The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes
Pablo R. Hardoim,Leonard S. van Overbeek,Gabriele Berg,Anna Maria Pirttilä,Stéphane Compant,Andrea Campisano,Matthias Döring,Angela Sessitsch +7 more
TLDR
This review addresses the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.Citations
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Plant–microbiome interactions: from community assembly to plant health
TL;DR: This Review explores how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment and how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.
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A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application
TL;DR: In this paper, the importance and functionalities of the bacterial plant microbiome and discusses challenges and concepts in regard to the application of plantassociated bacteria. But, the authors do not consider the impact of farming practices and genotype on the microbial community.
Journal ArticleDOI
Microbial interactions within the plant holobiont.
TL;DR: The fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health is discussed and a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis is provided.
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Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots
Samiran Banerjee,Florian Walder,Lucie Büchi,Marcel Meyer,Alain Y. Held,Andreas Gattinger,Andreas Gattinger,Thomas Keller,Raphaël Charles,Marcel G. A. van der Heijden +9 more
TL;DR: It is demonstrated that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome, and this is the first study to report mycorrhizal keystoneTaxa for agroecosystems.
Journal ArticleDOI
Forest microbiome: diversity, complexity and dynamics
TL;DR: The understanding of these processes can be only achieved by the exploration of the complex 'ecosystem microbiome' and its functioning using focused, integrative microbiological and ecological research performed across multiple habitats.
References
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast,Elmar Pruesse,Pelin Yilmaz,Jan Gerken,Timmy Schweer,Pablo Yarza,Jörg Peplies,Frank Oliver Glöckner +7 more
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
QUORUM SENSING: Cell-to-Cell Communication in Bacteria
TL;DR: This review focuses on the architectures of bacterial chemical communication networks; how chemical information is integrated, processed, and transduced to control gene expression; how intra- and interspecies cell-cell communication is accomplished; and the intriguing possibility of prokaryote-eukaryote cross-communication.
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