Proposed minimal standards for description of new taxa of the class Halobacteria

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2024, Номер 74(3)

Опубликована: Март 8, 2024

Halophilic archaea of the class Halobacteria are most salt-requiring prokaryotes within domain Archaea . In 1997, minimal standards for description new taxa in order Halobacteriales were proposed. From then on, taxonomy provides an excellent example how changing concepts on prokaryote and development methods implemented. The last decades have witnessed a rapid expansion number described coinciding with era genome sequencing development. current members International Committee Systematics Prokaryotes Subcommittee Taxonomy propose these revisions to recommended encourage use advanced technologies taxonomic Most previously required some retained present revision, but changes been proposed line methodologies. addition 16S rRNA gene, rpoB′ gene is important molecular marker identification Phylogenomic analysis based concatenated conserved, single-copy genes infer status taxa. overall relatedness indexes proven be determinative classification Average nucleotide identity, digital DNA–DNA hybridization, average amino acid identity values should calculated rigorous comparison among close relatives.

Язык: Английский

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The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2024, Номер 74(1)

Опубликована: Янв. 5, 2024

The naming of prokaryotes is governed by the International Code Nomenclature Prokaryotes (ICNP) and partially for Algae, Fungi Plants (ICN). Such codes must be able to determine names taxa in a universal unambiguous manner, thus serving as common language across different fields activities. This unity undermined when new code nomenclature emerges that overlaps scope with an established, time-tested uses same format but assigns nomenclatural status values names. resulting confusion not beneficial wider scientific community. ambiguity expected result from establishment ‘Code Described DNA Sequence Data’ (‘SeqCode’), which general specific conflict ICNP ICN. Shortcomings interpretation may have exacerbated incompatibility between codes. It reiterated why proposals accept sequences types species subspecies validly published names, now implemented SeqCode, been Committee on Systematics (ICSP), oversees ICNP. absence certain regulations yet uncultivated acceptable argument, although it does justify separate code. Moreover, rejected ICSP are unnecessary adequately regulate prokaryotes. To provide better service community, alternative proposal emend presented, would Candidatus being regulated analogously fully consistent previous decisions, preserves essential avoids confusion.

Язык: Английский

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Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2023, Номер 73(7)

Опубликована: Июль 24, 2023

Currently, there are four mainstream taxonomic opinions on the classification of class Halobacteria at family and order levels. The International Committee Systematics Prokaryotes Subcommittee Taxonomy (ICSP), List Prokaryotic names with Standing in Nomenclature (LPSN) National Centre for Biotechnology Information (NCBI) adopted taxonomies have three to orders up eight families, while Genome Database (GTDB) taxonomy proposes only one nine families. To resolve inconsistency, phylogenomic analyses based concatenated single-copy orthologous proteins 122 conserved marker were conducted infer status current representatives 76 genera validly published able be assigned into families order. On basis these results, it is proposed that species should remerged Halobacteriales, then Haladaptataceae, Haloarculaceae, Halobacteriaceae, Halococcaceae, Haloferacaceae, Natronoarchaeaceae, Natrialbaceae Halorubellaceae. Thus, Haladaptataceae fam. nov. described Haladaptatus, Halomicrococcus Halorussus Halorubellaceae incorporating Haloarchaeobius Halorubellus, respectively.

Язык: Английский

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Novel insights into the diversity of halophilic microorganisms and their functioning in hypersaline ecosystems

npj Biodiversity, Год журнала: 2024, Номер 3(1)

Опубликована: Авг. 2, 2024

Abstract Our understanding of the microbial diversity inhabiting hypersaline environments, here defined as containing >100–150 g/L salts, has greatly increased in past five years. Halophiles are found each three domains life. Many novel types have been cultivated, and metagenomics other cultivation-independent approaches revealed existence many previously unrecognized lineages. Syntrophic interactions between different phylogenetic lineages discovered, such symbiosis members archaeal class Halobacteria ‘ Candidatus Nanohalarchaeota’. Metagenomics techniques also shed light on biogeography halophiles, especially genera Salinibacter ( Bacteria ) Haloquadratum Halorubrum Archaea ). Exploration microbiome lakes led to discovery metabolism unknown occur at high salt concentrations. Studies environments with concentrations chaotropic ions magnesium, calcium, lithium refined our limits

Язык: Английский

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Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2023, Номер 73(9)

Опубликована: Окт. 3, 2023

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.

Язык: Английский

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Halobacterium hubeiense sp. nov., a haloarchaeal species isolated from a bore core drilled in Hubei Province, PR China

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2024, Номер 74(3)

Опубликована: Март 21, 2024

Eight colonies of live microbes were isolated from an extensively surface-sterilized halite sample which had been retrieved a depth 2000 m salt mine in the Qianjiang Depression, Hubei Province, PR China. The eight colonies, obtained after 4 weeks incubation, named JI20-1 T –JI20-8 and was selected as type strain. strains have previously described, including genomic analysis based on complete genome for strain draft genomes other strains. In that study, name Halobacterium hubeiense suggested, location drilling site. Previous phylogenomic showed is most closely related to Permian isolate noricense Alpine rock salt. orthologous average nucleotide identity (orthoANI) digital DNA–DNA hybridization (dDDH) percentages between are 100–99.6 % 99.8–96.4 %, respectively. orthoANI dDDH values these with respect species genus 89.9–78.2 37.3–21.6 respectively, supporting their placement novel extremely halophilic archaeal species. tree comparison sequences 632 core-orthologous proteins confirmed status haloarchaea. polar lipid profile includes phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfate, sulfated galactosyl mannosyl glucosyl diether, compatible . Based genomic, phenotypic, chemotaxonomic characterization, we propose (=DSM 114402 = HAMBI 3616 ) , sp. nov.

Язык: Английский

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Roles of core nosZ denitrifiers in enhancing denitrification activity under long-term rice straw retention

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Фев. 7, 2025

The denitrification process is known to contribute soil nitrogen (N) loss, which strongly affected by fertilization strategies; however, the effects of distinct straw retention modes on activity have rarely been discriminated and underlying mechanisms remain unclear. This study coupled field incubation experiments explore characteristics activity, standing water physicochemical properties, abundance, community diversity, co-occurrence network nosZ denitrifiers, based a paddy implementing 10-year under rice-wheat rotation system. Four treatments with equivalent chemical fertilizers were applied, namely no (NS), wheat only (WS), rice (RS), (WRS). Results indicated significant increase (by 41.93-45.80% when compared that NS) in RS WRS. Correspondingly, resulted development similar composition (P < 0.05), structure = 0.001), more positively interconnected network, as well specific keystone taxa relative those non-rice mode. Under long-term conditions, core nosZ-denitrifying phylogroups shifted (r 0.83, P recruitment from phyla Bacteroidetes Euryarchaeota playing key role enhancing stimulating N loss. Accordingly, field, practice single season recommended because it will not markedly sacrifice availability impaired process.

Язык: Английский

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Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(10), С. 1856 - 1869

Опубликована: Авг. 12, 2024

Язык: Английский

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Global distribution and diversity of haloarchaeal pL6-family plasmids

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 8, 2024

Abstract Australian isolates of Haloquadratum walsbyi , a square-shaped haloarchaeon, often harbor small cryptic plasmids the pL6-family, approximately 6 kb in size. These exhibit highly conserved gene arrangement and encode replicase similar to those betapleolipoviruses. To assess their global distribution recover more examples for analysis, fifteen additional were reconstructed from metagenomes seven hypersaline sites across four countries: Argentina, Australia, Puerto Rico, Spain. Including five previously described plasmids, average plasmid size is 6,002 bp, with an G+C content 52.5%. The tetramers GGCC CTAG are either absent or significantly under-represented, except two highest %G+C. All share arrange-ment genes organized as outwardly facing replication ATPase modules, but variations observed some core genes, such F2, had acquired accessory genes. Two pCOLO-c1 pISLA-c6 shared 92.7% nt identity despite originating Argentina Spain, respectively. Numerous metagenomic CRISPR spacers matched sequences indicating frequent invasion haloarchaea. Spacers could be assigned haloarchaeal genera by mapping associated direct repeats (DR), half these matching . Finally, strand-specific metatranscriptome (RNA-seq) data used demonstrate active transcription pL6-family including antisense transcripts.

Язык: Английский

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Global Distribution and Diversity of Haloarchaeal pL6-Family Plasmids

Genes, Год журнала: 2024, Номер 15(9), С. 1123 - 1123

Опубликована: Авг. 26, 2024

Australian isolates of

Язык: Английский

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