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Rescooped by Stéphane Hacquard from MycorWeb Plant-Microbe Interactions
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Belowground biodiversity and ecosystem functioning : Nature

Belowground biodiversity and ecosystem functioning : Nature | The Plant Microbiome | Scoop.it
Evidence is mounting that the immense diversity of microorganisms and animals that live belowground contributes significantly to shaping aboveground biodiversity and the functioning of terrestrial ecosystems. Our understanding of how this belowground biodiversity is distributed, and how it regulates the structure and functioning of terrestrial ecosystems, is rapidly growing. Evidence also points to soil biodiversity as having a key role in determining the ecological and evolutionary responses of terrestrial ecosystems to current and future environmental change. Here we review recent progress and propose avenues for further research in this field.

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eLIFE: Antibacterial gene transfer across the tree of life

eLIFE: Antibacterial gene transfer across the tree of life | The Plant Microbiome | Scoop.it

Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, transfer of a potent antibacterial gene across the universal tree seemingly bestows a niche-transcending adaptation that trumps the barriers against parallel HGT to all domains. The discoveries also comprise the first characterization of an antibacterial gene in archaea and support the pursuit of antibiotics in this underexplored group.

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New Phytol: Towards a holistic understanding of the beneficial interactions across the Populus microbiome

New Phytol: Towards a holistic understanding of the beneficial interactions across the Populus microbiome | The Plant Microbiome | Scoop.it

Interactions between trees and microorganisms are tremendously complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi-component interactions necessary for holistic ecosystem-level understanding. We review recent studies in Populus to emphasize the importance of such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems.

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Nature Review Microbiology: The importance of sample archiving in microbial ecology

For many microbial ecology studies, the samples collected are irreplaceable — microbial ecologists must therefore develop robust strategies for long-term storage and archiving of samples in order to fully develop, and protect, the scientific record.

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Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe : Scientific Reports : Nature Publishing Group

Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe : Scientific Reports : Nature Publishing Group | The Plant Microbiome | Scoop.it
The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.

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Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data

Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data | The Plant Microbiome | Scoop.it

Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that have rested controversial claims upon sequencing data that appear to support the presence of unexpected exogenous species. I used reads that preferentially aligned to alternate genomes to infer the distribution of potential contaminant species in a set of independent sequencing experiments. I confirmed that dilute samples are more exposed to contaminating DNA, and, focusing on four single-cell sequencing experiments, found that these contaminants appear to originate from a wide diversity of clades. Although negative control libraries prepared from ‘blank’ samples recovered the highest-frequency contaminants, low-frequency contaminants, which appeared to make heterogeneous contributions to samples prepared in parallel within a single experiment, were not well controlled for. I used these results to show that, despite heavy replication and plausible controls, contamination can explain all of the observations used to support a recent claim that complete genes pass from food to human blood. Contamination must be considered a potential source of signals of exogenous species in sequencing data, even if these signals are replicated in independent experiments, vary across conditions, or indicate a species which seems a priori unlikely to contaminate. Negative control libraries processed in parallel are essential to control for contaminant DNAs, but their limited ability to recover low-frequency contaminants must be recognized.


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Botrytis species: relentless necrotrophic thugs or endophytes gone rogue?

Botrytis species: relentless necrotrophic thugs or endophytes gone rogue? | The Plant Microbiome | Scoop.it

Plant pathology has a long-standing tradition of classifying microbes as pathogens, endophytes or saprophytes. Lifestyles of pathogens are categorized as biotrophic, necrotrophic or hemibiotrophic. Botrytis species are considered by many to be archetypal examples of necrotrophic fungi, with B. cinerea being the most extensively studied species because of its broad host range and economic impact. In this review, we discuss recent work which illustrates that B. cinerea is capable of colonizing plants internally, presumably as an endophyte, without causing any disease or stress symptoms. The extent of the facultative endophytic behaviour of B. cinerea and its relevance in the ecology and disease epidemiology may be vastly underestimated. Moreover, we discuss the recent discovery of a novel Botrytis species, B. deweyae, which normally grows as an endophyte in ornamental daylilies (Hemerocallis), but displays facultative pathogenic behaviour, and is increasingly causing economic damage. We propose that the emergence of endophytes ‘gone rogue’ as novel diseases may be related to increased inbreeding of hybrid lines and reduced genetic diversity. These observations lead us to argue that the sometimes inflexible classification of pathogenic microbes by their lifestyles requires serious reconsideration. There is much more variety to the interactions of Botrytis with its hosts than the eye (or the plant pathologist) can see, and this may be true for other microbes interacting with plants.


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New Phytol: Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation

New Phytol: Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation | The Plant Microbiome | Scoop.it

Plants rapidly release photoassimilated carbon (C) to the soil via direct root exudation and associated mycorrhizal fungi, with both pathways promoting plant nutrient availability. This study aimed to explore these pathways from the root's vascular bundle to soil microbial communities.
Using nanoscale secondary ion mass spectrometry (NanoSIMS) imaging and 13C-phospho- and neutral lipid fatty acids, we traced in-situ flows of recently photoassimilated C of 13CO2-exposed wheat (Triticum aestivum) through arbuscular mycorrhiza (AM) into root- and hyphae-associated soil microbial communities.
Intraradical hyphae of AM fungi were significantly 13C-enriched compared to other root-cortex areas after 8 h of labelling. Immature fine root areas close to the root tip, where AM features were absent, showed signs of passive C loss and co-location of photoassimilates with nitrogen taken up from the soil solution. A significant and exclusively fresh proportion of 13C-photosynthates was delivered through the AM pathway and was utilised by different microbial groups compared to C directly released by roots.
Our results indicate that a major release of recent photosynthates into soil leave plant roots via AM intraradical hyphae already upstream of passive root exudations. AM fungi may act as a rapid hub for translocating fresh plant C to soil microbes.

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Phyllosphere bacterial community of floating macrophytes in paddy soil environments as revealed by Illumina high-throughput sequencing

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities, but remains largely unknown. We took Wolffia australiana as a representative floating plant, and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. Results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited significantly different structures from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species-sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, this study reveals the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.
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Standing genetic variation in host preference for mutualist microbial symbionts

Many models of mutualisms show that mutualisms are unstable if hosts lack mechanisms enabling preferential associations with mutualistic symbiotic partners over exploitative partners. Despite the theoretical importance of mutualism-stabilizing mechanisms, we have little empirical evidence to infer their evolutionary dynamics in response to exploitation by non-beneficial partners. Using a model mutualism—the interaction between legumes and nitrogen-fixing soil symbionts—we tested for quantitative genetic variation in plant responses to mutualistic and exploitative symbiotic rhizobia in controlled greenhouse conditions. We found significant broad-sense heritability in a legume host's preferential association with mutualistic over exploitative symbionts and selection to reduce frequency of associations with exploitative partners. We failed to detect evidence that selection will favour the loss of mutualism-stabilizing mechanisms in the absence of exploitation, as we found no evidence for a fitness cost to the host trait or indirect selection on genetically correlated traits. Our results show that genetic variation in the ability to preferentially reduce associations with an exploitative partner exists within mutualisms and is under selection, indicating that micro-evolutionary responses in mutualism-stabilizing traits in the face of rapidly evolving mutualistic and exploitative symbiotic bacteria can occur in natural host populations.

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New Phytol: The effect of elevated carbon dioxide on the interaction between Eucalyptus grandis and diverse isolates of Pisolithus sp. is associated with a complex shift in the root transcriptome

New Phytol: The effect of elevated carbon dioxide on the interaction between Eucalyptus grandis and diverse isolates of Pisolithus sp. is associated with a complex shift in the root transcriptome | The Plant Microbiome | Scoop.it

Using the newly available genome for Eucalyptus grandis, we sought to determine the genome-wide traits that enable this host to form mutualistic interactions with ectomycorrhizal (ECM) Pisolithus sp. and to determine how future predicted concentrations of atmospheric carbon dioxide (CO2) will affect this relationship.
We analyzed the physiological and transcriptomic responses of E. grandis during colonization by different Pisolithus sp. isolates under conditions of ambient (400 ppm) and elevated (650 ppm) CO2 to tease out the gene expression profiles associated with colonization status.
We demonstrate that E. grandis varies in its susceptibility to colonization by different Pisolithus isolates in a manner that is not predictable by geographic origin or the internal transcribed spacer (ITS)-based phylogeny of the fungal partner. Elevated concentrations of CO2 alter the receptivity of E. grandis to Pisolithus, a change that is correlated to a dramatic shift in the transcriptomic profile of the root.
These data provide a starting point for understanding how future environmental change may alter the signaling between plants and their ECM partners and is a step towards determining the mechanism behind previously observed shifts in Eucalypt-associated fungal communities exposed to elevated concentrations of atmospheric CO2.

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Spatial structuring of bacterial communities within individual Ginkgo biloba trees

Plant-associated microorganisms affect the health of their hosts in diverse ways, yet the distribution of these organisms within individual plants remains poorly understood. To address this knowledge gap, we assessed the spatial variability in bacterial community diversity and composition found on and in aboveground tissues of individual Ginkgo biloba trees. We sampled bacterial communities from > 100 locations per tree, including leaf, branch, and trunk samples, and used high-throughput sequencing of the 16S rRNA gene to determine the diversity and composition of these communities. Bacterial community structure differed strongly between bark and leaf samples, with bark samples harboring much greater bacterial diversity and a community composition distinct from leaves. Within sample types, we observed clear spatial patterns in bacterial diversity and community composition that corresponded to the samples’ proximity to the exterior of the tree. The composition of the bacterial communities found on trees is highly variable, but this variability is predictable and dependent on sampling location. Moreover, this work highlights the importance of carefully considering plant spatial structure when characterizing the microbial communities associated with plants and their impacts on plant hosts.

Via Jean-Michel Ané, Francis Martin
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New Phytologist: Root structural and functional dynamics in terrestrial biosphere models – evaluation and recommendations

New Phytologist: Root structural and functional dynamics in terrestrial biosphere models – evaluation and recommendations | The Plant Microbiome | Scoop.it
There is wide breadth of root function within ecosystems that should be considered when modeling the terrestrial biosphere. Root structure and function are closely associated with control of plant water and nutrient uptake from the soil, plant carbon (C) assimilation, partitioning and release to the soils, and control of biogeochemical cycles through interactions within the rhizosphere. Root function is extremely dynamic and dependent on internal plant signals, root traits and morphology, and the physical, chemical and biotic soil environment. While plant roots have significant structural and functional plasticity to changing environmental conditions, their dynamics are noticeably absent from the land component of process-based Earth system models used to simulate global biogeochemical cycling. Their dynamic represen- tation in large-scale models should improve model veracity. Here, we describe current root inclusion in models across scales, ranging from mechanistic processes of single roots to parameterized root processes operating at the landscape scale. With this foundation we discuss how existing and future root functional knowledge, new data compilation efforts, and novel modeling platforms can be leveraged to enhance root functionality in large-scale terrestrial biosphere models by improving parameterization within models, and introducing new components such as dynamic root distribution and root functional traits linked to resource extraction.
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The inter-kingdom volatile signal indole promotes root development by interfering with auxin signalling

The inter-kingdom volatile signal indole promotes root development by interfering with auxin signalling | The Plant Microbiome | Scoop.it
Recently, emission of volatile organic compounds (VOCs) has emerged as a mode of communication between bacteria and plants. Although some bacterial VOCs that promote plant growth have been identified, their underlying mechanism of action is unknown. Here we demonstrate that indole, which was identified using a screen for Arabidopsis growth promotion by VOCs from soil-borne bacteria, is a potent plant-growth modulator. Its prominent role in increasing the plant secondary root network is mediated by interfering with the auxin-signalling machinery. Using auxin reporter lines and classic auxin physiological and transport assays we show that the indole signal invades the plant body, reaches zones of auxin activity and acts in a polar auxin transport-dependent bimodal mechanism to trigger differential cellular auxin responses. Our results suggest that indole, beyond its importance as a bacterial signal molecule, can serve as a remote messenger to manipulate plant growth and development.

Via Francis Martin, Nicolas Denancé, Jean-Michel Ané
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Spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases

Spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases | The Plant Microbiome | Scoop.it

Symbiosis Receptor-like Kinase (SYMRK) is indispensable for the development of phosphate-acquiring arbuscular mycorrhiza (AM) as well as nitrogen-fixing root nodule symbiosis, but the mechanisms that discriminate between the two distinct symbiotic developmental fates have been enigmatic. In this study, we show that upon ectopic expression, the receptor-like kinase genes Nod Factor Receptor 1 (NFR1), NFR5, and SYMRK initiate spontaneous nodule organogenesis and nodulation-related gene expression in the absence of rhizobia. Furthermore, overexpressed NFR1 or NFR5 associated with endogenous SYMRK in roots of the legume Lotus japonicus. Epistasis tests revealed that the dominant active SYMRK allele initiates signalling independently of either the NFR1 or NFR5 gene and upstream of a set of genes required for the generation or decoding of calcium-spiking in both symbioses. Only SYMRK but not NFR overexpression triggered the expression of AM-related genes, indicating that the receptors play a key role in the decision between AM- or root nodule symbiosis-development. - See more at: http://elifesciences.org/content/3/e03891#sthash.7GMN2VZ5.dpuf


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Jean-Michel Ané's curator insight, November 25, 8:07 PM

That's a BIG paper in our field... a must read for all my lab members :-)

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Frontiers | Expanding genomics of mycorrhizal symbiosis | Microbial Symbioses

Frontiers | Expanding genomics of mycorrhizal symbiosis | Microbial Symbioses | The Plant Microbiome | Scoop.it
The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant and soil health, and carbon and nutrient cycles. The symbiosis evolved repeatedly and independently as multiple morphological types (e.g. arbuscular [AM], ectomycorrhizal [ECM]) in multiple fungal clades (e.g. phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and culturability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first 3 mycorrhizal fungal genomes, representing 3 fungal phyla and 2 mycorrhizal types. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant-degrading enzymes (PDEs) and expansion of lineage-specific gene families, including short secreted protein (SSP) effectors and other symbiosis genes. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of gene families in contrast to Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other 2 fungi, the symbiosis can involve similar solutions as loss of PDEs and mycorrhiza-induced SSPs. The mycorrhizal community is building on these studies with 3 large-scale initiatives. The Mycorrhizal Genomics Initiative (MGI) is sequencing 35 genomes of multiple fungal clades and mycorrhizal types for phylogenomic and population analyses. 17 MGI species whose symbiosis is reconstitutable in vitro are targeted for comprehensive transcriptomics of mycorrhiza formation. MGI genomes are seeding a set of 50+ reference fungal genomes for annotating metatranscriptomes sampled from 7 diverse well-described soil sites. These 3 projects address fundamental questions about the nature and role of a vital mutualism.

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Scientific Reports: Removal of floral microbiota reduces floral terpene emissions

Scientific Reports: Removal of floral microbiota reduces floral terpene emissions | The Plant Microbiome | Scoop.it
The emission of floral terpenes plays a key role in pollination in many plant species. We hypothesized that the floral phyllospheric microbiota could significantly influence these floral terpene emissions because microorganisms also produce and emit terpenes. We tested this hypothesis by analyzing the effect of removing the microbiota from flowers. We fumigated Sambucus nigra L. plants, including their flowers, with a combination of three broad-spectrum antibiotics and measured the floral emissions and tissular concentrations in both antibiotic-fumigated and non-fumigated plants. Floral terpene emissions decreased by ca. two thirds after fumigation. The concentration of terpenes in floral tissues did not decrease, and floral respiration rates did not change, indicating an absence of damage to the floral tissues. The suppression of the phyllospheric microbial communities also changed the composition and proportion of terpenes in the volatile blend. One week after fumigation, the flowers were not emitting β-ocimene, linalool, epoxylinalool, and linalool oxide. These results show a key role of the floral phyllospheric microbiota in the quantity and quality of floral terpene emissions and therefore a possible key role in pollination.
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Nature Com: Genome-wide association study of Arabidopsis thaliana leaf microbial community

Nature Com: Genome-wide association study of Arabidopsis thaliana leaf microbial community | The Plant Microbiome | Scoop.it

Identifying the factors that influence the outcome of host–microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

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Evolution of species interactions determines microbial community productivity in new environments

Evolution of species interactions determines microbial community productivity in new environments | The Plant Microbiome | Scoop.it
Diversity generally increases ecosystem productivity over short timescales. Over longer timescales, both ecological and evolutionary responses to new environments could alter productivity and diversity–productivity relationships. In turn, diversity might affect how component species adapt to new conditions. We tested these ideas by culturing artificial microbial communities containing between 1 and 12 species in three different environments for ~60 generations. The relationship between community yields and diversity became steeper over time in one environment. This occurred despite a general tendency for the separate yields of isolates of constituent species to be lower at the end if they had evolved in a more diverse community. Statistical comparisons of community and species yields showed that species interactions had evolved to be less negative over time, especially in more diverse communities. Diversity and evolution therefore interacted to enhance community productivity in a new environment.

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Reagent contamination can critically impact sequence-based microbiome analyses

Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Concurrent sequencing of negative control samples is strongly advised.


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New Phytol: Temporal variation in mycorrhizal diversity and carbon and nitrogen stable isotope abundance in the wintergreen meadow orchid Anacamptis morio

New Phytol: Temporal variation in mycorrhizal diversity and carbon and nitrogen stable isotope abundance in the wintergreen meadow orchid Anacamptis morio | The Plant Microbiome | Scoop.it

Many adult orchids, especially photoautotrophic species, associate with a diverse range of mycorrhizal fungi, but little is known about the temporal changes that might occur in the diversity and functioning of orchid mycorrhiza during vegetative and reproductive plant growth.
Temporal variations in the spectrum of mycorrhizal fungi and in stable isotope natural abundance were investigated in adult plants of Anacamptis morio, a wintergreen meadow orchid.
Anacamptis morio associated with mycorrhizal fungi belonging to Tulasnella, Ceratobasidium and a clade of Pezizaceae (Ascomycetes). When a complete growing season was investigated, multivariate analyses indicated significant differences in the mycorrhizal fungal community. Among fungi identified from manually isolated pelotons, Tulasnella was more common in autumn and winter, the pezizacean clade was very frequent in spring, and Ceratobasidium was more frequent in summer. By contrast, relatively small variations were found in carbon (C) and nitrogen (N) stable isotope natural abundance, A. morio samples showing similar 15N enrichment and 13C depletion at the different sampling times.
These observations suggest that, irrespective of differences in the seasonal environmental conditions, the plant phenological stages and the associated fungi, the isotopic content in mycorrhizal A. morio remains fairly constant over time.

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Searching for new branches on the tree of life

Searching for new branches on the tree of life | The Plant Microbiome | Scoop.it

Ever since Woese's seminal work nearly 40 years ago (1), life has been divided into three domains: Archaea, Bacteria, and Eukaryota. But could there be life that does not fit into any of these domains? Novel techniques for exploring microbes that cannot readily be grown in the laboratory offer hope that scientists can discover such life, if it exists (see the first figure). These methods include metagenomics, which involves the sequencing of DNA extracted from environmental samples, and single-cell genomics, where individual microbial cells are isolated from the environment and their genomes amplified and sequenced.

On the basis of these and other approaches, we propose that microbial life be operationally divided into three categories: explored, unexplored, and undiscovered. It is among the latter that potential signs of additional branches on the tree of life beyond the three known domains may be found.

EXPLORED, UNEXPLORED, UNDISCOVERED. ...


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EM: Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation

EM: Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation | The Plant Microbiome | Scoop.it
Plant-associated bacteria are intensively investigated concerning their characteristics for plant growth promotion, biocontrol mechanisms and enhanced phytoremediation efficiency. To obtain endophytes, different sampling and isolation protocols are used although their representativeness is not always clearly demonstrated. The objective of this study was to acquire representative pictures of the cultivable bacterial root, stem and leaf communities for all Brassica napus L. individuals growing on the same field. For each plant organ genotypic identifications of the endophytic communities were performed using 3 replicates. Root replicates were composed of 3 total root systems, whereas stem and leaf replicates needed to consist of 6 independent plant parts in order to be representative. Greater variations between replicates were found when considering phenotypic characteristics. Correspondence analysis revealed reliable phenotypic results for roots and even shoots, but less reliable ones for leaves. Additionally, realistic Shannon-Wiener biodiversity indices were calculated for all 3 organs and showed similar Evenness factors. Furthermore, it was striking that all replicates and thus the whole plant contained Pseudomonas and Bacillus strains although above- and below-ground plant tissues differed in most dominant bacterial genera and characteristics.
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MPMI: The pattern of secreted molecules during the co-inoculation of alfalfa plants with Sinorhizobium meliloti and Delftia sp. JD2: an interaction that improves plant yield

MPMI: The pattern of secreted molecules during the co-inoculation of alfalfa plants with Sinorhizobium meliloti and Delftia sp. JD2: an interaction that improves plant yield | The Plant Microbiome | Scoop.it

Delftia sp. JD2 is a plant-growth-promoting bacterium that enhances legume nodulation and growth, acting as nodule-assisting bacterium during the co-inoculation of plants with rhizobial strains. In this work we evaluate how the co-inoculation of alfalfa with Sinorhizobium meliloti U143 and JD2 increases plant yield under greenhouse conditions and we analyze the pattern of secreted bioactive compounds which may be involved in the microbe-plant communication. The chemical composition of extracellular cultures (ECs) produced in hydroponic conditions (collected 4, 7 and 14 days after bacterial treatment) were characterized using different chromatographic and elucidation techniques. In addition, we assessed the effect that plant irrigation with cell-free ECs, produced during co-inoculation experiments, would have on plant yield. Results showed increased alfalfa shoot and root matter suggesting that U143-JD2 co-inoculation might be a beneficial agricultural practice. The pattern of secreted secondary metabolites among treatments showed important differences. Qualitative and quantitative changes in phenolic compounds (including flavonoids), organic acids and volatile compounds were detected during the early microbe-plant interaction, suggesting that the production of some molecules positively affect the microbe-plant association. Finally, the irrigation of co-inoculated plants with cell free ECs, under greenhouse conditions, increased plant yield over agronomic expectations. This effect might be attributed to the bioactive secondary metabolites incorporated during the irrigation.

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Bacterial networks and co-occurrence relationships in the lettuce root microbiota

Lettuce is one of the most common raw foods world-wide, but occasionally also involved in pathogen outbreaks. To understand the correlative structure of the bacterial community as a network, we studied root microbiota of eight ancient and modern Lactuca sativa cultivars and the wild ancestor L. serriola by pyrosequencing of 16S rRNA gene amplicon libraries. The lettuce microbiota was dominated by Proteobacteria and Bacteriodetes, as well as abundant Chloroflexi and Actinobacteria. Cultivar-specificity comprised 12.5% of the species. Diversity indices were not different between lettuce cultivar groups but higher than in L. serriola, suggesting that domestication lead to bacterial diversification in lettuce root system. Spearman correlations between OTUs showed that co-occurrence prevailed over co-exclusion, and complementary FISH-CLSM analyses revealed that this pattern results from both potential interactions and habitat sharing. Predominant taxa, such as Pseudomonas, Flavobacterium, and Sphingomonadaceae rather suggested interactions, even though these are not necessarily part of significant modules in the co-occurrence networks. Without any need for complex interactions, single organisms are able to invade into this microbial network and to colonize lettuce plants; a fact which can influence the susceptibility to pathogens. The approach to combine co-occurrence analysis and FISH-CLSM allows reliably reconstructing and interpreting microbial interaction networks.

Via Jean-Michel Ané
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