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Advances in next generation sequencing technologies, omics, and bioinformatics are revealing a tremendous and unsuspected diversity of microbes, both at a compositional and functional level. Moreover, the expansion of ecological concepts into microbial ecology has greatly advanced our comprehension of the role microbes play in the functioning of ecosystems across a wide range of biomes. Super-imposed on this new information about microbes, their functions and how they are organized, environmental gradients are changing rapidly, largely driven by direct and indirect human activities. In the context of global change, understanding the mechanisms that shape microbial communities is pivotal to predict microbial responses to novel selective forces and their implications at the local as well as global scale. One of the main features of microbial communities is their ability to react to changes in the environment. Thus, many studies have reported changes in the performance and composition of communities along environmental gradients. However, the mechanisms underlying these responses remain unclear. It is assumed that the response of microbes to changes in the environment is mediated by a complex combination of shifts in the physiological properties, single-cell activities, or composition of communities: it may occur by means of physiological adjustments of the taxa present in a community or selecting towards more tolerant/better adapted phylotypes. Knowing whether certain factors trigger one, many, or all mechanisms would greatly increase confidence in predictions of future microbial composition and processes. This Research Topic brings together studies that applied the latest molecular techniques for studying microbial composition and functioning and integrated ecological, biogeochemical and/or modeling approaches to provide a comprehensive and mechanistic perspective of the responses of micro-organisms to environmental changes. This Research Topic presents new findings on environmental parameters influencing microbial communities, the type and magnitude of response and differences in the response among microbial groups, and which collectively deepen our current understanding and knowledge of the underlying mechanisms of microbial structural and functional responses to environmental changes and gradients in both aquatic and terrestrial ecosystems. The body of work has, furthermore, identified many challenges and questions that yet remain to be addressed and new perspectives to follow up on.

microbial community composition --- ecosystem functioning --- next-generation sequencing --- micro-organism --- environmental change --- microbial diversity --- microbial ecology

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Advances in next generation sequencing technologies, omics, and bioinformatics are revealing a tremendous and unsuspected diversity of microbes, both at a compositional and functional level. Moreover, the expansion of ecological concepts into microbial ecology has greatly advanced our comprehension of the role microbes play in the functioning of ecosystems across a wide range of biomes. Super-imposed on this new information about microbes, their functions and how they are organized, environmental gradients are changing rapidly, largely driven by direct and indirect human activities. In the context of global change, understanding the mechanisms that shape microbial communities is pivotal to predict microbial responses to novel selective forces and their implications at the local as well as global scale. One of the main features of microbial communities is their ability to react to changes in the environment. Thus, many studies have reported changes in the performance and composition of communities along environmental gradients. However, the mechanisms underlying these responses remain unclear. It is assumed that the response of microbes to changes in the environment is mediated by a complex combination of shifts in the physiological properties, single-cell activities, or composition of communities: it may occur by means of physiological adjustments of the taxa present in a community or selecting towards more tolerant/better adapted phylotypes. Knowing whether certain factors trigger one, many, or all mechanisms would greatly increase confidence in predictions of future microbial composition and processes. This Research Topic brings together studies that applied the latest molecular techniques for studying microbial composition and functioning and integrated ecological, biogeochemical and/or modeling approaches to provide a comprehensive and mechanistic perspective of the responses of micro-organisms to environmental changes. This Research Topic presents new findings on environmental parameters influencing microbial communities, the type and magnitude of response and differences in the response among microbial groups, and which collectively deepen our current understanding and knowledge of the underlying mechanisms of microbial structural and functional responses to environmental changes and gradients in both aquatic and terrestrial ecosystems. The body of work has, furthermore, identified many challenges and questions that yet remain to be addressed and new perspectives to follow up on.

microbial community composition --- ecosystem functioning --- next-generation sequencing --- micro-organism --- environmental change --- microbial diversity --- microbial ecology

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Animal Microbiome will address all aspects of non-human animal-associated microbiomes, including (but not limited to): domestic, wild and livestock animals. We will also welcome studies encompassing (but not limited to): marker gene surveys; '-omics' surveys (including culturomics, metagenomic, metatransciptomic, metaproteomic, and metabolomic), bioinformatic and other analytical tools, which have an underlying strong hypothesis for using such techniques.

Veterinary microbiology --- Microbiology --- Microorganisms --- Microbiota. --- Animals. --- Veterinary microbiology. --- Microorganisms. --- Microbiology. --- Animalia --- Animal --- Metazoa --- Microbial Community --- Microbial Community Composition --- Microbial Community Structure --- Human Microbiome --- Microbiome --- Microbiome, Human --- Community Composition, Microbial --- Community Structure, Microbial --- Community, Microbial --- Composition, Microbial Community --- Human Microbiomes --- Microbial Communities --- Microbial Community Compositions --- Microbial Community Structures --- Microbiomes --- Microbiotas --- Metagenome --- Germs --- Micro-organisms --- Microbes --- Microscopic organisms --- Organisms --- Agricultural microbiology --- Medical microbiology --- Communicable diseases in animals --- Microbial biology --- Biology --- animal microbiome --- microbiology --- animal-microbiome interactions

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Numerous studies have demonstrated that the plant microbiome is highly relevant for the growth and fitness of plants. Plants in ecosystems and agroecosystems can recruit a wide variety of microorganisms, including beneficial microbes which are being studied and applied as biostimulators to improve nutrition and tolerance of plants and as biocontrol of phytopathogens. In this context, this Book contains a selection of articles describing diverse ecological and biotechnological aspects of microbiomes in native and agronomic plants (e.g., pepper, potato, rice and lettuce) created by researchers from Italy, China, Korea, Egypt, Oman, Germany, the USA, and Chile.

Research & information: general --- Biology, life sciences --- bioprospecting --- inoculants --- plant growth-promoting bacteria --- plant microbiome --- plant–microbe interactions --- plant microbiota --- cultivation-dependent of plant microbiota --- plant broth-based culture media --- “in-situ-similis” culturing strategy --- vegan nutrition --- clover bacterial endophytes --- co-occurrence network --- fungal community --- fungal functional role --- plastic shed cultivation --- rhizosphere --- rhizosphere microbiome --- shotgun metagenomic sequencing --- partial least squares (PLS) regression analysis --- rice --- recombinant inbred lines --- root and shoot biomass --- heading and physiological maturity stage --- Codonopsis tangshen --- continuous cropping --- 454 pyrosequencing --- bacterial community --- bacterial structure --- soil chemical properties --- Streptomyces biocontrol agent --- cucumber --- microbial community composition --- microbial function --- Cadophora spp. --- corm rot --- dark septate endophytes --- functional guild --- internal transcribed spacer --- Talaromyces spp. --- aquaponics --- metabarcoding --- bacterial communities --- carbohydrases --- phytases --- endosymbiont --- microbial diversity --- fig and fig wasp --- Ficus hirta --- interaction --- alpha and beta diversity --- diversity --- metagenomics --- Streptomyces spp. spatial location --- variety --- volcanoes --- Andean Altiplano --- wild rice --- microbial community --- rhizosphere microorganism --- plant growth promoting --- extreme environments --- Atacama Desert --- 2,4-diacetylphloroglucinol --- biocontroller

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Numerous studies have demonstrated that the plant microbiome is highly relevant for the growth and fitness of plants. Plants in ecosystems and agroecosystems can recruit a wide variety of microorganisms, including beneficial microbes which are being studied and applied as biostimulators to improve nutrition and tolerance of plants and as biocontrol of phytopathogens. In this context, this Book contains a selection of articles describing diverse ecological and biotechnological aspects of microbiomes in native and agronomic plants (e.g., pepper, potato, rice and lettuce) created by researchers from Italy, China, Korea, Egypt, Oman, Germany, the USA, and Chile.

Research & information: general --- Biology, life sciences --- bioprospecting --- inoculants --- plant growth-promoting bacteria --- plant microbiome --- plant–microbe interactions --- plant microbiota --- cultivation-dependent of plant microbiota --- plant broth-based culture media --- “in-situ-similis” culturing strategy --- vegan nutrition --- clover bacterial endophytes --- co-occurrence network --- fungal community --- fungal functional role --- plastic shed cultivation --- rhizosphere --- rhizosphere microbiome --- shotgun metagenomic sequencing --- partial least squares (PLS) regression analysis --- rice --- recombinant inbred lines --- root and shoot biomass --- heading and physiological maturity stage --- Codonopsis tangshen --- continuous cropping --- 454 pyrosequencing --- bacterial community --- bacterial structure --- soil chemical properties --- Streptomyces biocontrol agent --- cucumber --- microbial community composition --- microbial function --- Cadophora spp. --- corm rot --- dark septate endophytes --- functional guild --- internal transcribed spacer --- Talaromyces spp. --- aquaponics --- metabarcoding --- bacterial communities --- carbohydrases --- phytases --- endosymbiont --- microbial diversity --- fig and fig wasp --- Ficus hirta --- interaction --- alpha and beta diversity --- diversity --- metagenomics --- Streptomyces spp. spatial location --- variety --- volcanoes --- Andean Altiplano --- wild rice --- microbial community --- rhizosphere microorganism --- plant growth promoting --- extreme environments --- Atacama Desert --- 2,4-diacetylphloroglucinol --- biocontroller