Spring, Stefan

A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2T could be affiliated with the phylum Synergistota . Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2T (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2T (=DSM 107166T=NBRC 114655T) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.

Abstract Ther.mo.ha.lo.bac.te.ra.ce'ae. N.L. masc. n. Thermohalobacter , type genus of the family; suff. ‐aceae , ending to denote a family; N.L. fem. pl. n. Thermohalobacteraceae , the Thermohalobacter family. Free‐living bacteria that mainly occur in anoxic saline environments. Cells are not pigmented and have a Gram‐positive type of cell wall. Gram‐stain reaction can be negative or positive. Typically slender rod‐shaped cells that are motile by flagella. Several strains form heat‐resistant spores. Mainly euryhaline, moderately thermophilic and halophilic. Members of the family are strictly anaerobic bacteria that utilize carbohydrates or peptides by fermentation. Cellular fatty acid patterns are dominated by iso ‐C 15:0 and iso ‐C 15:0 DMA. The family currently accommodates members of the genera Thermohalobacter , Caldisalinibacter , Caloranaerobacter , Brassicibacter , Sporosalibacterium , and Clostridiisalibacter , which were previously affiliated with the family Clostridiaceae . The affiliation of novel species to this family depends on the phylogenetic position, which should be determined on the basis of comparative sequence analyses of 16S rRNA genes or genomes. DNA G + C content (mol%): 28–33. Type genus: Thermohalobacter Cayol et al. 2000. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Thermohalobacteraceae is: synonym (last update, February 2025) * . Correct name: Clostridiaceae LPSN classification: Bacteria / Bacillati / Bacillota / Clostridia / Eubacteriales / Clostridiaceae The family Thermohalobacteraceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Thermohalobacteraceae (version v220) ** . GTDB classification: d__Bacteria / p__Bacillota_A / c__Clostridia / o__Tissierellales / f__Thermohalobacteraceae * 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

Summary The anaerobic, mesophilic and moderately halophilic strain L21‐Spi‐D4 T was recently isolated from the suboxic zone of a hypersaline cyanobacterial mat using protein‐rich extracts of Arthrospira (formerly Spirulina ) platensis as substrate. Phylogenetic analyses based on 16S rRNA genes indicated an affiliation of the novel strain with the Bacteroidetes clade MgMjR‐022, which is widely distributed and abundant in hypersaline microbial mats and heretofore comprised only sequences of uncultured bacteria. Analyses of the complete genome sequence of strain L21‐Spi‐D4 T revealed a possible specialization on the degradation of cyanobacterial biomass. Besides genes for enzymes degrading specific cyanobacterial proteins a conspicuous transport complex for the polypeptide cyanophycin could be identified that is homologous to typical polysaccharide utilization loci of Bacteroidetes . A distinct and reproducible co‐occurrence pattern of environmental 16S rRNA gene sequences of the MgMjR‐022 clade and cyanobacteria in the suboxic zone of hypersaline mats points to a specific dependence of members of this clade on decaying cyanobacteria. Based on a comparative analysis of phenotypic, genomic and ecological characteristics we propose to establish the novel taxa Salinivirga cyanobacteriivorans gen. nov., sp. nov., represented by the type strain L21‐Spi‐D4 T , and Salinivirgaceae fam. nov., comprising sequences of the MgMjR‐022 clade.

Abstract The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-ABT and related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.

Abstract Mag.ne'to.bac.te'ri.um. Gr. n. magnes magnet, comb. form magneto‐; Gr. n. bakterion a small rod; M.L. neut. n. Magnetobacterium a magnetic rod. Rod‐shaped, large, magnetic cells occurring in freshwater sediments. The original description is based on bacteria enriched from the littoral sediment of a freshwater lake in Southern Germany (Chiemsee); similar types of bacteria were also observed in sediments of other freshwater lakes and ponds in Southern Germany and Brazil. Counts of active bacteria in different vertical layers of Chiemsee sediment indicated that “ Candidatus M. bavaricum” is a typical gradient organism, particularly adapted to zones characterized by low levels of oxygen, where it reaches the highest abundance (Spring et al., 1993). A minor fraction of these bacteria was also found in the anoxic zone, whereas high concentrations of oxygen can apparently not be tolerated by this bacterium over longer periods of time. Type species : “ Candidatus Magnetobacterium bavaricum ” Spring, Amann, Ludwig, Schleifer, van Gemerden and Petersen 1993, 2398. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Magnetobacterium is: synonym (and no standing) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Nitrospirota / Nitrospiria / Nitrospirales / Nitrospiraceae / Candidatus Magnetobacterium The genus Candidatus Magnetobacterium can also be recovered in the Genome Taxonomy Database (GTDB) as g__Magnetobacterium (version v220) ** . GTDB classification: d__Bacteria / p__Nitrospirota / c__Thermodesulfovibrionia / o__Thermodesulfovibrionales / f__Magnetobacteriaceae / g__Magnetobacterium * 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

A combination of polymerase chain reaction-assisted rRNA sequence retrieval and fluorescent oligonucleotide probing was used to identify in situ a hitherto unculturable, big, magnetotactic, rod-shaped organism in freshwater sediment samples collected from Lake Chiemsee. Tentatively named “Magnetobacterium bavaricum,” this bacterium is evolutionarily distant from all other phylogenetically characterized magnetotactic bacteria and contains unusually high numbers of magnetosomes (up to 1,000 magnetosomes per cell). The spatial distribution in the sediment was studied, and up to 7 × 10 5 active cells per cm 3 were found in the microaerobic zone. Considering its average volume (25.8 ± 4.1 μm 3 ) and relative abundance (0.64 ± 0.17%), “M. bavaricum” may account for approximately 30% of the microbial biovolume and may therefore be a dominant fraction of the microbial community in this layer. Its microhabitat and its high content of sulfur globules and magnetosomes suggest that this organism has an iron-dependent way of energy conservation which depends on balanced gradients of oxygen and sulfide.