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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Crop Bioprotection Research » Research » Publications at this Location » Publication #373569
Research Project: Use of Microorganisms to Manage Weeds and Insect Pests in Turf and Agricultural Systems

Location: Crop Bioprotection Research

Title: Roadmap for naming uncultivated Archaea and Bacteria

Author
item MURRAY, ALISON - Desert Research Institute
item FREUDENSTEIN, JOHN - The Ohio State University
item GRIBALDO, SIMONETTA - Institut Pasteur - France
item HATZENPICHLER, ROLAND - Montana State University
item HUGENHOLTZ, PHILIP - University Of Queensland
item KÄMPFER, PETER - Justus-Liebig University
item KONSTANTINIDIS, KONSTANTINOS - Georgia Tech
item LANE, CHRISTOPHER - University Of Rhode Island
item PAPKE, ROBERTSON - University Of Connecticut
item PARKS, DONOVAN - University Of Queensland
item ROSSELLO-MORA, RAMON - Universitat De Les Illes Balears
item STOTT, MATTHEW - Canterbury Christchurch College
item SUTCLIFFE, IAIN - Northumbria University
item THRASH, JAMES - University Of Southern California
item VENTER, STEPHANUS - University Of Pretoria
item WHITMAN, WILLIAM - University Of Georgia
item ACINAS, SILVIA - Institute Of Advanced Chemistry Of Catalonia(CSIC)
item AMANN, RUDOLF - Max Planck Society
item ANANTHARAMAN, KARTHIK - University Of Wisconsin
item ARMENGAUD, JEAN - Cea Marcoule
item BAKER, BRETT - Marine Science Institute
item BARCO, ROMAN - University Of Southern California
item BODE, HELGE - Goethe University
item BOYD, ERIC - Montana State University
item BRADY, CARRIE - Western New England University
item CARINI, PAUL - University Of Arizona
item CHAIN, PATRICK S - Los Alamos National Research Laboratory
item COLMAN, DANIEL - Montana State University
item DEANGELIS, KRISTEN - University Of Massachusetts
item DE LOS RIOS, MARIA ASUNCION - Consejo Superior De Investigaciones Cientificas (CSIC)
item DE LOS SANTOS, PAULINA ESTRADA - Laboratorio Avi-Mex, Sa De Cv
item Dunlap, Christopher
item EISEN, JONATHAN - University Of California, Davis
item EMERSON, DAVID - Bigelow Laboratory For Ocean Sciences
item ETTEMA, THIJS J - Wageningen University And Research Center
item EVEILLARD, DAMIEN - University Of Nantes
item GIRGUIS, PETER - Harvard University
item HENTSCHEL, UTE - Helmholtz Centre
item HOLLIBAUGH, JAMES - University Of Georgia
item HUG, LAURA - University Of Waterloo
item INSKEEP, WILLIAM - Montana State University
item IVANOVA, ELENA - Melbourne University
item KLENK, HANS-PETER - Newcastle University
item LI, WEN-JUN - Sun Yat-Sen University
item LLOYD, KAREN - University Of Tennessee
item LOEFFLER, FRANK - University Of Tennessee
item MAKHALANYANE, THULANI - University Of Pretoria
item MOSER, DUANE - Desert Research Institute
item NUNOURA, TAKURO - Japan Agency For Marine-Earth Science And Technology (JAMSTEC)
item PALMER, MARIKE - University Of Nevada
item PARRO, VICTOR - Instituto Nacional De Investigacion Y Tecnologia Agraria Y Alimentaria
item PEDROS-ALIO, CARLOS - Ciudad University - Spain
item PROBST, ALEXANDER - University Of Duisburg-Essen
item SMITS, THEO H - Zurich University Of Applied Sciences
item STEEN, ANDREW - University Of Tennessee
item STEENKAMP, EMMA - University Of Pretoria
item SPANG, ANJA - Royal Netherlands Society For Agricultural Science (KLV)
item STEWART, FRANK - Georgia Tech
item TIEDJE, JAMES - Michigan State University
item VANDAMME, PETER - Ghent University
item WAGNER, MICHAEL - University Of Vienna
item WANG, FENG-PING - Shanghai Jiaotong University
item YARZA, PABLO - Ribocon Gmbh
item HEDLUND, BRIAN - University Of Nevada Las Vegas, Las Vegas, Nv
item REYSENBACH, ANNA-LOUISE - Portland State University

Submitted to: Nature Microbiology
Publication Type: Other
Publication Acceptance Date: 5/1/2020
Publication Date: 6/8/2020
Citation: Murray, A.E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K.T., Lane, C.E., Papke, R.T., Parks, D.H., Rossello-Mora, R., Stott, M.B., Sutcliffe, I.C., Thrash, J.C., Venter, S.N., Whitman, W.B., Acinas, S.G., Amann, R.I., Anantharaman, K., Armengaud, J., Baker, B.J., Barco, R.A., Bode, H.B., Boyd, E.S., Brady, C.L., Carini, P., Chain, P.S.G., Colman, D.R., Deangelis, K.M., De Los Rios, M.A., De Los Santos, P.E., Dunlap, C.A., Eisen, J.A., Emerson, D., Ettema, T.J.G., Eveillard, D., Girguis, P.R., Hentschel, U., Hollibaugh, J.T., Hug, L.A., Inskeep, W.P., Ivanova, E.P., Klenk, H-P., Li, W-J., Lloyd, K.G., Loeffler, F.E., Makhalanyane, T., Moser, D.P., Nunoura, T., Palmer, M., Parro, V., Pedros-Alio, C., Probst, A.J., Smits, T.M., Steen, A.D., Steenkamp, E.T., Spang, A., Stewart, F.J., Tiedje, J.M., Vandamme, P., Wagner, M., Wang, F-P., Yarza, P., Hedlund, B.P., Reysenbach, A-L. 2020. Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology . 5:987-994. https://doi.org/10.1038/s41564-020-0733-x.
DOI: https://doi.org/10.1038/s41564-020-0733-x

Interpretive Summary: Advances in our analytical abilities have allowed us to identify bacteria that we cannot grow in the laboratory, but we can routinely observe in the environment. Historically, bacteria were required to be grown and stored in the laboratory before they were given a name. It is important to give these uncultivatable bacteria standardized names so they can be discussed and communicated about in the scientific community. This manuscript provides a roadmap on developing such a naming system. This research benefits all agricultural producers and consumers as it allows us to more effectively communicate about these bacteria that are found in all environments.

Technical Abstract: Assembly of single-amplified genomes and metagenome-assembled genomes has led to a recent explosion in genome-based discoveries of Bacteria and Archaea, bringing with it an urgent need to develop guidelines for nomenclature of uncultivated microorganisms. Currently, the International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as “type material”, thereby preventing naming of uncultivated organisms. Here, we consider two potential paths to solve this nomenclatural conundrum. One option requires adopting already proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other creates a parallel nomenclatural code for uncultivated prokaryotes that could ultimately be merged with the ICNP if deemed appropriate at a future point in time. In either case, we believe that timely action is needed and that the scientific community needs to organize in order to develop consistent nomenclature rules for uncultivated taxa to provide stability, communicate diversity, and reduce confusion.