis of recombinant inbred lines (RILs) revealed the quantitative trait loci (QTLs) associated with NopP interactions. A soybean genomic region containing two overlapping QTLs was analyzed in greater detail. A transcriptome analysis and qRT-PCR assay were used to identify candidate genes encoding proteins that interact with NopP. In some germplasms, NopP positively and negatively affected the NN and NDW, while NopP had different effects on NN and NDW in other germplasms. The QTL region in chromosome 12 was further analyzed. The expression patterns of candidate genes Glyma.12g031200 and Glyma.12g073000 were determined by qRT-PCR, and were confirmed to be influenced by NopP.}, } @article {pmid30399353, year = {2018}, author = {Wiedenmann, J and D'Angelo, C}, title = {Symbiosis: High-Carb Diet of Reef Corals as Seen from Space.}, journal = {Current biology : CB}, volume = {28}, number = {21}, pages = {R1263-R1265}, doi = {10.1016/j.cub.2018.09.056}, pmid = {30399353}, issn = {1879-0445}, abstract = {High levels of phytoplankton visible in satellite imagery are correlated with an increased uptake of carbon compounds by corals. This suggests that corals rely less on carbon production by photosynthetic symbionts when other resources are plentiful, and that the changes in the acquisition mode of carbon can be inferred by remote-sensing techniques.}, } @article {pmid30395788, year = {2018}, author = {Xu, Y and Liu, F and Li, X and Cheng, B}, title = {The mycorrhiza-induced maize ZmPt9 gene affects root development and phosphate availability in nonmycorrhizal plant.}, journal = {Plant signaling & behavior}, volume = {}, number = {}, pages = {1-3}, doi = {10.1080/15592324.2018.1542240}, pmid = {30395788}, issn = {1559-2324}, abstract = {The arbuscular mycorrhizal (AM)-induced ZmPt9 gene is an orthologous to some AM-inducible phosphate (Pi) transporter genes involved in Pi-starvation responses. Promoter GFP assay confirmed its transcript was localized surrounding arbuscule in arbuscule-containing cells. But this gene was not an AM fungi-specific gene. Its function in nonmycorrhizal seedlings was verified through phenotypic analysis of ZmPt9-overexpression Arabidopsis. Overexpression of ZmPt9 in Arabidopsis exhibited increased primary root length and lateral root formation. Furthermore, ZmPt9-overexpression Arabidopsis plants contained more phosphorus (P) than that of wild type. The affection of ZmPt9 in nonmycorrhizal Arabidopsis leads to the hypothesis that symbiosis-inducible genes are also involved in root development and Pi accumulation in AM-independent manner.}, } @article {pmid30392013, year = {2018}, author = {Hendrikx, T and Schnabl, B}, title = {Antimicrobial proteins: intestinal guards to protect against liver disease.}, journal = {Journal of gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00535-018-1521-8}, pmid = {30392013}, issn = {1435-5922}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; U01 AA021856/AA/NIAAA NIH HHS/United States ; U01 AA024726/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, abstract = {Alterations of gut microbes play a role in the pathogenesis and progression of many disorders including liver and gastrointestinal diseases. Both qualitative and quantitative changes in gut microbiota have been associated with liver disease. Intestinal dysbiosis can disrupt the integrity of the intestinal barrier leading to pathological bacterial translocation and the initiation of an inflammatory response in the liver. In order to sustain symbiosis and protect from pathological bacterial translocation, antimicrobial proteins (AMPs) such as a-defensins and C-type lectins are expressed in the gastrointestinal tract. In this review, we provide an overview of the role of AMPs in different chronic liver disease such as alcoholic steatohepatitis, non-alcoholic fatty liver disease, and cirrhosis. In addition, potential approaches to modulate the function of AMPs and prevent bacterial translocation are discussed.}, } @article {pmid30390540, year = {2018}, author = {Meng, F and Xi, L and Liu, D and Huang, W and Lei, Z and Zhang, Z and Huang, W}, title = {Effects of light intensity on oxygen distribution, lipid production and biological community of algal-bacterial granules in photo-sequencing batch reactors.}, journal = {Bioresource technology}, volume = {272}, number = {}, pages = {473-481}, doi = {10.1016/j.biortech.2018.10.059}, pmid = {30390540}, issn = {1873-2976}, abstract = {The effects of light intensity (0-225 µmol m-2 s-1) on oxygen distribution, lipid production and biological community structure of algal-bacterial granules were investigated in six identical photo-sequencing batch reactors (with a dark/light cycle of 12 h/12 h). Typically green algal-bacterial granules could be developed at a light intensity of ≥135 µmol m-2 s-1. The lipid content was significantly increased under higher light intensity, while the percentage of saturated fatty acid methyl esters was remarkably decreased. Results showed that light intensity ≥90 µmol m-2 s-1 yielded enough O2 production from algae, creating aerobic/anoxic zone (0.3-0.6 mg-O2/L) in the core of granules and thus efficient algal-bacterial symbiosis system. Enhanced nitrogen and phosphorus removals were achieved in the reactors with stronger light illumination, probably attributable to the enrichment of ammonia oxidizing bacteria (Comamonadaceae and Nitrosomonadaceae) and algae (Navicula and Stigeoclonium). Illuminance ≥180 µmol m-2 s-1 was found to be unfavorable for Nitrospiraceae.}, } @article {pmid30390012, year = {2018}, author = {Kim, TH and Kim, D and Gautam, A and Lee, H and Kwak, MH and Park, MC and Park, S and Wu, G and Lee, BL and Lee, Y and Kwon, HJ}, title = {CpG-DNA exerts antibacterial effects by protecting immune cells and producing bacteria-reactive antibodies.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16236}, doi = {10.1038/s41598-018-34722-y}, pmid = {30390012}, issn = {2045-2322}, support = {2016M3A9B6916708//National Research Foundation of Korea (NRF)/ ; 2017R1A2B2007373//National Research Foundation of Korea (NRF)/ ; }, abstract = {CpG-DNA activates various immune cells, contributing to the host defense against bacteria. Here, we examined the biological function of CpG-DNA in the production of bacteria-reactive antibodies. The administration of CpG-DNA increased survival in mice following infection with methicillin-resistant S. aureus and protected immune cell populations in the peritoneal cavity, bone marrow, and spleen. CpG-DNA injection likewise increased bacteria-reactive antibodies in the mouse peritoneal fluid and serum, which was dependent on TLR9. B cells isolated from the peritoneal cavity produced bacteria-reactive antib