Whitman, William B.

AbstractMost prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, includingCandidatusnames, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.

Abstract Me.tha.no.tri.cha'les. N.L. fem. n. Methanothrix type genus of the order; suff. ‐ ales the ending to denote an order; N.L. fem. pl. n. Methanotrichales the order of Methanothrix . Cells are nonmotile, sheathed rods with flat ends. Gram‐stain negative. Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Species are oxygen‐tolerant anaerobe. However, growth and methanogenesis can only occur in strictly anaerobic and highly reducing conditions. Energy is obtained by splitting acetate into methane and CO 2 . When cocultured with electrogenic Geobacter spp., CO 2 is reduced to methane via direct interspecies electron transfer (DIET). Optimum growth pH range is 7.0–7.8. Mesophilic and thermophilic. Optimum growth temperatures are 34–37°C for mesophilic strains and 55–60°C for thermophilic strains. They occupy a wide range of anoxic habitats including anaerobic river mud, paddy field soil, hot springs, thermal lakes, thermophilic, and mesophilic anaerobic wastewater digesters treating domestic wastes; granular sludge, anaerobic fixed‐bed reactors, and other types of anaerobic systems. Genome sequences have been determined for strains of all three of the described species in the order, and the genome size ranges from 1.9 to 3.0 Mb. The order Methanotrichales consists of one family Methanotrichaceae . Although all three described species are currently classified in a single genus Methanothrix , phylogenomic analyses suggest that two species should be transferred to novel genera. DNA G + C content (mol%) : 51–61 (Genome). Type genus : Methanothrix Huser et al. 1982, VL10. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Methanotrichales is: synonym (and no standing) (last update, February 2025) * . Correct name: Methanosarcinales LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanosarcinia / Methanosarcinales The order Methanotrichales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Methanotrichales (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanosarcinia / o__Methanotrichales * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Me.tha'no.thrix. N.L. neut. n. methanum methane; Gr. fem. n. thrix , hair; N.L. fem. n. Methanothrix , methane (‐producing) hair. Straight, rod‐shaped cells with flat ends, usually 0.8–1.3 μm wide by 2.0–6.0 μm long enclosed in a tubular sheath. Forms short (∼5–25 μm) to long (>150 μm) flexible chains of cells within the sheath. Nonmotile. Gram‐stain‐negative. Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Oxygen‐tolerant anaerobe. Organotrophic, splitting acetate into methane and CO 2 for energy generation. Some strains split formate into H 2 and CO 2 without producing methane. CO 2 can be reduced to methane in coculture with Geobacter spp. via direct interspecies electron transfer (DIET). Growth factors such as vitamins are stimulatory. Yeast extract is required, stimulatory or inhibitory, depending on the strain. NaCl is not required for growth. Optimal temperatures range from 34 to 37°C for mesophilic strains and 55 to 60°C for thermophilic strains; optimal pH range is 7.0–7.8. Gas vacuoles are generally found in thermophilic strains. Occur in both mesophilic and thermophilic anaerobic sludge digesters as well as anaerobic sediments. Synonymous with the genus Methanosaeta . DNA G + C content (mol%) : 51–61 (genome). Type species : Methanothrix soehngenii Huser et al. 1982, VL10. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Methanothrix is: correct name (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanosarcinia / Methanosarcinales / Methanotrichaceae / Methanothrix The genus Methanothrix can also be recovered in the Genome Taxonomy Database (GTDB) as g__Methanothrix (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanosarcinia / o__Methanotrichales / f__Methanotrichaceae / g__Methanothrix * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Me.tha.no.tri.cha.ce'ae. N.L. fem. n. Methanothrix type genus of the family; suff. – aceae ending to denote a family; N.L. fem. pl. n. Methanotrichaceae the Methanothrix family. Sheathed, rod‐shaped cells with flat ends, usually 0.8–1.3 μm wide by 2.0–6.0 μm long. Nonmotile. Gram‐stain‐negative. Oxygen‐tolerant anaerobe. Slow‐growing organotrophic, splitting acetate into methane and CO 2 for energy generation. Some strains split formate into hydrogen and CO 2 without generating methane. CO 2 can be reduced into methane when cocultured with electrogenic Geobacter spp. via direct interspecies electron transfer (DIET). Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Genome sequences have been determined for all described species. Habitats : Widely distributed in anaerobic river mud, paddy field soil, hot springs, thermal lakes, thermophilic and mesophilic anaerobic wastewater digestors treating domestic wastes, granular sludge, anaerobic fixed‐bed reactors, and other types of anaerobic systems. DNA G + C content (mol%) : 51–61 (Genome). Type genus : Methanothrix Huser et al. 1982, VL10. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Methanotrichaceae is: correct name (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanosarcinia / Methanosarcinales / Methanotrichaceae The family Methanotrichaceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Methanotrichaceae (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanosarcinia / o__Methanotrichales / f__Methanotrichaceae * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776