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

MBio
Kateryna ZhalninaTrent R Northen

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.

References

May 11, 2002·Science·Vigdis TorsvikTron Frede Thingstad
Jan 1, 1964·Annual Review of Microbiology·M ALEXANDER
Apr 28, 2004·Trends in Biotechnology·Royston GoodacreDouglas B Kell
Jun 15, 2005·Nature Reviews. Microbiology·Douglas B KellStephen G Oliver
Mar 14, 2007·Molecular Systems Biology·Sergey StolyarDavid A Stahl
May 24, 2008·Science·Paul G FalkowskiEdward F Delong
Jul 11, 2008·The ISME Journal·Richard D BardgettNicholas J Ostle
Oct 8, 2011·Nature·Michael W I SchmidtSusan E Trumbore
Dec 22, 2011·The Plant Cell·Guido GrossmannMatthias Meier
Mar 28, 2012·Nature Reviews. Microbiology·Karsten Zengler, Bernhard O Palsson
Apr 5, 2013·FEMS Microbiology Reviews·Michiel VosGeorge A Kowalchuk
Nov 30, 2013·Science·Itai Sharon, Jillian F Banfield
Jan 17, 2014·Nature Reviews. Genetics·Aarash BordbarBernhard O Palsson
May 2, 2014·Nature Methods·Sriram Kosuri, George M Church
May 2, 2014·Frontiers in Microbiology·Susanne SchreiterKornelia Smalla
Jan 1, 2013·Metabolites·Rainer BreitlingEriko Takano
Sep 23, 2014·Chemistry & Biology·Aleksandr MilshteynSean F Brady
Sep 23, 2014·Nature Biotechnology·Robert J CitorikTimothy K Lu
Nov 12, 2014·The ISME Journal·Francesca FiegnaTimothy G Barraclough
Jan 1, 2015·Proceedings of the National Academy of Sciences of the United States of America·David BerryMichael Wagner
Jan 7, 2015·Methods in Molecular Biology·Peter LandgrafDaniela C Dieterich
Feb 20, 2015·Plant Methods·David RousseauFrançois Chapeau-Blondeau
Aug 19, 2015·Proceedings of the National Academy of Sciences of the United States of America·Louis J CohenSean F Brady
Aug 19, 2015·Nature Chemical Biology·Eunji KimYeo Joon Yoon
Nov 21, 2015·Journal of Industrial Microbiology & Biotechnology·Micah KatzSean F Brady
Nov 26, 2015·Nature·Diana H WallJohan Six
Dec 2, 2015·Proceedings of the National Academy of Sciences of the United States of America·Mallory EmbreeKarsten Zengler
Jan 6, 2016·Plant Physiology·Dagmar van DusschotenSiegfried Jahnke
Feb 3, 2016·Trends in Plant Science·Vittorio Venturi, Christoph Keel
Apr 27, 2016·Current Opinion in Biotechnology·Nico JehmlichMartin von Bergen
May 4, 2016·Proceedings of the National Academy of Sciences of the United States of America·Kenneth J Locey, Jay T Lennon
Jul 1, 2016·Proceedings of the National Academy of Sciences of the United States of America·Roland HatzenpichlerVictoria J Orphan
Aug 31, 2016·Nature Microbiology·Laura A HugJillian F Banfield
Oct 25, 2016·Trends in Cell Biology·Bob Goldstein, Nicole King
Oct 25, 2016·Nature Chemical Biology·John ChuSean F Brady
Nov 29, 2016·Nature Communications·Cynthia M KallenbachA Stuart Grandy
Dec 23, 2016·Nature·David BursteinJillian F Banfield

❮ Previous
Next ❯

Citations

Jun 23, 2019·Nature Methods·Karsten ZenglerTrent R Northen
Jul 25, 2019·Nature Microbiology·Manish KumarJens Nielsen
Sep 25, 2019·Nature Reviews. Microbiology·Christopher E LawsonKatherine D McMahon
Feb 10, 2021·Current Opinion in Biotechnology·Livia S ZaramelaKarsten Zengler
Mar 10, 2021·Nature Communications·Felipe Senne de Oliveira LinoMorten Otto Alexander Sommer
Apr 13, 2021·Frontiers in Microbiology·Mon Oo YeeRomy Chakraborty
Jun 4, 2021·Microbial Biotechnology·Neeraj KumarThomas Clavel
Aug 8, 2021·International Journal of Molecular Sciences·Lauren K JabuschTrent R Northen
Nov 21, 2018·Biochemistry·Xinyun CaoOphelia S Venturelli

❮ Previous
Next ❯

Methods Mentioned

BETA
imaging techniques

Software Mentioned

EcoFABs
GLO

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.