Microbe-Microbe Interactions
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An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts

An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts | Microbe-Microbe Interactions | Scoop.it
Arbuscular mycorrhizal fungi (AMF) are obligate plant biotrophs that may contain endobacteria in their cytoplasm. Genome sequencing of Candidatus Glomeribacter gigasporarum revealed a reduced genome and dependence on the fungal host.RNA-seq analysis of the AMF Gigaspora margarita in the presence and absence of the endobacterium indicated that endobacteria have an important role in the fungal pre-symbiotic phase by enhancing fungal bioenergetic capacity. To improve the understanding of fungal–endobacterial interactions, iTRAQ (isobaric tags for relative and absolute quantification) quantitative proteomics was used to identify differentially expressed proteins in G. margarita germinating spores with endobacteria (B+), without endobacteria in the cured line (B−) and after application of the synthetic strigolactone GR24.Proteomic, transcriptomic and biochemical data identified several fungal and bacterial proteins involved in interspecies interactions. Endobacteria influenced fungal growth, calcium signalling and metabolism. The greatest effects were on fungal primary metabolism and respiration, which was 50% higher in B+ than in B−. A shift towards pentose phosphate metabolism was detected in B−. Quantification of carbonylated proteins indicated that the B− line had higher oxidative stress levels, which were also observed in two host plants.This study shows that endobacteria generate a complex interdomain network that affects AMF and fungal–plant interactions
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Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples - Science

Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species’ growth rate. We demonstrate this in vitro and in vivo, under different growth conditions, and in complex bacterial communities. For several bacterial species, peak-to-trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes.


Via Max-Bernhard Ballhausen
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Max-Bernhard Ballhausen's curator insight, September 4, 2015 3:20 AM

Growth rate estimations in metagenomic samples, an important puzzle piece for studies in microbial community ecology!

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Socially mediated induction and suppression of antibiosis during bacterial coexistence

Antibiotics have profoundly changed human medicine, yet we know surprisingly little about the role of antibiotics in nature for the bacteria that produce them. Here we examine antibiotic use in the prolific antibiotic-producing genus Streptomyces across divergent social and competitive growth conditions. Our results provide clear experimental evidence that antibiotics are weapons whose use is strongly modified by intermicrobial social interactions. Simultaneously, using experiments and computer simulations, we show that social and competitive dynamics between bacteria have a crucial and previously unrecognized influence on the maintenance of microbial diversity in soil environments. These insights have implications for both bacterial coexistence and diversity and also for drug discovery.

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Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea

Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea | Microbe-Microbe Interactions | Scoop.it

In this work we have studied the antagonistic interactions existing among cultivable bacteria isolated from three ecological niches (rhizospheric soil, roots, and stem/leaves) of the traditional natural medicinal plant Echinacea purpurea. The three compartments harbored different taxonomic assemblages of strains, which were previously reported to display different antibiotic resistance patterns, suggesting the presence of differential selective pressure due to antagonistic molecules in the three compartments. Antagonistic interactions were assayed by the cross-streak method and interpreted using a network-based analysis. In particular “within-niche inhibition” and “cross-niche inhibition'’ were evaluated among isolates associated with each compartment as well as between isolates retrieved from the three different compartments, respectively. Data obtained indicated that bacteria isolated from the stem/leaves compartment were much more sensitive to the antagonistic activity than bacteria from roots and rhizospheric soil. Moreover, both the taxonomical position and the ecological niche might influence the antagonistic ability/sensitivity of different strains. Antagonism could play a significant role in contributing to the differentiation and structuring of plant-associated bacterial communities.

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Metabolic dependencies drive species co-occurrence in diverse microbial communities

Metabolic dependencies drive species co-occurrence in diverse microbial communities | Microbe-Microbe Interactions | Scoop.it

Although metabolic interactions have long been implicated in the assembly of microbial communities, their general prevalence has remained largely unknown. In this study, we systematically survey, by using a metabolic modeling approach, the extent of resource competition and metabolic cross-feeding in over 800 microbial communities from diverse habitats. We show that interspecies metabolic exchanges are widespread in natural communities, and that such exchanges can provide group advantage under nutrient-poor conditions. Our results highlight metabolic dependencies as a major driver of species co-occurrence. The presented methodology and mechanistic insights have broad implications for understanding compositional variation in natural communities as well as for facilitating the design of synthetic microbial communities.

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Hsiao-Han Lin's curator insight, May 5, 2015 9:51 PM

microbe are not the same, and they communicate and exchange

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Host genotype is an important determinant of the cereal phyllosphere mycobiome

Host genotype is an important determinant of the cereal phyllosphere mycobiome | Microbe-Microbe Interactions | Scoop.it
SummaryThe phyllosphere mycobiome in cereals is an important determinant of crop health. However, an understanding of the factors shaping this community is lacking.Fungal diversity in leaves from a range of cultivars of winter wheat (Triticum aestivum), winter and spring barley (Hordeum vulgare) and a smaller number of samples from oat (Avena sativa), rye (Secale cereale) and triticale (Triticum × Secale) was studied using next-generation sequencing. The effects of host genotype, fungicide treatment and location on fungal communities were explored.In total, 635 251 fungal internal transcribed spacer (ITS) reads were obtained from 210 leaf samples. Visual disease assessments and relative read abundance of Zymoseptoria tritici and Ramularia collo-cygni were strongly positively related. Crop genotype at the species level explained 43% of the variance in the total dataset, followed by fungicide treatment (13%) and location (4%). Indicator species, including plant pathogens, responding to factors such as crop species, location and treatment were identified.Host genotype at both the species and cultivar level is important in shaping phyllosphere fungal communities, whereas fungicide treatment and location have minor effects. We found many host-specific fungal pathogens, but also a large diversity of fungi that were relatively insensitive to host genetic background, indicating that host-specific pathogens live in a ‘sea’ of nonspecific fungi.
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Spatial heterogeneity of plant–soil feedback affects root interactions and interspecific competition

Spatial heterogeneity of plant–soil feedback affects root interactions and interspecific competition | Microbe-Microbe Interactions | Scoop.it
Plant–soil feedback is receiving increasing interest as a factor influencing plant competition and species coexistence in grasslands. However, we do not know how spatial distribution of plant–soil feedback affects plant below-ground interactions. We investigated the way in which spatial heterogeneity of soil biota affects competitive interactions in grassland plant species.We performed a pairwise competition experiment combined with heterogeneous distribution of soil biota using four grassland plant species and their soil biota. Patches were applied as quadrants of ‘own’ and ‘foreign’ soils from all plant species in all pairwise combinations. To evaluate interspecific root responses, species-specific root biomass was quantified using real-time PCR.All plant species suffered negative soil feedback, but strength was species-specific, reflected by a decrease in root growth in own compared with foreign soil. Reduction in root growth in own patches by the superior plant competitor provided opportunities for inferior competitors to increase root biomass in these patches. These patterns did not cascade into above-ground effects during our experiment.We show that root distributions can be determined by spatial heterogeneity of soil biota, affecting plant below-ground competitive interactions. Thus, spatial heterogeneity of soil biota may contribute to plant species coexistence in species-rich grasslands.
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PNAS: Molecular cartography of the human skin surface in 3D

PNAS: Molecular cartography of the human skin surface in 3D | Microbe-Microbe Interactions | Scoop.it

The human skin is an organ with a surface area of 1.5–2 m2 that provides our interface with the environment. The molecular composition of this organ is derived from host cells, microbiota, and external molecules. The chemical makeup of the skin surface is largely undefined. Here we advance the technologies needed to explore the topographical distribution of skin molecules, using 3D mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. Our 3D maps reveal that the molecular composition of skin has diverse distributions and that the composition is defined not only by skin cells and microbes but also by our daily routines, including the application of hygiene products. The technological development of these maps lays a foundation for studying the spatial relationships of human skin with hygiene, the microbiota, and environment, with potential for developing predictive models of skin phenotypes tailored to individual health.


Via Stéphane Hacquard, Max-Bernhard Ballhausen
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Max-Bernhard Ballhausen's curator insight, March 31, 2015 2:11 AM

Not really soil related, but just too cool to not post it :-)

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Molecular Ecology - The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

Molecular Ecology - The interaction of Saccharomyces paradoxus with its natural competitors on oak bark | Microbe-Microbe Interactions | Scoop.it

The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high-throughput environmental sequencing to show that S. paradoxus is a very rare member of the oak bark microbial community. We find that S. paradoxus can grow well on sterile medium made from oak bark, but that its growth is strongly suppressed when the other members of the community are present. We purified a set of twelve common fungal and bacterial species from the oak bark community and tested how each affected the growth of S. paradoxus in direct competition on oak bark medium at summer and winter temperatures, identifying both positive and negative interactions. One Pseudomonas species produces a diffusible toxin that suppresses S. paradoxus as effectively as either the whole set of twelve species together or the complete community present in nonsterilized oak medium. Conversely, one of the twelve species, Mucilaginibacter sp., had the opposite effect and promoted S. paradoxus growth at low temperatures. We conclude that, in its natural oak tree habitat, S. paradoxus is a rare species whose success depends on the much more abundant microbial species surrounding it.

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The ISME Journal - Selection on soil microbiomes reveals reproducible impacts on plant function

The ISME Journal - Selection on soil microbiomes reveals reproducible impacts on plant function | Microbe-Microbe Interactions | Scoop.it

Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools.

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The Great Escape: Pathogen Versus Host

The Great Escape: Pathogen Versus Host | Microbe-Microbe Interactions | Scoop.it

When bodily surface barriers have been breached, invading microorganisms are confronted by the innate immune system [1]. The first step in mounting a protective response is the rapid activation of an acute inflammatory response characterized by the migration and accumulation of immune cells at the site of invasion. As a primary defense against microbial infections, professional phagocytic cells such as macrophages will attempt to engulf and dispose of the invading microorganisms and their products. The recognition by effector cells of the innate immune system initiates signaling cascades, resulting in phagocytosis, secretion of microbicidal compounds and production of proinflammatory mediators. These early events culminate in the activation of adaptive immune responses; therefore, if launched early and effectively, innate immune responses limit the establishment of infectious foci and curb the severity of infections. However, it becomes more and more evident that microbial pathogens have developed very efficient strategies to circumvent and misguide host defenses, and therefore, their presence in the host results either in their elimination or in infection. Because of the critical role the innate immune system has in controlling microbial burden during the early stages of infection, the mechanisms employed by invading pathogens to thwart host immune defenses have attracted increasing interest. Here we synopsize some of the strategies exploited by two ubiquitous yet important human pathogens, the fungal species Candida albicans and the bacterial species Staphylococcus aureus [2,3]. In addition to possessing an array of virulence factors, these diverse species share many pathogenic characteristics, including the ability to form biofilms on host and abiotic surfaces, rapid development of antimicrobial resistance, and the ability to alter their transcriptome in response to stresses inflicted upon them by host immune cells. Importantly, although C. albicans and S. aureus are commensal species commonly colonizing various niches in the human host, they are the most frequent combination of organisms isolated from polymicrobial infections [4].

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A novel intracellular nitrogen-fixing symbiosis made by Ustilago maydis and Bacillus spp.

A novel intracellular nitrogen-fixing symbiosis made by Ustilago maydis and Bacillus spp. | Microbe-Microbe Interactions | Scoop.it

We observed that the maize pathogenic fungus Ustilago maydis grew in nitrogen (N)-free media at a rate similar to that observed in media containing ammonium nitrate, suggesting that it was able to fix atmospheric N2. Because only prokaryotic organisms have the capacity to reduce N2, we entertained the possibility that U. maydis was associated with an intracellular bacterium.The presence of nitrogenase in the fungus was analyzed by acetylene reduction, and capacity to fix N2 by use of 15N2. Presence of an intracellular N2-fixing bacterium was analyzed by PCR amplification of bacterial 16S rRNA and nifH genes, and by microscopic observations.Nitrogenase activity and 15N incorporation into the cells proved that U. maydis fixed N2. Light and electron microscopy, and fluorescence in situ hybridization (FISH) experiments revealed the presence of intracellular bacteria related to Bacillus pumilus, as evidenced by sequencing of the PCR-amplified fragments.These observations reveal for the first time the existence of an endosymbiotic N2-fixing association involving a fungus and a bacterium.


Via Kevin Garcia, Francis Martin
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PNAS: Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages—which provide a larger spatiotemporal scale relative to within stage analyses—revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended—and experimentally testable—conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.


Via Stéphane Hacquard
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Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism | Microbe-Microbe Interactions | Scoop.it

The global biogeography of microorganisms remains largely unknown, in contrast to the well-studied diversity patterns of macroorganisms. We used arbuscular mycorrhizal (AM) fungus DNA from 1014 plant-root samples collected worldwide to determine the global distribution of these plant symbionts. We found that AM fungal communities reflected local environmental conditions and the spatial distance between sites. However, despite AM fungi apparently possessing limited dispersal ability, we found 93% of taxa on multiple continents and 34% on all six continents surveyed. This contrasts with the high spatial turnover of other fungal taxa and with the endemism displayed by plants at the global scale. We suggest that the biogeography of AM fungi is driven by unexpectedly efficient dispersal, probably via both abiotic and biotic vectors, including humans.


Via Francis Martin, Stéphane Hacquard
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PLoS Biology: Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.


Via Stéphane Hacquard, Francis Martin
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Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies

Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies | Microbe-Microbe Interactions | Scoop.it
Naturally occurring antagonists towards pathogens play an important role to avoid pathogen outbreaks in ecosystems, and they can be applied as biocontrol agents for crops. Lichens present long-living symbiotic systems continuously exposed to pathogens. To analyze the antagonistic potential in lichens, we studied the bacterial community active against model bacteria and fungi by an integrative approach combining isolate screening, omics techniques and high resolution mass spectrometry. The highly diverse microbiome of the lung lichen (Lobaria pulmonaria (L.) Hoffm.) included an abundant antagonistic community dominated by Stenotrophomonas, Pseudomonas and Burkholderia. While antagonists represent 24.5% of the isolates, they were identified with only 7% in the metagenome; which means that they were overrepresented in the culturable fraction. Isolates of the dominant antagonistic genus Stenotrophomonas produced spermidine as main bioactive component. Moreover, spermidine-related genes, especially for the transport, were identified in the metagenome. The majority of hits identified belonged to Alphaproteobacteria, while Stenotrophomonas-specific spermidine synthases were not present in the dataset. Evidence for plant growth promoting effects was found for lichen-associated strains of Stenotrophomonas. Linking of metagenomic and culture data was possible but showed partly contradictory results, which required a comparative assessment. However, we have shown that lichens are important reservoirs for antagonistic bacteria, which open broad possibilities for biotechnological applications.
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Biotic interactions mediate soil microbial feedbacks to climate change

Decomposition of organic material by soil microbes generates an annual global release of 50–75 Pg carbon to the atmosphere, ∼7.5–9 times that of anthropogenic emissions worldwide. This process is sensitive to global change factors, which can drive carbon cycle–climate feedbacks with the potential to enhance atmospheric warming. Although the effects of interacting global change factors on soil microbial activity have been a widespread ecological focus, the regulatory effects of interspecific interactions are rarely considered in climate feedback studies. We explore the potential of soil animals to mediate microbial responses to warming and nitrogen enrichment within a long-term, field-based global change study. The combination of global change factors alleviated the bottom-up limitations on fungal growth, stimulating enzyme production and decomposition rates in the absence of soil animals. However, increased fungal biomass also stimulated consumption rates by soil invertebrates, restoring microbial process rates to levels observed under ambient conditions. Our results support the contemporary theory that top-down control in soil food webs is apparent only in the absence of bottom-up limitation. As such, when global change factors alleviate the bottom-up limitations on microbial activity, top-down control becomes an increasingly important regulatory force with the capacity to dampen the strength of positive carbon cycle–climate feedbacks.

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Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters | Microbe-Microbe Interactions | Scoop.it
Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies ‘talk’ between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms.
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Shao Qian's curator insight, May 17, 2015 4:32 AM

Remember the secondary metabolites produced by fungus during the discussion of article ?.. The journal below may provide one of the excellent example.

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Below-ground abiotic and biotic heterogeneity shapes above-ground infection outcomes and spatial divergence in a host–parasite interaction

Below-ground abiotic and biotic heterogeneity shapes above-ground infection outcomes and spatial divergence in a host–parasite interaction | Microbe-Microbe Interactions | Scoop.it
We investigated the impact of below-ground and above-ground environmental heterogeneity on the ecology and evolution of a natural plant–pathogen interaction.We combined field measurements and a reciprocal inoculation experiment to investigate the potential for natural variation in abiotic and biotic factors to mediate infection outcomes in the association between the fungal pathogen Melampsora lini and its wild flax host, Linum marginale, where pathogen strains and plant lines originated from two ecologically distinct habitat types that occur in close proximity (‘bog’ and ‘hill’).The two habitat types differed strikingly in soil moisture and soil microbiota. Infection outcomes for different host–pathogen combinations were strongly affected by the habitat of origin of the plant lines and pathogen strains, the soil environment and their interactions. Our results suggested that tradeoffs play a key role in explaining the evolutionary divergence in interaction traits among the two habitat types.Overall, we demonstrate that soil heterogeneity, by mediating infection outcomes and evolutionary divergence, can contribute to the maintenance of variation in resistance and pathogenicity within a natural host–pathogen metapopulation.
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Metabolic connectivity as a driver of host and endosymbiont integration

The origin of oxygenic photosynthesis in the Archaeplastida common ancestor was foundational for the evolution of multicellular life. It is very likely that the primary endosymbiosis that explains plastid origin relied initially on the establishment of a metabolic connection between the host cell and captured cyanobacterium. We posit that these connections were derived primarily from existing host-derived components. To test this idea, we used phylogenomic and network analysis to infer the phylogenetic origin and evolutionary history of 37 validated plastid innermost membrane (permeome) metabolite transporters from the model plant Arabidopsis thaliana. Our results show that 57% of these transporter genes are of eukaryotic origin and that the captured cyanobacterium made a relatively minor (albeit important) contribution to the process. We also tested the hypothesis that the bacterium-derived hexose-phosphate transporter UhpC might have been the primordial sugar transporter in the Archaeplastida ancestor. Bioinformatic and protein localization studies demonstrate that this protein in the extremophilic red algae Galdieria sulphuraria and Cyanidioschyzon merolae are plastid targeted. Given this protein is also localized in plastids in the glaucophyte alga Cyanophora paradoxa, we suggest it played a crucial role in early plastid endosymbiosis by connecting the endosymbiont and host carbon storage networks. In summary, our work significantly advances understanding of plastid integration and favors a host-centric view of endosymbiosis. Under this view, nuclear genes of either eukaryotic or bacterial (noncyanobacterial) origin provided key elements of the toolkit needed for establishing metabolic connections in the primordial Archaeplastida lineage.

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The Soil Microbiome Influences Grapevine-Associated Microbiota

The Soil Microbiome Influences Grapevine-Associated Microbiota | Microbe-Microbe Interactions | Scoop.it
Grapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g., Rhizobiaceae and Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management.

Via Jean-Michel Ané, Christophe Jacquet, Stéphane Hacquard
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Jean-Michel Ané's curator insight, March 25, 2015 6:41 PM

It always ticks me off when people claim the presence of "diazotrophic bacteria" based on that kind of study... They have no idea if these bacteria fix nitrogen and, in fact, it is very likely that they don't in the grape rhizoshere. 

Stijn Spaepen's comment, March 26, 2015 1:09 PM
Totally agree with your comment, Jean-Michel!
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Throwback (2009): Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana

Throwback (2009): Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana | Microbe-Microbe Interactions | Scoop.it

We constructed an experimental model system to study the effects of grazing by a common soil amoeba, Acanthamoeba castellanii, on the composition of bacterial communities in the rhizosphere of Arabidopsis thaliana. Amoebae showed distinct grazing preferences for specific bacterial taxa, which were rapidly replaced by grazing tolerant taxa in a highly reproducible way. The relative proportion of active bacteria increased although bacterial abundance was strongly decreased by amoebae. Specific bacterial taxa had disappeared already two days after inoculation of amoebae. The decrease in numbers was most pronounced in Betaproteobacteria and Firmicutes. In contrast, Actinobacteria, Nitrospira, Verrucomicrobia and Planctomycetes increased. Although other groups, such as betaproteobacterial ammonia oxidizers and Gammaproteobacteria did not change in abundance, denaturing gradient gel electrophoresis with specific primers for pseudomonads (Gammaproteobacteria) revealed both specific changes in community composition as well as shifts in functional genes (gacA) involved in bacterial defence responses. The resulting positive feedback on plant growth in the amoeba treatment confirms that bacterial grazers play a dominant role in structuring bacteria–plant interactions. This is the first detailed study documenting how rapidly protozoan grazers induce shifts in rhizosphere bacterial community composition.

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Nature Reviews Microbiology: Ecology and exploration of the rare biosphere

Nature Reviews Microbiology: Ecology and exploration of the rare biosphere | Microbe-Microbe Interactions | Scoop.it

The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations — the 'rare biosphere' — have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.

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Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria rich microbiome

Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria rich microbiome | Microbe-Microbe Interactions | Scoop.it
Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in CAZymes, despite a large expansion in genome size, both of which are consistent with what is seen in T. melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy-like long terminal repeats (LTR), and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics, and the evolution of the ectomycorrhizal association.

Via Francis Martin
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Evolution: Long-term nitrogen addition causes the evolution of less-cooperative mutualists

Evolution: Long-term nitrogen addition causes the evolution of less-cooperative mutualists | Microbe-Microbe Interactions | Scoop.it

Human activities have altered the global nitrogen (N) cycle, and as a result, elevated N inputs are causing profound ecological changes in diverse ecosystems. The evolutionary consequences of this global change have been largely ignored even though elevated N inputs are predicted to cause mutualism breakdown and the evolution of decreased cooperation between resource mutualists. Using a long-term (22 years) N-addition experiment, we find that elevated N inputs have altered the legume–rhizobium mutualism (where rhizobial bacteria trade N in exchange for photosynthates from legumes), causing the evolution of less-mutualistic rhizobia. Plants inoculated with rhizobium strains isolated from N-fertilized treatments produced 17–30% less biomass and had reduced chlorophyll content compared to plants inoculated with strains from unfertilized control plots. Because the legume–rhizobium mutualism is the major contributor of naturally fixed N to terrestrial ecosystems, the evolution of less-cooperative rhizobia may have important environmental consequences.


Via Stéphane Hacquard
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