Roadmap for naming uncultivated Archaea and Bacteria

Alison E Murray¹, John Freudenstein², Simonetta Gribaldo³, Roland Hatzenpichler⁴, Philip Hugenholtz⁵, Peter Kämpfer⁶, Konstantinos T Konstantinidis⁷, Christopher E Lane⁸, R Thane Papke⁹, Donovan H Parks⁵, Ramon Rossello-Mora¹⁰, Matthew B Stott¹¹, Iain C Sutcliffe¹², J Cameron Thrash¹³, Stephanus N Venter¹⁴, William B Whitman¹⁵, Silvia G Acinas¹⁶, Rudolf I Amann¹⁷, Karthik Anantharaman¹⁸, Jean Armengaud¹⁹, Brett J Baker²⁰, Roman A Barco²¹, Helge B Bode^{22

23}, Eric S Boyd²⁴, Carrie L Brady²⁵, Paul Carini²⁶, Patrick S G Chain²⁷, Daniel R Colman²⁴, Kristen M DeAngelis²⁸, Maria Asuncion de Los Rios²⁹, Paulina Estrada-de Los Santos³⁰, Christopher A Dunlap³¹, Jonathan A Eisen³², David Emerson³³, Thijs J G Ettema³⁴, Damien Eveillard³⁵, Peter R Girguis³⁶, Ute Hentschel³⁷, James T Hollibaugh³⁸, Laura A Hug³⁹, William P Inskeep⁴⁰, Elena P Ivanova⁴¹, Hans-Peter Klenk⁴², Wen-Jun Li⁴³, Karen G Lloyd⁴⁴, Frank E Löffler^{45

46}, Thulani P Makhalanyane⁴⁷, Duane P Moser⁴⁸, Takuro Nunoura⁴⁹, Marike Palmer⁵⁰, Victor Parro⁵¹, Carlos Pedrós-Alió⁵², Alexander J Probst⁵³, Theo H M Smits⁵⁴, Andrew D Steen⁵⁵, Emma T Steenkamp¹⁴, Anja Spang^{56

57}, Frank J Stewart²⁴, James M Tiedje⁵⁸, Peter Vandamme⁵⁹, Michael Wagner⁶⁰, Feng-Ping Wang⁶¹, Pablo Yarza⁶², Brian P Hedlund⁶³, Anna-Louise Reysenbach⁶⁴

Affiliations

¹ Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA. alison.murray@dri.edu.
² Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
³ Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France.
⁴ Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
⁵ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
⁶ Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany.
⁷ School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA.
⁸ Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
⁹ Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA.
¹⁰ Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain.
¹¹ School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
¹² Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK.
¹³ Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
¹⁴ Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
¹⁵ Department of Microbiology, University of Georgia, Athens, GA, USA.
¹⁶ Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain.
¹⁷ Max Planck Institute for Marine Microbiology, Bremen, Germany.
¹⁸ Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
¹⁹ CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France.
²⁰ Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA.
²¹ Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.
²² Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.
²³ Senckenberg Society for Nature Research, Frankfurt am Main, Germany.
²⁴ Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
²⁵ University of the West of England, Bristol, England.
²⁶ Department of Environmental Science, University of Arizona, Tuscon, AZ, USA.
²⁷ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
²⁸ Microbiology Department, University of Massachusetts, Amherst, MA, USA.
²⁹ National Museum of Natural Sciences, CSIC, Madrid, Spain.
³⁰ Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
³¹ National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA.
³² Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA.
³³ Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
³⁴ Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
³⁵ LS2N, Université de Nantes, CNRS, Nantes, France.
³⁶ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
³⁷ GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany.
³⁸ Department of Marine Sciences, University of Georgia, Athens, GA, USA.
³⁹ Department of Biology, University of Waterloo, Waterloo, Canada.
⁴⁰ Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
⁴¹ School of Science, RMIT University, Melbourne, Victoria, Australia.
⁴² School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
⁴³ School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
⁴⁴ Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
⁴⁵ Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.
⁴⁶ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
⁴⁷ Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
⁴⁸ Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA.
⁴⁹ Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
⁵⁰ School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
⁵¹ Astrobiology Center (CSIC-INTA), Madrid, Spain.
⁵² National Biotechnology Center, Cantoblanco, Madrid, Spain.
⁵³ Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany.
⁵⁴ Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland.
⁵⁵ Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA.
⁵⁶ Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.
⁵⁷ Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
⁵⁸ Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
⁵⁹ Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium.
⁶⁰ Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
⁶¹ International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
⁶² Ribocon GmbH, Bremen, Germany.
⁶³ School of Life Sciences, University of Nevada, Las Vegas, NV, USA. brian.hedlund@unlv.edu.
⁶⁴ Biology Department, Portland State University, Portland, OR, USA. bwar@pdx.edu.

PMID: 32514073
PMCID: PMC7381421
DOI: 10.1038/s41564-020-0733-x

Review

Roadmap for naming uncultivated Archaea and Bacteria

Alison E Murray et al. Nat Microbiol. 2020 Aug.

. 2020 Aug;5(8):987-994.

doi: 10.1038/s41564-020-0733-x. Epub 2020 Jun 8.

Authors

Affiliations

¹ Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA. alison.murray@dri.edu.
² Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
³ Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France.
⁴ Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
⁵ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
⁶ Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany.
⁷ School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA.
⁸ Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
⁹ Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA.
¹⁰ Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain.
¹¹ School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
¹² Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK.
¹³ Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
¹⁴ Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
¹⁵ Department of Microbiology, University of Georgia, Athens, GA, USA.
¹⁶ Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain.
¹⁷ Max Planck Institute for Marine Microbiology, Bremen, Germany.
¹⁸ Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
¹⁹ CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France.
²⁰ Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA.
²¹ Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.
²² Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.
²³ Senckenberg Society for Nature Research, Frankfurt am Main, Germany.
²⁴ Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
²⁵ University of the West of England, Bristol, England.
²⁶ Department of Environmental Science, University of Arizona, Tuscon, AZ, USA.
²⁷ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
²⁸ Microbiology Department, University of Massachusetts, Amherst, MA, USA.
²⁹ National Museum of Natural Sciences, CSIC, Madrid, Spain.
³⁰ Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
³¹ National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA.
³² Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA.
³³ Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
³⁴ Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
³⁵ LS2N, Université de Nantes, CNRS, Nantes, France.
³⁶ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
³⁷ GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany.
³⁸ Department of Marine Sciences, University of Georgia, Athens, GA, USA.
³⁹ Department of Biology, University of Waterloo, Waterloo, Canada.
⁴⁰ Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
⁴¹ School of Science, RMIT University, Melbourne, Victoria, Australia.
⁴² School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
⁴³ School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
⁴⁴ Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
⁴⁵ Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.
⁴⁶ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
⁴⁷ Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
⁴⁸ Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA.
⁴⁹ Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
⁵⁰ School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
⁵¹ Astrobiology Center (CSIC-INTA), Madrid, Spain.
⁵² National Biotechnology Center, Cantoblanco, Madrid, Spain.
⁵³ Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany.
⁵⁴ Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland.
⁵⁵ Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA.
⁵⁶ Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.
⁵⁷ Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
⁵⁸ Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
⁵⁹ Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium.
⁶⁰ Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
⁶¹ International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
⁶² Ribocon GmbH, Bremen, Germany.
⁶³ School of Life Sciences, University of Nevada, Las Vegas, NV, USA. brian.hedlund@unlv.edu.
⁶⁴ Biology Department, Portland State University, Portland, OR, USA. bwar@pdx.edu.

PMID: 32514073
PMCID: PMC7381421
DOI: 10.1038/s41564-020-0733-x

Erratum in

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.
Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Murray AE, et al. Nat Microbiol. 2021 Jan;6(1):136. doi: 10.1038/s41564-020-00827-2. Nat Microbiol. 2021. PMID: 33184503 Free PMC article. No abstract available.

Abstract

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

PubMed Disclaimer

Conflict of interest statement

The authors have no competing interests.

Figures

**Fig. 1. Proposed roadmaps for nomenclature of uncultivated Archaea and Bacteria.**
Plans A and B provide two alternatives for inclusion of uncultivated Archaea and Bacteria into the classical Linnaean nomenclature system.

**Fig. 2. Scenario for naming uncultivated Archaea and Bacteria.**
In cases where naming a new species is warranted, the steps outlined here are a likely process for nomenclature regardless of whether plan A or plan B (Fig. 1) is adopted.

See this image and copyright information in PMC

References

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Roadmap for naming uncultivated Archaea and Bacteria

Affiliations

Roadmap for naming uncultivated Archaea and Bacteria

Authors

Affiliations

Erratum in

Abstract

Conflict of interest statement

Figures

References

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