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Bibliography on: Symbiosis

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.


ESP: PubMed Auto Bibliography 17 Jan 2019 at 01:44 Created: 


Symbiosis refers to an interaction between two or more different organisms living in close physical association, typically to the advantage of both. Symbiotic relationships were once thought to be exceptional situations. Recent studies, however, have shown that every multicellular eukaryote exists in a tight symbiotic relationship with billions of microbes. The associated microbial ecosystems are referred to as microbiome and the combination of a multicellular organism and its microbiota has been described as a holobiont. It seems "we are all lichens now."

Created with PubMed® Query: symbiosis NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-01-15

Baturina OA, Muntyan VS, Afonin AM, et al (2019)

Draft Genome Sequence of Sinorhizobium meliloti Strain CXM1-105.

Microbiology resource announcements, 8(2): pii:MRA01621-18.

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.

RevDate: 2019-01-15

Faure E, Not F, Benoiston AS, et al (2019)

Mixotrophic protists display contrasted biogeographies in the global ocean.

The ISME journal pii:10.1038/s41396-018-0340-5 [Epub ahead of print].

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.

RevDate: 2019-01-15

Banerjee J, Mishra N, Damle G, et al (2019)

Beyond LDL-c: The importance of serum oxidized LDL in predicting risk for type 2 diabetes in the middle-aged Asian Indians.

Diabetes & metabolic syndrome, 13(1):206-213.

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.

RevDate: 2019-01-15
CmpDate: 2019-01-15

Sui X, Wu Q, Chang W, et al (2018)

Proteomic analysis of the response of Funnelifor mismosseae/Medicago sativa to atrazine stress.

BMC plant biology, 18(1):289.

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.

RevDate: 2019-01-15
CmpDate: 2019-01-15

Kaczanowski S, Klim J, U Zielenkiewicz (2018)

An Apoptotic and Endosymbiotic Explanation of the Warburg and the Inverse Warburg Hypotheses.

International journal of molecular sciences, 19(10):.

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.

RevDate: 2019-01-15
CmpDate: 2019-01-15

Wang LX, Ren LL, Liu XB, et al (2019)

Effects of endophytic fungi in Mongolian pine on the selection behavior of woodwasp (Sirex noctilio) and the growth of its fungal symbiont.

Pest management science, 75(2):492-505.

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.

RevDate: 2019-01-15
CmpDate: 2019-01-15

Gile GH, James ER, Tai V, et al (2018)

New Species of Spirotrichonympha from Reticulitermes and the Relationships Among Genera in Spirotrichonymphea (Parabasalia).

The Journal of eukaryotic microbiology, 65(2):159-169.

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.

RevDate: 2019-01-14

Ingavle GC, Gionet-Gonzales M, Vorwald CE, et al (2019)

Injectable mineralized microsphere-loaded composite hydrogels for bone repair in a sheep bone defect model.

Biomaterials, 197:119-128 pii:S0142-9612(19)30005-5 [Epub ahead of print].

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.

RevDate: 2019-01-14

Rabillé H, Billoud B, Tesson B, et al (2019)

The brown algal mode of tip growth: Keeping stress under control.

PLoS biology, 17(1):e2005258 pii:pbio.2005258 [Epub ahead of print].

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.

RevDate: 2019-01-14

Bayer K, Jahn MT, Slaby BM, et al (2018)

Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade.

mSystems, 3(6): pii:mSystems00150-18.

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.

RevDate: 2019-01-14

Suesdek L (2018)

Microevolution of medically important mosquitoes - A review.

Acta tropica, 191:162-171 pii:S0001-706X(18)30994-X [Epub ahead of print].

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Frynta D, Kaftanová-Eliášová B, Žampachová B, et al (2018)

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.

Behavioural processes, 157:133-141.

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Rossitto De Marchi B, Kinene T, Mbora Wainaina J, et al (2018)

Comparative transcriptome analysis reveals genetic diversity in the endosymbiont Hamiltonella between native and exotic populations of Bemisia tabaci from Brazil.

PloS one, 13(7):e0201411.

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Matsuo M, Katahata A, Satoh S, et al (2018)

Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer.

PloS one, 13(7):e0200961.

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Ravanbakhsh M, Sasidharan R, Voesenek LACJ, et al (2018)

Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences.

Microbiome, 6(1):52.

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Weis AM, Soto R, JL Round (2018)

Commensal regulation of T cell survival through Erdr1.

Gut microbes, 9(5):458-464.

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Cieplak T, Soffer N, Sulakvelidze A, et al (2018)

A bacteriophage cocktail targeting Escherichia coli reduces E. coli in simulated gut conditions, while preserving a non-targeted representative commensal normal microbiota.

Gut microbes, 9(5):391-399.

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Brener-Raffalli K, Clerissi C, Vidal-Dupiol J, et al (2018)

Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato.

Microbiome, 6(1):39.

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Bellucci M, De Marchis F, A Pompa (2017)

The endoplasmic reticulum is a hub to sort proteins toward unconventional traffic pathways and endosymbiotic organelles.

Journal of experimental botany, 69(1):7-20.

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.

RevDate: 2019-01-13

Morin E, Miyauchi S, San Clemente H, et al (2019)

Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina.

The New phytologist [Epub ahead of print].

• 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.

RevDate: 2019-01-13

Miri M, Janakirama P, Huebert T, et al (2019)

Inside out: root cortex-localized LHK1 cytokinin receptor limits epidermal infection of Lotus japonicus roots by Mesorhizobium loti.

The New phytologist [Epub ahead of print].

•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.

RevDate: 2019-01-12

Belcaid M, Casaburi G, McAnulty SJ, et al (2019)

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.

Proceedings of the National Academy of Sciences of the United States of America pii:1817322116 [Epub ahead of print].

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.

RevDate: 2019-01-12

Simon JC, Marchesi JR, Mougel C, et al (2019)

Host-microbiota interactions: from holobiont theory to analysis.

Microbiome, 7(1):5 pii:10.1186/s40168-019-0619-4.

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.

RevDate: 2019-01-11

Wang J, Andersen SU, P Ratet (2018)

Editorial: Molecular and Cellular Mechanisms of the Legume-Rhizobia Symbiosis.

Frontiers in plant science, 9:1839.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Gupta R, Singh A, Srivastava M, et al (2019)

Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress.

Microbiological research, 218:87-96.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Yu F, Jing X, Li X, et al (2019)

Recombineering Pseudomonas protegens CHA0: An innovative approach that improves nitrogen fixation with impressive bactericidal potency.

Microbiological research, 218:58-65.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Chen L, Shi H, Heng J, et al (2019)

Antimicrobial, plant growth-promoting and genomic properties of the peanut endophyte Bacillus velezensis LDO2.

Microbiological research, 218:41-48.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Meng A, Marchet C, Corre E, et al (2018)

A de novo approach to disentangle partner identity and function in holobiont systems.

Microbiome, 6(1):105.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Benjamino J, Lincoln S, Srivastava R, et al (2018)

Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration.

Microbiome, 6(1):86.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Sorek M, Schnytzer Y, Ben-Asher HW, et al (2018)

Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium.

Microbiome, 6(1):83.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Deutscher AT, Burke CM, Darling AE, et al (2018)

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae.

Microbiome, 6(1):85.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

van de Guchte M, Blottière HM, J Doré (2018)

Humans as holobionts: implications for prevention and therapy.

Microbiome, 6(1):81.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Rosenberg E, I Zilber-Rosenberg (2018)

The hologenome concept of evolution after 10 years.

Microbiome, 6(1):78.

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".

RevDate: 2019-01-11
CmpDate: 2019-01-11

Vannier N, Mony C, Bittebiere AK, et al (2018)

A microorganisms' journey between plant generations.

Microbiome, 6(1):79.

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.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Ye Z, Vollhardt IMG, Girtler S, et al (2017)

An effective molecular approach for assessing cereal aphid-parasitoid-endosymbiont networks.

Scientific reports, 7(1):3138.

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.

RevDate: 2019-01-10

Reyes ML, Laughton AM, Parker BJ, et al (2019)

The influence of symbiotic bacteria on reproductive strategies and wing polyphenism in pea aphids responding to stress.

The Journal of animal ecology [Epub ahead of print].

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.

RevDate: 2019-01-10

Dombrowski N, Lee JH, Williams TA, et al (2019)

Genomic diversity, lifestyles and evolutionary origins of DPANN archaea.

FEMS microbiology letters pii:5281434 [Epub ahead of print].

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.

RevDate: 2019-01-10

Caputo A, Nylander JAA, RA Foster (2019)

The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.

FEMS microbiology letters pii:5281432 [Epub ahead of print].

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.

RevDate: 2019-01-10

Piromyou P, Songwattana P, Teamtisong K, et al (2019)

Mutualistic co-evolution of T3SSs during the establishment of symbiotic relationships between Vigna radiata and Bradyrhizobia.

MicrobiologyOpen [Epub ahead of print].

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.

RevDate: 2019-01-10

Fokin SI, Serra V, Ferrantini F, et al (2019)

"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.

Microbial ecology pii:10.1007/s00248-018-1311-0 [Epub ahead of print].

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.

RevDate: 2019-01-10

Hsu CC, Lai PH, Chen TC, et al (2019)

PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids.

BMC genomics, 20(1):25 pii:10.1186/s12864-018-5420-4.

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.

RevDate: 2019-01-10

Chou M, Sun Y, Yang J, et al (2019)

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.

The Science of the total environment, 656:1346-1357.

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.

RevDate: 2019-01-10
CmpDate: 2019-01-10

Huang J, Zhang PJ, Zhang J, et al (2017)

An ant-coccid mutualism affects the behavior of the parasitoid Aenasius bambawalei, but not that of the ghost ant Tetramorium bicarinatum.

Scientific reports, 7(1):5175.

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.

RevDate: 2019-01-10
CmpDate: 2019-01-10

Xing X, Men J, S Guo (2017)

Phylogenetic constrains on Polyporus umbellatus-Armillaria associations.

Scientific reports, 7(1):4226.

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.

RevDate: 2019-01-09

Liu L, Xu L, Jia Q, et al (2019)

Arms race: diverse effector proteins with conserved motifs.

Plant signaling & behavior [Epub ahead of print].

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.

RevDate: 2019-01-09
CmpDate: 2019-01-09

Ferrier-Pagès C, Sauzéat L, V Balter (2018)

Coral bleaching is linked to the capacity of the animal host to supply essential metals to the symbionts.

Global change biology, 24(7):3145-3157.

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.

RevDate: 2019-01-08

Liu A, Contador CA, Fan K, et al (2018)

Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes.

Frontiers in plant science, 9:1860.

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.

RevDate: 2019-01-08

Bedini A, Mercy L, Schneider C, et al (2018)

Unraveling the Initial Plant Hormone Signaling, Metabolic Mechanisms and Plant Defense Triggering the Endomycorrhizal Symbiosis Behavior.

Frontiers in plant science, 9:1800.

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.

RevDate: 2019-01-08

Nguyen HP, Ratu STN, Yasuda M, et al (2018)

InnB, a Novel Type III Effector of Bradyrhizobium elkanii USDA61, Controls Symbiosis With Vigna Species.

Frontiers in microbiology, 9:3155.

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.

RevDate: 2019-01-08

Huitzil S, Sandoval-Motta S, Frank A, et al (2018)

Modeling the Role of the Microbiome in Evolution.

Frontiers in physiology, 9:1836.

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.

RevDate: 2019-01-08

Bogar L, Peay K, Kornfeld A, et al (2019)

Plant-mediated partner discrimination in ectomycorrhizal mutualisms.

Mycorrhiza pii:10.1007/s00572-018-00879-7 [Epub ahead of print].

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.

RevDate: 2019-01-08

Dessì D, Margarita V, Cocco AR, et al (2019)

Trichomonas vaginalis and Mycoplasma hominis: new tales of two old friends.

Parasitology pii:S0031182018002135 [Epub ahead of print].

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.

RevDate: 2019-01-08
CmpDate: 2019-01-08

Zhang B, Du N, Li Y, et al (2018)

Distinct biogeographic patterns of rhizobia and non-rhizobial endophytes associated with soybean nodules across China.

The Science of the total environment, 643:569-578.

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.

RevDate: 2019-01-07

Zhang XF, Hu ZH, Yan TX, et al (2019)

Arbuscular mycorrhizal fungi alleviate Cd phytotoxicity by altering Cd subcellular distribution and chemical forms in Zea mays.

Ecotoxicology and environmental safety, 171:352-360 pii:S0147-6513(18)31395-2 [Epub ahead of print].

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.

RevDate: 2019-01-07

Zhang XW, Dunn DW, Wen XL, et al (2019)

Differential deployment of sanctioning mechanisms by male and female host trees in a gynodioecious fig-wasp mutualism.

Ecology [Epub ahead of print].

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.

RevDate: 2019-01-07

Shang N, Ding M, Dai M, et al (2019)

Biodegradation of malachite green by an endophytic bacterium Klebsiella aerogenes S27 involving a novel oxidoreductase.

Applied microbiology and biotechnology pii:10.1007/s00253-018-09583-0 [Epub ahead of print].

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.

RevDate: 2019-01-07

Ramírez-Puebla ST, Hernández MAR, Guerrero Ruiz G, et al (2018)

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.

Systematic and applied microbiology pii:S0723-2020(18)30455-7 [Epub ahead of print].

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Ohtsuka S, Nishikawa J, GA Boxshall (2018)

A new species of Peniculus (Copepoda: Siphonostomatoida) parasitizing mesopelagic myctophid fish: first discovery of colonization of the genus in deep water.

Parasite (Paris, France), 25:58.

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Yang CY, DC Tarng (2018)

Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients.

Nephrology (Carlton, Vic.), 23 Suppl 4:16-20.

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Shane JL, Grogan CL, Cwalina C, et al (2018)

Blood meal-induced inhibition of vector-borne disease by transgenic microbiota.

Nature communications, 9(1):4127.

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Clanner-Engelshofen BM, Ruzicka T, M Reinholz (2018)

Efficient isolation and observation of the most complex human commensal, Demodex spp.

Experimental & applied acarology, 76(1):71-80.

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Kanté Tagueu S, Farikou O, Njiokou F, et al (2018)

Prevalence of Sodalis glossinidius and different trypanosome species in Glossina palpalis palpalis caught in the Fontem sleeping sickness focus of the southern Cameroon.

Parasite (Paris, France), 25:44.

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Albrecht J, Classen A, Vollstädt MGR, et al (2018)

Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient.

Nature communications, 9(1):3177.

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Medina V, Sardoy PM, Soria M, et al (2018)

Characterized non-transient microbiota from stinkbug (Nezara viridula) midgut deactivates soybean chemical defenses.

PloS one, 13(7):e0200161.

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Tetz G, V Tetz (2018)

Tetz's theory and law of longevity.

Theory in biosciences = Theorie in den Biowissenschaften, 137(2):145-154.

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.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Redanz S, Cheng X, Giacaman RA, et al (2018)

Live and let die: Hydrogen peroxide production by the commensal flora and its role in maintaining a symbiotic microbiome.

Molecular oral microbiology, 33(5):337-352.

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.

RevDate: 2019-01-06

Jelassi R, Khemaissia H, Ghemari C, et al (2019)

Ecotoxicological effects of trace element contamination in talitrid amphipod Orchestia montagui Audouin, 1826.

Environmental science and pollution research international pii:10.1007/s11356-018-3974-y [Epub ahead of print].

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.

RevDate: 2019-01-06

Voříšková A, Jansa J, Püschel D, et al (2019)

Abiotic contexts consistently influence mycorrhiza functioning independently of the composition of synthetic arbuscular mycorrhizal fungal communities.

Mycorrhiza pii:10.1007/s00572-018-00878-8 [Epub ahead of print].

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.

RevDate: 2019-01-06

Cui G, Ai S, Chen K, et al (2019)

Arbuscular mycorrhiza augments cadmium tolerance in soybean by altering accumulation and partitioning of nutrient elements, and related gene expression.

Ecotoxicology and environmental safety, 171:231-239 pii:S0147-6513(18)31392-7 [Epub ahead of print].

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.

RevDate: 2019-01-06

Kamm K, Schierwater B, R DeSalle (2019)

Innate immunity in the simplest animals - placozoans.

BMC genomics, 20(1):5 pii:10.1186/s12864-018-5377-3.

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.

RevDate: 2019-01-05

Liu J, Rutten L, Limpens E, et al (2019)

A Remote cis-Regulatory Region Is Required for NIN Expression in the Pericycle to Initiate Nodule Primordium Formation in Medicago truncatula.

The Plant cell pii:tpc.18.00478 [Epub ahead of print].

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.

RevDate: 2019-01-04

Shinde S, Zerbs S, Collart FR, et al (2019)

Pseudomonas fluorescens increases mycorrhization and modulates expression of antifungal defense response genes in roots of aspen seedlings.

BMC plant biology, 19(1):4 pii:10.1186/s12870-018-1610-0.

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.

RevDate: 2019-01-04
CmpDate: 2019-01-04

Cagide C, Riviezzi B, Minteguiaga M, et al (2018)

Identification of Plant Compounds Involved in the Microbe-Plant Communication During the Coinoculation of Soybean with Bradyrhizobium elkanii and Delftia sp. strain JD2.

Molecular plant-microbe interactions : MPMI, 31(11):1192-1199.

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.

RevDate: 2019-01-03

Suzaki T, Takeda N, Nishida H, et al (2019)

LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonius.

PLoS genetics, 15(1):e1007865 pii:PGENETICS-D-18-01183.

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.

RevDate: 2019-01-03

Franzini VI, Azcón R, Ruiz-Lozano JM, et al (2019)

Rhizobial symbiosis modifies root hydraulic properties in bean plants under non-stressed and salinity-stressed conditions.

Planta pii:10.1007/s00425-018-03076-0 [Epub ahead of print].

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.

RevDate: 2019-01-03

Muñoz-Marín MDC, Shilova IN, Shi T, et al (2019)

The Transcriptional Cycle Is Suited to Daytime N2 Fixation in the Unicellular Cyanobacterium "Candidatus Atelocyanobacterium thalassa" (UCYN-A).

mBio, 10(1): pii:mBio.02495-18.

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.

RevDate: 2019-01-03

Hall RJ, Flanagan LA, Bottery MJ, et al (2019)

A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet.

mBio, 10(1): pii:mBio.02106-18.

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.

RevDate: 2019-01-03

Rubin-Blum M, Dubilier N, M Kleiner (2019)

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria.

mSphere, 4(1): pii:4/1/e00394-18.

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.

RevDate: 2019-01-03

Chen YY, Chen DQ, Chen L, et al (2019)

Microbiome-metabolome reveals the contribution of gut-kidney axis on kidney disease.

Journal of translational medicine, 17(1):5 pii:10.1186/s12967-018-1756-4.

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.

RevDate: 2019-01-03
CmpDate: 2019-01-03

Rangel SM, AS Paller (2018)

Bacterial colonization, overgrowth, and superinfection in atopic dermatitis.

Clinics in dermatology, 36(5):641-647.

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.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Kanté ST, Melachio T, Ofon E, et al (2018)

Detection of Wolbachia and different trypanosome species in Glossina palpalis palpalis populations from three sleeping sickness foci of southern Cameroon.

Parasites & vectors, 11(1):630 pii:10.1186/s13071-018-3229-2.

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.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Fontúrbel FE, Bruford MW, Salazar DA, et al (2019)

The hidden costs of living in a transformed habitat: Ecological and evolutionary consequences in a tripartite mutualistic system with a keystone mistletoe.

The Science of the total environment, 651(Pt 2):2740-2748.

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.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Butler S, JP O'Dwyer (2018)

Stability criteria for complex microbial communities.

Nature communications, 9(1):2970.

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.

RevDate: 2019-01-01
CmpDate: 2019-01-01

Ezugwu AE, Adeleke OJ, S Viriri (2018)

Symbiotic organisms search algorithm for the unrelated parallel machines scheduling with sequence-dependent setup times.

PloS one, 13(7):e0200030 pii:PONE-D-18-05231.

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.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Melati BG, LC Leal (2018)

Aggressive bodyguards are not always the best: Preferential interaction with more aggressive ant species reduces reproductive success of plant bearing extrafloral nectaries.

PloS one, 13(6):e0199764.

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.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Hörandl E, D Speijer (2018)

How oxygen gave rise to eukaryotic sex.

Proceedings. Biological sciences, 285(1872):.

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.

RevDate: 2018-12-31

Fukudome M, Watanabe E, Osuki KI, et al (2018)

Stably-Transformed Lotus japonicus Plants Overexpressing Phytoglobin LjGlb1-1 Show Decreased Nitric Oxide Levels in Roots and Nodules as well as Delayed Nodule Senescence.

Plant & cell physiology pii:5265248 [Epub ahead of print].

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.

RevDate: 2018-12-31

Shu L, Brock DA, Geist KS, et al (2018)

Symbiont location, host fitness, and possible coadaptation in a symbiosis between social amoebae and bacteria.

eLife, 7: pii:42660 [Epub ahead of print].

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Sun L, Zuo W, Tian Y, et al (2019)

Performance and microbial community analysis of an algal-activated sludge symbiotic system: Effect of activated sludge concentration.

Journal of environmental sciences (China), 76:121-132.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Regan T, Barnett MW, Laetsch DR, et al (2018)

Characterisation of the British honey bee metagenome.

Nature communications, 9(1):4995.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Váczi P, Gauslaa Y, KA Solhaug (2019)

Reprint of Efficient fungal UV-screening provides a remarkably high UV-B tolerance of photosystem II in lichen photobionts.

Plant physiology and biochemistry : PPB, 134:123-128.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Wintermantel WM (2018)

Integration of Omics Approaches toward Understanding Whitefly Transmission of Viruses.

Advances in virus research, 102:199-223.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Carr JP, Donnelly R, Tungadi T, et al (2018)

Viral Manipulation of Plant Stress Responses and Host Interactions With Insects.

Advances in virus research, 102:177-197.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Pastore M, E Sforza (2018)

Exploiting symbiotic interactions between Chlorella protothecoides and Brevundimonas diminuta for an efficient single-step urban wastewater treatment.

Water science and technology : a journal of the International Association on Water Pollution Research, 78(1-2):216-224.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Cornuault JK, Petit MA, Mariadassou M, et al (2018)

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes.

Microbiome, 6(1):65.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Robledo M, García-Tomsig NI, JI Jiménez-Zurdo (2018)

Primary Characterization of Small RNAs in Symbiotic Nitrogen-Fixing Bacteria.

Methods in molecular biology (Clifton, N.J.), 1734:277-295.

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.

RevDate: 2018-12-28

Fisinin VI, Egorov IA, Laptev GY, et al (2017)

[Antibiotic-free poultry production based on innovative nutritional programs with the involvement of probiotics].

Voprosy pitaniia, 86(6):114-124.

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.

RevDate: 2018-12-27

Thürich J, Meichsner D, Furch ACU, et al (2018)

Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins.

PloS one, 13(12):e0209658 pii:PONE-D-18-13453.

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.

RevDate: 2018-12-27

Swain Ewald HA, PW Ewald (2018)

Natural Selection, The Microbiome, and Public Health.

The Yale journal of biology and medicine, 91(4):445-455.

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.

RevDate: 2018-12-25

Lebon C, Benlali A, Atyame C, et al (2018)

Construction of a genetic sexing strain for Aedes albopictus: a promising tool for the development of sterilizing insect control strategies targeting the tiger mosquito.

Parasites & vectors, 11(Suppl 2):658 pii:10.1186/s13071-018-3212-y.

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.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )