Proposed minimal standards for description of methanogenic archaea

Prakash, Om; Dodsworth, Jeremy A.; Dong, Xiuzhu; Ferry, James G.; L’Haridon, Stephane; Imachi, Hiroyuki; Kamagata, Yoichi; Rhee, Sung-Keun; Sagar, Isita; Shcherbakova, Viktoria; Wagner, Dirk; Whitman, William B.

doi:10.1099/ijsem.0.005500

Proposed minimal standards for description of methanogenic archaea

Journal Article · Tue Apr 25 04:00:00 EDT 2023 · International Journal of Systematic and Evolutionary Microbiology

DOI:https://doi.org/10.1099/ijsem.0.005500· OSTI ID:2419447

Prakash, Om ^[1]; ^[2]; Dong, Xiuzhu ^[3]; Ferry, James G. ^[4]; ^[5]; ^[6]; ^[7]; Rhee, Sung-Keun ^[8]; Sagar, Isita ^[9]; ^[10]; ^[11]; ^[12]

Symbiosis Centre for Climate Change and Sustainability, Symbiosis International (Deemed University), Lavale, Pune-412115, Maharashtra, India; National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India; OSTI
Department of Biology, California State University, San Bernardino, CA 92407, USA
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, F-29280, Plouzané, France
Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8560, Japan
Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
Laboratory of Anaerobic Microorganisms, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 3, Pushchino, Moscow, 142290, Russian Federation
Institut of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg A71-359, 14473 Potsdam, Germany
Department of Microbiology, University of Georgia, Athens, GA 30602, USA

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA–DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of themcrAgene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description ofCandidatusmethanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.

Research Organization:: Pennsylvania State Univ., University Park, PA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: FG02-95ER20198

OSTI ID:: 2419447

Journal Information:: International Journal of Systematic and Evolutionary Microbiology, Journal Name: International Journal of Systematic and Evolutionary Microbiology Journal Issue: 4 Vol. 73; ISSN 1466-5026

Publisher:: International Union of Microbiological Societies

Country of Publication:: United States

Language:: English

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