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Network Modeling to Understand Plant Immunity

Network Modeling to Understand Plant Immunity | MycorWeb Plant-Microbe Interactions | Scoop.it

Deciphering the networks that underpin complex biological processes using experimental data remains a significant, but promising, challenge, a task made all the harder by the added complexity of host-pathogen interactions. The aim of this article is to review the progress in understanding plant immunity made so far by applying network modeling algorithms and to show how this computational/mathematical strategy is facilitating a systems view of plant defense. We review the different types of network modeling that have been used, the data required, and the type of insight that such modeling can provide. We discuss the current challenges in modeling the regulatory networks that underlie plant defense and the future developments that may help address these challenges.


Via Christophe Jacquet
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Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions

Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions | MycorWeb Plant-Microbe Interactions | Scoop.it

Marine sandy beaches represent dynamic environments often subject to harsh conditions and climate fluctuations, where natural and anthropogenic inputs of freshwater from fluvial and pluvial sources alter salinity, which has been recognized as a key variable affecting the distribution of aquatic organisms and influencing critical physiological processes. The marine arenicolous fungus Corollospora maritima is a worldwide-distributed saprobe that has been reported to present tolerance to freshwater. Here, we present a transcriptome analysis that will provide the first insight of the genomic content for this fungus and a gene expression comparison between two different salinity conditions. We also identified genes that are candidates for being differentially expressed in response to environmental variations on salinity during the fungal growth. The de novo reconstruction of C. maritima transcriptome Illumina sequencing provided a total of 14,530 transcripts (16 megabases). The comparison between the two growth conditions rendered 103 genes specifically overexpressed in seawater, and 132 genes specifically up-regulated under freshwater. Using fungal isolates collected from different beaches, the specific environmental regulation of particular transcript differential expression was confirmed by RT-qPCR. To our knowledge, this is the first analysis that explores the marine fungus C. maritima molecular responses to overcome freshwater stress, and these data could shed light to understand the fungal adaptation and plasticity mechanisms to the marine habitat.

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FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species

FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species | MycorWeb Plant-Microbe Interactions | Scoop.it

Systematically extracting biological meaning from omics data is a major challenge in systems biology. Enrichment analysis is often used to identify characteristic patterns in candidate lists. FungiFun is a user-friendly Web tool for functional enrichment analysis of fungal genes and proteins. The novel tool FungiFun2 uses a completely revised data management system and thus allows enrichment analysis for 298 currently available fungal strains published in standard databases. FungiFun2 offers a modern Web interface and creates interactive tables, charts and figures, which users can directly manipulate to their needs.

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INRA - Analyse de la sécheresse 2015

INRA - Analyse de la sécheresse 2015 | MycorWeb Plant-Microbe Interactions | Scoop.it
2015 est l’année la plus chaude jamais mesurée au plan mondial d’après les relevés sur les 7 premiers mois. L’Inra a, depuis 10 ans, développé des outils et indicateurs pour évaluer la situation climatique en cours, la situer par rapport à des références historiques et montrer les effets attendus sur le fonctionnement des peuplements végétaux, le rendement des cultures ou la santé des forêts. Application à l’année 2015…
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Genomic evidence for the Pleistocene and recent population history of Native Americans

Genomic evidence for the Pleistocene and recent population history of Native Americans | MycorWeb Plant-Microbe Interactions | Scoop.it
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
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Increasing human dominance of tropical forests

Increasing human dominance of tropical forests | MycorWeb Plant-Microbe Interactions | Scoop.it
Tropical forests house over half of Earth’s biodiversity and are an important influence on the climate system. These forests are experiencing escalating human influence, altering their health and the provision of important ecosystem functions and services. Impacts started with hunting and millennia-old megafaunal extinctions (phase I), continuing via low-intensity shifting cultivation (phase II), to today’s global integration, dominated by intensive permanent agriculture, industrial logging, and attendant fires and fragmentation (phase III). Such ongoing pressures, together with an intensification of global environmental change, may severely degrade forests in the future (phase IV, global simplification) unless new “development without destruction” pathways are established alongside climate change–resilient landscape designs.
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Boreal forest health and global change

Boreal forest health and global change | MycorWeb Plant-Microbe Interactions | Scoop.it
The boreal forest, one of the largest biomes on Earth, provides ecosystem services that benefit society at levels ranging from local to global. Currently, about two-thirds of the area covered by this biome is under some form of management, mostly for wood production. Services such as climate regulation are also provided by both the unmanaged and managed boreal forests. Although most of the boreal forests have retained the resilience to cope with current disturbances, projected environmental changes of unprecedented speed and amplitude pose a substantial threat to their health. Management options to reduce these threats are available and could be implemented, but economic incentives and a greater focus on the boreal biome in international fora are needed to support further adaptation and mitigation actions.
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Second Act: Forest ecologist Robin Chazdon is helping show that regenerating tropical forests aren't wastelands

Second Act: Forest ecologist Robin Chazdon is helping show that regenerating tropical forests aren't wastelands | MycorWeb Plant-Microbe Interactions | Scoop.it

When ecologist Robin Chazdon began studying tropical forests in the 1990s, she took the road less traveled. Whereas many researchers were scrambling to study undisturbed forests before they disappeared, she focused on what grew back once the trees were burned or logged. Rather than working in the forest's shaded understory, an ecosystem celebrated in Hollywood films, she labored in scraggly deforested plots in the broiling sun, covered head to toe to keep prickly bushes and biting chiggers at bay.

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Battling a giant killer

Battling a giant killer | MycorWeb Plant-Microbe Interactions | Scoop.it
On a frigid morning this past March, arborist Will Blozan snuck behind a small church here and headed down into a gorge thick with rhododendron. He crashed through the shrubs until he spotted the gorge's treasure: the world's largest known living eastern hemlock tree, known as the Cheoah.

In 2006, Blozan had climbed the nearly 50-meter-tall giant and calculated that it contained 44.29 cubic meters of wood—then a record. Blozan would later discover two even larger hemlocks in the nearby Great Smoky Mountains National Park. Both of those champions, however, are now dead.
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Orchid phylogenomics and multiple drivers of their extraordinary diversification

Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras), and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp−1 My−1) is 6.8 times that at the Asparagales crown.
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Orchids' dazzling diversity explained

Orchids' dazzling diversity explained | MycorWeb Plant-Microbe Interactions | Scoop.it

Evolutionary biologists never lost their fascination with orchids. With more than 25,000 species, they're the biggest group within the plant kingdom, comprising roughly 8% of all vascular plant species. Biologists have proposed various explanations for this extraordinary diversity, but it has been impossible to nail down their relative importance.

Now, a new family tree of the orchids is a major step in that direction. “For the first time, they have a well-supported phylogeny for all main branches,” says orchidologist Barbara Gravendeel of the Naturalis Biodiversity Center in Leiden, the Netherlands, who was not involved in the work. “It's a great study,” Gravendeel says, and it shows how orchids owe their diversity to a series of innovations—above all, the ability to grow in tropical mountains—that individually or jointly touched off explosions of new species.

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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 | MycorWeb Plant-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.

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PeerJ Collection: Top Microbiology Papers - August 2015

PeerJ Collection: Top Microbiology Papers - August 2015 | MycorWeb Plant-Microbe Interactions | Scoop.it
Microbiology is the study of microscopic organisms and includes many sub-disciplines such as virology, mycology, parasitology, and bacteriology. PeerJ is pleased to have published some outstanding work in microbiology and this Collection represents some of the most noteworthy papers we have published, as of August 2015.
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Standardizing metadata and taxonomic identification in metabarcoding studies - Springer

Standardizing metadata and taxonomic identification in metabarcoding studies - Springer | MycorWeb Plant-Microbe Interactions | Scoop.it

High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.

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Cellular Subcompartments through Cytoplasmic Streaming

Cellular Subcompartments through Cytoplasmic Streaming | MycorWeb Plant-Microbe Interactions | Scoop.it
Cytoplasmic streaming occurs in diverse cell types, where it generally serves a transport function. Here, we examine streaming in multicellular fungal hyphae and identify an additional function wherein regimented streaming forms distinct cytoplasmic subcompartments. In the hypha, cytoplasm flows directionally from cell to cell through septal pores. Using live-cell imaging and computer simulations, we identify a flow pattern that produces vortices (eddies) on the upstream side of the septum. Nuclei can be immobilized in these microfluidic eddies, where they form multinucleate aggregates and accumulate foci of the HDA-2 histone deacetylase-associated factor, SPA-19. Pores experiencing flow degenerate in the absence of SPA-19, suggesting that eddy-trapped nuclei function to reinforce the septum. Together, our data show that eddies comprise a subcellular niche favoring nuclear differentiation and that subcompartments can be self-organized as a consequence of regimented cytoplasmic streaming.
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Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors

Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors | MycorWeb Plant-Microbe Interactions | Scoop.it

TOPLESS (TPL) and TOPLESS-related (TPR) proteins comprise a conserved family of plant transcriptional corepressors that are related to Tup1, Groucho, and TLE (transducin-like enhancer of split) corepressors in yeast, insects, and mammals. In plants, TPL/TPR corepressors regulate development, stress responses, and hormone signaling through interaction with small ethylene response factor–associated amphiphilic repression (EAR) motifs found in diverse transcriptional repressors. How EAR motifs can interact with TPL/TPR proteins is unknown. We confirm the amino-terminal domain of the TPL family of corepressors, which we term TOPLESS domain (TPD), as the EAR motif–binding domain. To understand the structural basis of this interaction, we determined the crystal structures of the TPD of rice (Os) TPR2 in apo (apo protein) state and in complexes with the EAR motifs from Arabidopsis NINJA (novel interactor of JAZ), IAA1 (auxin-responsive protein 1), and IAA10, key transcriptional repressors involved in jasmonate and auxin signaling. The OsTPR2 TPD adopts a new fold of nine helices, followed by a zinc finger, which are arranged into a disc-like tetramer. The EAR motifs in the three different complexes adopt a similar extended conformation with the hydrophobic residues fitting into the same surface groove of each OsTPR2 monomer. Sequence alignments and structure-based mutagenesis indicate that this mode of corepressor binding is highly conserved in a large set of transcriptional repressors, thus providing a general mechanism for gene repression mediated by the TPL family of corepressors.

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Response to Comment on “Global diversity and geography of soil fungi”

Response to Comment on “Global diversity and geography of soil fungi” | MycorWeb Plant-Microbe Interactions | Scoop.it

Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)–free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.

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Planted forest health: The need for a global strategy

Planted forest health: The need for a global strategy | MycorWeb Plant-Microbe Interactions | Scoop.it

Several key tree genera are used in planted forests worldwide, and these represent valuable global resources. Planted forests are increasingly threatened by insects and microbial pathogens, which are introduced accidentally and/or have adapted to new host trees. Globalization has hastened tree pest emergence, despite a growing awareness of the problem, improved understanding of the costs, and an increased focus on the importance of quarantine. To protect the value and potential of planted forests, innovative solutions and a better-coordinated global approach are needed. Mitigation strategies that are effective only in wealthy countries fail to contain invasions elsewhere in the world, ultimately leading to global impacts. Solutions to forest pest problems in the future should mainly focus on integrating management approaches globally, rather than single-country strategies. A global strategy to manage pest issues is vitally important and urgently needed.

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Temperate forest health in an era of emerging megadisturbance

Temperate forest health in an era of emerging megadisturbance | MycorWeb Plant-Microbe Interactions | Scoop.it

Although disturbances such as fire and native insects can contribute to natural dynamics of forest health, exceptional droughts, directly and in combination with other disturbance factors, are pushing some temperate forests beyond thresholds of sustainability. Interactions from increasing temperatures, drought, native insects and pathogens, and uncharacteristically severe wildfire are resulting in forest mortality beyond the levels of 20th-century experience. Additional anthropogenic stressors, such as atmospheric pollution and invasive species, further weaken trees in some regions. Although continuing climate change will likely drive many areas of temperate forest toward large-scale transformations, management actions can help ease transitions and minimize losses of socially valued ecosystem services.

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Forest health and global change

Forest health and global change | MycorWeb Plant-Microbe Interactions | Scoop.it

Humans rely on healthy forests to supply energy, building materials, and food and to provide services such as storing carbon, hosting biodiversity, and regulating climate. Defining forest health integrates utilitarian and ecosystem measures of forest condition and function, implemented across a range of spatial scales. Although native forests are adapted to some level of disturbance, all forests now face novel stresses in the form of climate change, air pollution, and invasive pests. Detecting how intensification of these stresses will affect the trajectory of forests is a major scientific challenge that requires developing systems to assess the health of global forests. It is particularly critical to identify thresholds for rapid forest decline, because it can take many decades for forests to restore the services that they provide.

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The new North

The new North | MycorWeb Plant-Microbe Interactions | Scoop.it
With its millions of square kilometers of pristine timber, thick carpet of moss and needles, and organic-rich frozen soil, the boreal forest stores more carbon than any other land ecosystem. And more than any other forest, it is bearing the brunt of climate change, warming roughly twice as fast as the rest of the planet. The effects on its cold-adapted trees are already evident. “We are on the cusp of a transformation,” says ecologist Michelle Mack of Northern Arizona University in Flagstaff.

The early signs can be seen from space, where orbiting sensors that monitor photosynthesis show that much of the boreal belt is “browning”: not literally turning brown but losing its vigor. They can be seen on the ground, in tree-ring studies that show trees are struggling to grow during the increasingly hot summers. They can be seen in insect outbreaks that are killing trees hundreds of kilometers farther north than they did 20 years ago. Most dramatically, the transformation can be seen in forest fires so fierce and voracious that they kick the forest into a new state, with a different mix of species and untold impacts on wildlife and climate.
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Forestry in the Anthropocene

Forestry in the Anthropocene | MycorWeb Plant-Microbe Interactions | Scoop.it

Human activity has had enormous effects on the species composition of floras and faunas, creating new ecological biomes worldwide. A principal challenge in forestry research and conservation is how to deal with these novel ecosystems. Most attention to this phenomenon is centered on the negative effects of species introductions and the need to stem the tide of species invasion. However, we need to scientifically understand new ecosystems and learn to recognize adaptive species combinations that will function sustainably in changing environmental conditions.

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The genome sequence of the orchid Phalaenopsis equestris : Nature Genetics

The genome sequence of the orchid Phalaenopsis equestris : Nature Genetics | MycorWeb Plant-Microbe Interactions | Scoop.it

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

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The fungi that ate my house

The fungi that ate my house | MycorWeb Plant-Microbe Interactions | Scoop.it
During my first years at Rutgers, I worked on issues related to women in science while reinventing my research career. In my new laboratory, as I had promised myself after Hurricane Katrina, my team adapted genetic models to study the possible physiological effects of fungal volatile organic compounds (VOCs). We found that several common fungal VOCs are neurotoxic in a Drosophila (fruit fly) model. Somewhat surprisingly, we also found that the VOCs from the most common fungus isolated from my flooded home, a Trichoderma species, can make the plant Arabidopsis and tomatoes grow better. Although I haven't been able to demonstrate that the gases from molds contribute to sick building syndrome, I have been able to show that they have many profound physiological effects.
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Architecture of the fungal nuclear pore inner ring complex

The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kDa inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin hetero-trimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation.
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Linking Jasmonic Acid Signaling, Root Exudates, and Rhizosphere Microbiomes — Molecular Plant-Microbe Interactions

Linking Jasmonic Acid Signaling, Root Exudates, and Rhizosphere Microbiomes — Molecular Plant-Microbe Interactions | MycorWeb Plant-Microbe Interactions | Scoop.it
Jasmonic acid (JA) is an essential hormone in plant development and defense responses in Arabidopsis thaliana. Exogenous treatment with JA has recently been shown to alter root exudate profiles and the composition of root-associated bacterial communities. However, it is currently unknown whether disruptions of the JA in the rhizosphere affect root exudation profiles and the relative abundance of bacteria and archaea in the rhizosphere. In the present study, two Arabidopsis mutants that are disrupted in different branches of the jasmonate pathway, namely myc2 and med25, were cultivated in nutrient solution and soil to profile root exudates and bacterial and archaeal communities, respectively. Compared with the wild type, both mutants showed distinct exudation patterns, including lower amounts of asparagine, ornithine, and tryptophan, as well as distinct bacterial and archaeal community composition, as illustrated by an increased abundance of Streptomyces, Bacillus, and Lysinibacillus taxa in the med25 rhizosphere and an Enterobacteriaceae population in myc2. Alternatively, the Clostridiales population was less abundant in the rhizosphere of both mutants. Similarities between plant genotypes were highly correlated, as determined by operational taxonomic units in the rhizosphere and metabolites in root exudates. This strongly suggests that root exudates play a major role in modulating changes in microbial community composition upon plant defense responses.
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