Plant-Microbe-Interactions
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Rescooped by Hassani Med Amine from Soil microbial interactions
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Microbial interactions and community assembly at microscales - Current Opinion in Microbiology

Microbial interactions and community assembly at microscales - Current Opinion in Microbiology | Plant-Microbe-Interactions | Scoop.it
In most environments, microbial interactions take place within microscale cell aggregates. At the scale of these aggregates (∼100 μm), interactions are likely to be the dominant driver of population structure and dynamics. In particular, organisms that exploit interspecific interactions to increase ecological performance often co-aggregate. Conversely, organisms that antagonize each other will tend to spatially segregate, creating distinct micro-communities and increased diversity at larger length scales. We argue that, in order to understand the role that biological interactions play in microbial community function, it is necessary to study microscale spatial organization with enough throughput to measure statistical associations between taxa and possible alternative community states. We conclude by proposing strategies to tackle this challenge.

Via Max-Bernhard Ballhausen
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Max-Bernhard Ballhausen's curator insight, May 27, 3:50 AM
Working on a microbe-relevant scale. One of the most important, most difficult and most interesting subjects in Microbial Ecology :-)
Rescooped by Hassani Med Amine from MycorWeb Plant-Microbe Interactions
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Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest | Plant-Microbe-Interactions | Scoop.it

Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG—CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle.


Via Francis Martin
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Rescooped by Hassani Med Amine from MycorWeb Plant-Microbe Interactions
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A microbial ecosystem beneath the West Antarctic ice sheet : Nature

A microbial ecosystem beneath the West Antarctic ice sheet : Nature | Plant-Microbe-Interactions | Scoop.it
Liquid water has been known to occur beneath the Antarctic ice sheet for more than 40 years, but only recently have these subglacial aqueous environments been recognized as microbial ecosystems that may influence biogeochemical transformations on a global scale. Here we present the first geomicrobiological description of water and surficial sediments obtained from direct sampling of a subglacial Antarctic lake. Subglacial Lake Whillans (SLW) lies beneath approximately 800 m of ice on the lower portion of the Whillans Ice Stream (WIS) in West Antarctica and is part of an extensive and evolving subglacial drainage network. The water column of SLW contained metabolically active microorganisms and was derived primarily from glacial ice melt with solute sources from lithogenic weathering and a minor seawater component. Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. Our results confirm that aquatic environments beneath the Antarctic ice sheet support viable microbial ecosystems, corroborating previous reports suggesting that they contain globally relevant pools of carbon and microbes that can mobilize elements from the lithosphere and influence Southern Ocean geochemical and biological systems.

Via Francis Martin
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Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages

Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages | Plant-Microbe-Interactions | Scoop.it
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Agrobacterium tumefaciens Deploys a Superfamily of Type VI Secretion DNase Effectors as Weapons for Interbacterial Competition In Planta: Cell Host & Microbe

Agrobacterium tumefaciens Deploys a Superfamily of Type VI Secretion DNase Effectors as Weapons for Interbacterial Competition In Planta: Cell Host & Microbe | Plant-Microbe-Interactions | Scoop.it

The type VI secretion system (T6SS) is a widespread molecular weapon deployed by many Proteobacteria to target effectors/toxins into both eukaryotic and prokaryotic cells. We report that Agrobacterium tumefaciens, a soil bacterium that triggers tumorigenesis in plants, produces a family of type VI DNase effectors (Tde) that are distinct from previously known polymorphic toxins and nucleases. Tde exhibits an antibacterial DNase activity that relies on a conserved HxxD motif and can be counteracted by a cognate immunity protein, Tdi. In vitro, A. tumefaciens T6SS could kill Escherichia coli but triggered a lethal counterattack by Pseudomonas aeruginosa upon injection of the Tde toxins. However, in an in planta coinfection assay, A. tumefaciens used Tde effectors to attack both siblings cells and P. aeruginosa to ultimately gain a competitive advantage. Such acquired T6SS-dependent fitness in vivo and conservation of Tde-Tdi couples in bacteria highlights a widespread antibacterial weapon beneficial for niche colonization


Via Suayib Üstün
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Rescooped by Hassani Med Amine from Plant-Microbe Symbiosis
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Taxonomical and functional microbial community selection in soybean rhizosphere

This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors.

Via Jean-Michel Ané
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Rescooped by Hassani Med Amine from MycorWeb Plant-Microbe Interactions
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Evolution of microbial markets

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.


Via Francis Martin
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Rescooped by Hassani Med Amine from Rhizobium Research
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Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field

Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field | Plant-Microbe-Interactions | Scoop.it

Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.

  Sugiyama A, Ueda Y, Zushi T, Takase H, Yazaki K (2014). PLoS One. Jun 23;9(6):e100709.


Via IvanOresnik
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LIIS: A web-based system for culture collections and sample annotation | Forster | Journal of Open Research Software

LIIS: A web-based system for culture collections and sample annotation | Forster | Journal of Open Research Software | Plant-Microbe-Interactions | Scoop.it
LIIS: A web-based system for culture collections and sample annotation
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Rescooped by Hassani Med Amine from Plant roots and rhizosphere
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Transposon Mutagenesis of the Plant-Associated Bacillus amyloliquefaciens ssp. plantarum FZB42 Revealed That the nfrA and RBAM17410 Genes Are Involved in Plant-Microbe-Interactions

Transposon Mutagenesis of the Plant-Associated Bacillus amyloliquefaciens ssp. plantarum FZB42 Revealed That the nfrA and RBAM17410 Genes Are Involved in Plant-Microbe-Interactions | Plant-Microbe-Interactions | Scoop.it

Bacillus amyloliquefaciens ssp. plantarum FZB42 represents the prototype of Gram-positive plant growth promoting and biocontrol bacteria. In this study, we applied transposon mutagenesis to generate a transposon library, which was screened for genes involved in multicellular behavior and biofilm formation on roots as a prerequisite of plant growth promoting activity. Transposon insertion sites were determined by rescue-cloning followed by DNA sequencing. As in B. subtilis, the global transcriptional regulator DegU was identified as an activator of genes necessary for swarming and biofilm formation, and the DegU-mutant of FZB42 was found impaired in efficient root colonization. Direct screening of 3,000 transposon insertion mutants for plant-growth-promotion revealed the gene products of nfrA and RBAM_017140 to be essential for beneficial effects exerted by FZB42 on plants. We analyzed the performance of GFP-labeled wild-type and transposon mutants in the colonization of lettuce roots using confocal laser scanning microscopy. While the wild-type strain heavily colonized root surfaces, the nfrA mutant did not colonize lettuce roots, although it was not impaired in growth in laboratory cultures, biofilm formation and swarming motility on agar plates. The RBAM17410 gene, occurring in only a few members of the B. subtilis species complex, was directly involved in plant growth promotion. None of the mutant strains were affected in producing the plant growth hormone auxin. We hypothesize that the nfrA gene product is essential for overcoming the stress caused by plant response towards bacterial root colonization.


Via Christophe Jacquet
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Rescooped by Hassani Med Amine from Plant Immunity And Microbial Effectors
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Natural rice rhizospheric microbes suppress rice blast infections

Background:
The natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression.

Via IPM Lab
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Rescooped by Hassani Med Amine from The Plant Microbiome
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PNAS: Syntrophic exchange in synthetic microbial communities

PNAS: Syntrophic exchange in synthetic microbial communities | Plant-Microbe-Interactions | Scoop.it

Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.

 


Via Stéphane Hacquard
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Rescooped by Hassani Med Amine from Plant microbiome studies
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Root microbiome relates to plant host evolution in maize and other Poaceae

Root microbiome relates to plant host evolution in maize and other Poaceae | Plant-Microbe-Interactions | Scoop.it

Prokaryote-eukaryote interactions are primordial, but host selection of its bacterial community remains poorly understood. Since eukaryote evolution affects numerous traits shaping the ecology of their microbiome, we can expect that many evolutionary changes in the former will have the potential to impact on the composition of the latter. Consequently, the more phylogenetically distant the eukaryotic hosts, the more distinct their associated bacterial communities should be. We tested this with plants, by comparing the bacterial communities associated to maize genotypes or other Poaceae. 16S rRNA taxonomic microarray analysis showed that the genetic distance between rhizobacterial communities correlated significantly with the phylogenetic distance (derived from chloroplastic sequences) between Poaceae genotypes. This correlation was also significant when considering specific bacterial populations from all main bacterial divisions, instead of the whole rhizobacterial community. These results indicate that eukaryotic host's evolutionary history can be a significant factor shaping directly the assembly and composition of its associated bacterial compartment.


Via Stéphane Hacquard, Nina Dombrowski
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Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice: Trends in Biotechnology

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Microbiology: Microbiome science needs a healthy dose of scepticism

Microbiology: Microbiome science needs a healthy dose of scepticism | Plant-Microbe-Interactions | Scoop.it
To guard against hype, those interpreting research on the body's microscopic communities should ask five questions, says William P. Hanage.
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Rescooped by Hassani Med Amine from Plants and Microbes
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1000 Fungal Genome (1KFG) project: Graduate Student-Postdoc Challenge (2014)

1000 Fungal Genome (1KFG) project: Graduate Student-Postdoc Challenge (2014) | Plant-Microbe-Interactions | Scoop.it

The 1000 Fungal Genome (1KFG) project is a large-scale community sequencing project supported by the Joint Genome Institute (JGI).  The goal of 1KFG is to facilitate the sequencing of fungal genomes across the Kingdom Fungi with the objective to significantly advance genome-enabled mycology.  The sampling guideline is to sequence two species of fungi for every family-level clade of Fungi so that genomic data is representative of phylogenetic diversity of Fungi. In support of this endeavor, 1KFG is pleased to announce the Graduate Student/Postdoc Challenge.  From July 2014-June 30 2015 we will accept nominations to sequence up to 100 species of fungi in support of graduate student and postdoctoral research projects.  Students and postdocs are encouraged to nominate species and submit DNA and RNA samples for genomic sequencing.

 

Follow the link to find out how to nominate species.


Via Kamoun Lab @ TSL
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Rescooped by Hassani Med Amine from Microbe-Microbe Interactions
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Diversity and abundance of phyllosphere bacteria are linked to insect herbivory

Diversity and abundance of phyllosphere bacteria are linked to insect herbivory | Plant-Microbe-Interactions | Scoop.it

Simultaneous or sequential attack by herbivores and microbes is common in plants. Many seed plants exhibit a defence trade-off against chewing herbivorous insects and leaf-colonizing (‘phyllosphere’) bacteria, which arises from cross-talk between the phytohormones jasmonic acid (JA, induced by many herbivores) and salicylic acid (SA, induced by many bacteria). This cross-talk may promote reciprocal susceptibility in plants between phyllosphere bacteria and insect herbivores. In a population of native bittercress (Cardamine cordifolia, Brassicaceae), we tested whether simulating prior damage with JA or SA treatment induced resistance or susceptibility (respectively) to chewing herbivores. In parallel, we conducted culture-dependent surveys of phyllosphere bacteria to test the hypothesis that damage by chewing herbivores correlates positively with bacterial abundance in leaves. Finally, we tested whether bacterial infection induced susceptibility to herbivory by a major chewing herbivore of bittercress, Scaptomyza nigrita (Drosophilidae). Overall, our results suggest that reciprocal susceptibility to herbivory and microbial attack occurs in bittercress. We found that JA treatment reduced and SA treatment increased S. nigrita herbivory in bittercress in the field. Bacterial abundance was higher in herbivore-damaged vs. undamaged leaves (especially Pseudomonas syringae). However, Pedobacter spp. and Pseudomonas fluorescens infections were negatively associated with herbivory. Experimental Pseudomonas spp. infections increased S. nigritaherbivory in bittercress. Thus, plant defence signalling trade-offs can have important ecological consequences in nature that may be reflected in a positive correlation between herbivory and phyllosphere bacterial abundance and diversity. Importantly, the strength and direction of this association varies within and among prevalent bacterial groups.


Via Kemen Lab
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Rescooped by Hassani Med Amine from Plant-microbe interaction
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Agrobacterium tumefaciens Deploys a Superfamily of Type VI Secretion DNase Effectors as Weapons for Interbacterial Competition In Planta: Cell Host & Microbe

Agrobacterium tumefaciens Deploys a Superfamily of Type VI Secretion DNase Effectors as Weapons for Interbacterial Competition In Planta: Cell Host & Microbe | Plant-Microbe-Interactions | Scoop.it

The type VI secretion system (T6SS) is a widespread molecular weapon deployed by many Proteobacteria to target effectors/toxins into both eukaryotic and prokaryotic cells. We report that Agrobacterium tumefaciens, a soil bacterium that triggers tumorigenesis in plants, produces a family of type VI DNase effectors (Tde) that are distinct from previously known polymorphic toxins and nucleases. Tde exhibits an antibacterial DNase activity that relies on a conserved HxxD motif and can be counteracted by a cognate immunity protein, Tdi. In vitro, A. tumefaciens T6SS could kill Escherichia coli but triggered a lethal counterattack by Pseudomonas aeruginosa upon injection of the Tde toxins. However, in an in planta coinfection assay, A. tumefaciens used Tde effectors to attack both siblings cells and P. aeruginosa to ultimately gain a competitive advantage. Such acquired T6SS-dependent fitness in vivo and conservation of Tde-Tdi couples in bacteria highlights a widespread antibacterial weapon beneficial for niche colonization


Via Suayib Üstün
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Fungi borrowed bacterial gene again and again

Fungi borrowed bacterial gene again and again | Plant-Microbe-Interactions | Scoop.it
Multiple independent gene transfers gave fungi ability to colonize plant roots.
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Within-Host Competition Drives Selection for the Capsule Virulence Determinant of Streptococcus pneumoniae

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Rescooped by Hassani Med Amine from Microbe-Microbe Interactions
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Frontiers | Deciphering microbial interactions and detecting keystone species with co-occurrence networks

Frontiers | Deciphering microbial interactions and detecting keystone species with co-occurrence networks | Plant-Microbe-Interactions | Scoop.it

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.


Via Stéphane Hacquard, Kemen Lab
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Frontiers | Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce | Plant-Microbe Interaction

The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects ...
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Rescooped by Hassani Med Amine from Plants and Microbes
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9th International Conference on Pseudomonas syringae and related pathogens; 2-6 June, 2015, Málaga, Spain

9th International Conference on Pseudomonas syringae and related pathogens; 2-6 June, 2015, Málaga, Spain | Plant-Microbe-Interactions | Scoop.it

Via Kamoun Lab @ TSL
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Rescooped by Hassani Med Amine from MycorWeb Plant-Microbe Interactions
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Plant–microbe interactions as drivers of ecosystem functions relevant for the biodegradation of organic contaminants

Plant–microbe interactions as drivers of ecosystem functions relevant for the biodegradation of organic contaminants | Plant-Microbe-Interactions | Scoop.it

Highlights• Biotransformation is an ecosystem property.• Microbes are the main drivers in biotransformation.• Dispersal of chemicals and bacteria drives degradation effectiveness.• Ecosystem stability is increased by plant–microbe interactions


Via Francis Martin
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