The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation

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

Опубликована: Июль 24, 2023

Within the 16SrII phytoplasma group, subgroups A-X have been classified based on restriction fragment length polymorphism of their 16S rRNA gene, and two species described, namely 'Candidatus Phytoplasma aurantifolia' 'Ca. australasia'. Strains phytoplasmas are detected across a broad geographic range within Africa, Asia, Australia, Europe North South America. Historically, all members group share ≥97.5 % nucleotide sequence identity gene. In this study, we used whole genome sequences to identify boundaries group. Whole analyses were done using 42 strains into seven subgroups, five taxa without official 16Sr subgroup classifications, one 16SrXXV-A strain as an outgroup taxon. Based phylogenomic well average amino acid (ANI AAI), eight distinct equivalent identified, six which novel descriptions. same had ANI AAI values >97 %, shared ≥80 genomic segments analysis. Species also biological and/or ecological features. A often represented species, e.g., 16SrII-B members. Members 16SrII-A, 16SrII-D, 16SrII-V sweet potato little leaf fulfilled criteria be included single but with subspecies-level relationships each other. The taxon was described and, for other bacterial families, provided evidence that it could genus from phytoplasmas. As more become available, classification system these bacteria can further refined at genus, subspecies taxonomic ranks.

Язык: Английский

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Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems

Applied Microbiology and Biotechnology, Год журнала: 2021, Номер 105(19), С. 7123 - 7139

Опубликована: Сен. 11, 2021

Abstract Many biotechnological applications deal with nitrification, one of the main steps global nitrogen cycle. The biological oxidation ammonia to nitrite and further nitrate is critical avoid environmental damage its functioning has be retained even under adverse conditions. Bacteria performing second reaction, nitrate, are fastidious microorganisms that highly sensitive against disturbances. One important finding relevance for removal systems was discovery mainly cold-adapted Cand . Nitrotoga, whose activity seems essential recovery in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains this genus have been recently described ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives detected activated sludge. This review summarizes natural distribution driving forces defining niche separation artificial nitrification systems. Further aspects competition Nitrospira Nitrobacter discussed. Knowledge about physiological capacities limits can help define physico-chemical parameters example reactor need run temperatures. Key points • Characterization psychrotolerant oxidizer Comparison features those other NOB Identification beneficial environmental/operational proliferation

Язык: Английский

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How to grow your cable bacteria: Establishment of a stable single-strain culture in sediment and proposal of Candidatus Electronema aureum GS

Systematic and Applied Microbiology, Год журнала: 2021, Номер 44(5), С. 126236 - 126236

Опубликована: Июль 22, 2021

Cable bacteria are multicellular filamentous within the Desulfobulbaceae that couple oxidation of sulfide to reduction oxygen over centimeter distances via long distance electron transport (LDET). So far, none freshwater or marine cable species have been isolated into pure culture. Here we describe a method for establishing stable single-strain bacterium culture in partially sterilized sediment. By repeated transfers single filament from pond sediment autoclaved sediment, obtained strain GS, identified by its 16S rRNA gene as member Ca. Electronema. This was further propagated transferring clumps, and has now semi-natural microbial community several years. Its metagenome-assembled genome 93% complete, had size 2.76 Mbp, DNA G + C content 52%. Average Nucleotide Identity (ANI) Amino Acid (AAI) suggest affiliation GS Electronema novel species. Cell size, number outer ridges, detection LDET likewise consistent with Based on these combined features, therefore new candidate genus Electronema, which propose name Candidatus aureum sp.nov. Although not culture, this will be useful physiological omics-based studies; similar approaches single-cell single-filament natural medium may also aid characterization other difficult-to-culture microbes.

Язык: Английский

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Collection and curation of prokaryotic genome assemblies from type strains at NCBI

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2023, Номер 73(1)

Опубликована: Янв. 19, 2023

The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability its re-use users. Genomes from type materials can act as unambiguous reference for a taxonomic name play important role in comparative genomics, especially taxon verification or reclassification. National Center Biotechnology Information (NCBI) collects curates information on prokaryotic strains genomes strains. average nucleotide identity (ANI)-based quality control processes introduced at NCBI verify improve related records detailed here. Using curated reference, taxonomy over 1.1 million GenBank were verified 7000 new submissions before acceptance 1800 existing reclassified.

Язык: Английский

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Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2023, Номер 73(2)

Опубликована: Фев. 7, 2023

Observations made after introduction of the phylum category into International Code Nomenclature Prokaryotes (ICNP) indicate that addition a should usually be conducted before informal names at rank become widely used. It is thus investigated whether it would beneficial to add further categories. An extrapolation from number validly published under ICNP distinct principal categories was conducted. This indicated two ranks above also harbour if according were covered by ICNP. The appropriate kingdom and domain, regarded as separate ranks. benefit introducing these confirmed analysing previous taxonomic activity level nomenclatural problems associated with this activity. etymological examination way taxa genus are formed codes nomenclature provides hints for implementing additional According emendations proposed include domain means stabilizing prokaryotic nomenclature.

Язык: Английский

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