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  1. Abstract

    Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genusVariovoraxvia an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect theVariovoraxauxin degradation locus to define the genesiadDEas necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products:iac-like andiad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizingArabidopsisplants show that while all degrade IAA, only strains containingiad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests thatiad-like operon-containing bacterial strains, includingVariovoraxspecies, play a key ecological role in modulating auxins in the plant microbiome.

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    Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments. 
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  5. Plants have an innate immune system to fight off potential invaders that is based on the perception of nonself or modified-self molecules. Microbe-associated molecular patterns (MAMPs) are evolutionarily conserved microbial molecules whose extracellular detection by specific cell surface receptors initiates an array of biochemical responses collectively known as MAMP-triggered immunity (MTI). Well-characterized MAMPs include chitin, peptidoglycan, and flg22, a 22-amino acid epitope found in the major building block of the bacterial flagellum, FliC. The importance of MAMP detection by the plant immune system is underscored by the large diversity of strategies used by pathogens to interfere with MTI and that failure to do so is often associated with loss of virulence. Yet, whether or how MTI functions beyond pathogenic interactions is not well understood. Here we demonstrate that a community of root commensal bacteria modulates a specific and evolutionarily conserved sector of theArabidopsisimmune system. We identify a set of robust, taxonomically diverse MTI suppressor strains that are efficient root colonizers and, notably, can enhance the colonization capacity of other tested commensal bacteria. We highlight the importance of extracellular strategies for MTI suppression by showing that the type 2, not the type 3, secretion system is required for the immunomodulatory activity of one robust MTI suppressor. Our findings reveal that root colonization by commensals is controlled by MTI, which, in turn, can be selectively modulated by specific members of a representative bacterial root microbiota.

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  6. Biological hydrolysis of microcrystalline cellulose is an uncommon feature in the microbial world, especially among bacteria and archaea growing optimally above 70°C (the so‐called extreme thermophiles). In fact, among this group only certain species in the genusCaldicellulosiruptorare capable of rapid and extensive cellulose degradation. Four novel multidomain glycoside hydrolases (GHs) fromCaldicellulosiruptor morganiiandCaldicellulosiruptor danieliiwere produced recombinantly inCaldicellulosiruptor besciiand characterized. These GHs are structurally organized with two or three catalytic domains flanking carbohydrate binding modules from Family 3. Collectively, these enzymes represent GH families 5, 9, 10, 12, 44, 48, and 74, and hydrolyze crystalline cellulose, glucan, xylan, and mannan, the primary carbohydrates in plant biomass. Degradation of microcrystalline cellulose by cocktails of GHs from threeCaldicellulosiruptorspecies demonstrated that synergistic interactions enable mixtures of multiple enzymes to outperform single enzymes, suggesting a community mode of action for lignocellulose utilization in thermal environments. © 2018 American Institute of Chemical EngineersAIChE J, 64: 4218–4228, 2018

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