Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

ABSTRACT The chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities...

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Auteurs principaux:	Kateryna Zhalnina, Karsten Zengler, Dianne Newman, Trent R. Northen
Format:	article
Langue:	EN
Publié:	American Society for Microbiology 2018
Sujets:	chemistry of soil microbiomes exometabolomics laboratory ecosystems metabolic networks synthetic communities Microbiology QR1-502
Accès en ligne:	https://doaj.org/article/72c9c36cb2e74a00917d7d73181a8b4f
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spelling	oai:doaj.org-article:72c9c36cb2e74a00917d7d73181a8b4f2021-11-15T16:00:16ZNeed for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry10.1128/mBio.01175-182150-7511https://doaj.org/article/72c9c36cb2e74a00917d7d73181a8b4f2018-09-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01175-18https://doaj.org/toc/2150-7511ABSTRACT The chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.Kateryna ZhalninaKarsten ZenglerDianne NewmanTrent R. NorthenAmerican Society for Microbiologyarticlechemistry of soil microbiomesexometabolomicslaboratory ecosystemsmetabolic networkssynthetic communitiesMicrobiologyQR1-502ENmBio, Vol 9, Iss 4 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	chemistry of soil microbiomes exometabolomics laboratory ecosystems metabolic networks synthetic communities Microbiology QR1-502
spellingShingle	chemistry of soil microbiomes exometabolomics laboratory ecosystems metabolic networks synthetic communities Microbiology QR1-502 Kateryna Zhalnina Karsten Zengler Dianne Newman Trent R. Northen Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
description	ABSTRACT The chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.
format	article
author	Kateryna Zhalnina Karsten Zengler Dianne Newman Trent R. Northen
author_facet	Kateryna Zhalnina Karsten Zengler Dianne Newman Trent R. Northen
author_sort	Kateryna Zhalnina
title	Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
title_short	Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
title_full	Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
title_fullStr	Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
title_full_unstemmed	Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
title_sort	need for laboratory ecosystems to unravel the structures and functions of soil microbial communities mediated by chemistry
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/72c9c36cb2e74a00917d7d73181a8b4f
work_keys_str_mv	AT katerynazhalnina needforlaboratoryecosystemstounravelthestructuresandfunctionsofsoilmicrobialcommunitiesmediatedbychemistry AT karstenzengler needforlaboratoryecosystemstounravelthestructuresandfunctionsofsoilmicrobialcommunitiesmediatedbychemistry AT diannenewman needforlaboratoryecosystemstounravelthestructuresandfunctionsofsoilmicrobialcommunitiesmediatedbychemistry AT trentrnorthen needforlaboratoryecosystemstounravelthestructuresandfunctionsofsoilmicrobialcommunitiesmediatedbychemistry
_version_	1718426974285725696

Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

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