International Journal of Systematic and Evolutionary Microbiology

‘ Candidatus Ferrigenium straubiae’ strain KS (KCTC 25982, DSM 118991) is a neutrophilic, Fe(II)-oxidizing bacterium representing up to 98% of the community in culture KS, the most extensively studied mixed culture known for autotrophic nitrate-reducing Fe(II) oxidation. The phylogeny and genome of this bacterium were previously analysed and identified as ‘ Candidatus Ferrigenium straubiae’. In this study, we report the first-time successful isolation of ‘ Candidatus Ferrigenium straubiae’ strain KS and its experimental physiological characterization. The bacterium was identified as a non-stalk-forming, rod-shaped and non-halophilic strain with a Gram-negative classification. We characterized its physiology when grown in agarose-stabilized Fe(II)-O 2 gradient tubes where Fe(II) stemming from FeS functions as the electron donor and O 2 as the electron acceptor. It showed growth at temperatures of 20–30 °C (optimal at 25°C) and at pH levels of 6.0–7.5 (optimal at pH 6.5–7.0). The doubling time at 20 °C and pH 6.5 was 16 h. We further optimized the gradient tubes for sustainable culture maintenance using modified Wolfe’s mineral medium (MWMM; 1 g l −1 NH 4 Cl) supplemented with 7-vitamin solution, SL-10 trace elements, selenite-tungstate solution and selenite-molybdate-nickel-copper-arsenic-vanadium solution (final concentrations of 10 µM Se, 10 µM Mo, 0.1 µM Ni, 0.1 µM Cu, 0.1 µM As and 5 nM V). We also evaluated several Fe(II) sources (with O 2 as electron acceptor), as well as both inorganic and organic substrates for their influence on growth. Although a known member of the denitrifying community in culture KS, the isolated strain ‘ Candidatus Ferrigenium straubiae’ KS exhibited exclusively microaerobic and autotrophic growth in agarose-stabilized Fe(II)-O 2 gradients, utilizing Fe(II) from FeS as the electron donor.

A Gram-stain-negative, aerobic, non-motile and short rod-shaped bacterium, designated strain SCSIO 64248T, was isolated from the stony coral Fungia sp. collected from South China Sea. Phylogenetic analysis indicated that strain SCSIO 64248T belonged to the family Geminicoccaceae and showed the highest 16S rRNA gene similarities with the types of Marinimicrococcus flavescens (90.5%), Arboricoccus pini (90.2%) and Benzoalithermus flavus (89.8%). The whole genome of strain SCSIO 64248T was 4.9 Mbp with a 68.8mol% G+C content. It shared average amino acid identity (AAI) values of 52–56.2%, which is below the proposed AAI threshold at the genus level and when compared to the known species of Geminicoccaceae. Colonies of strain SCSIO 64248T are circular, pink and convex. It was able to grow in the range of 4–37 °C, at pH 6.0–10.0 and in the presence of up to 8.0% (w/v) NaCl concentration. The major cellular fatty acid (>9%) was summed feature 8, C19 : 0 cyclo ω8c and C16 : 0, and the sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified phospholipid. Data of polyphasic characteristics revealed that strain SCSIO 64248T represented a novel species of a new genus within the family Geminicoccaceae, for which the name Marinivivus gen. nov. is proposed with the type strain of the type species Marinivivus vitaminiproducens SCSIO 64248T (=MCCC 1K08013T=KCTC 92503T).

Most micro-organisms remain unculturable under standard laboratory conditions, limiting our understanding of microbial diversity and ecological interactions. One major cause of this uncultivability is the loss of access to essential cross-fed metabolites when bacteria are removed from their natural communities. During a bioprospecting campaign targeting actinomycetes of an Apis mellifera beehive, we identified five isolates (DT32, DT45T, DT55, DT59 and DT194) that required co-cultivation for growth recovery, suggesting a dependence on microbial interactions in their native habitat. Whole-genome sequencing and phylogenetic analysis positioned these isolates within a distinct lineage of Micromonosporaceae, separate from the five officially recognized clades of the Micromonospora genus. A combination of microscopic, chemotaxonomic and physiological characterizations further supported their uniqueness. Notably, they exhibited high auxotrophy, being unable to use all carbon sources tested, likely due to genome reduction (4.6 Mbp) compared to other Micromonosporaceae. Pangenomic comparisons with their closest Micromonospora relatives revealed gene losses in key metabolic pathways, including the glyoxylate bypass and the Entner–Doudoroff pathway, which may explain their metabolic reliance. These findings reveal a highly specialized, ecologically adapted lineage with deep evolutionary divergence and further support microbial interdependence isolation strategies to explore the microbial dark matter. We propose Melissospora conviva as a novel genus and species within the Actinomycetota phylum, with isolate DT45T as the representative type species and type strain, which has been deposited in public collections under the accession numbers DSM 117791 and LMG 33580.

A Gram-stain-negative, anaerobic and rod-shaped bacterium was isolated from gut of rainbow trout in Japan. The temperature range for the growth of 9N8T was 10–30 °C with an optimum at 20 °C. The organism produced acetate and butyrate when grown on AccuDia™ Gifu Anaerobic Medium broth, Modified. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain 9N8T was related to the genus Fusobacterium (<92.9% similarity) and formed a distinct phylogenetic lineage from existing genera within the family Fusobacteriaceae. Strain 9N8T has a genome size of 2.60 Mb. The genomic DNA G+C content was 29.4 mol%. Average amino acid identity values between strain 9N8T and strains in the family Fusobacteriaceae ranged from 39.2 to 57.5%. The major fatty acids of strain 9N8T were C14 : 0, C16 : 1 ω7c and C16 : 0. On the basis of the morphological, physiological, biochemical and genetic information, a novel genus and species, Piscibacter tructae, is proposed, with 9N8T (=NBRC 116745T=DSM 118263T) as the type strain.

A strictly aerobic, Gram-stain-negative, ovoid-shaped and non-motile bacterium, designated as strain MJ-SS7T, was isolated from tidal mudflat sediment collected at a macro-tidal clam farm in Gochang, Republic of Korea. Strain MJ-SS7T exhibited oxidase- and catalase-positive activities. Growth occurred at 20–37 °C (optimum: 30 °C), pH 6–8 (optimum: pH 7) and in the presence of 0–9% (w/v) NaCl (optimum: 3%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that MJ-SS7T belonged to the family Roseobacteraceae. Its closest relatives, based on sequence similarity, were Rhodophyticola porphyridii KACC 18805T (95.9%), Kangsaoukella pontilimi KCTC 72224T (95.8%) and Actibacterium pelagium JN33T (95.5%). The major fatty acids included summed feature 8 (C18:1  ω7c/C18:1  ω6c), C16:0, C16:0 2OH and C18:0. The major polar lipids consisted of phosphatidylglycerol, five unidentified phospholipids, four unidentified aminolipids, two unidentified aminophospholipids and four unidentified lipids. The major respiratory quinone was ubiquinone-10. The genome size was 5.20 Mb, with a DNA G+C content of 63.4 mol%, encoding 5,031 protein-coding genes, 3 rRNA genes and 46 tRNA genes. Comparative genomic analyses confirmed its novelty, with average nucleotide identity (<73%) and average amino acid identity (<70%) values below the species delineation thresholds. Based on polyphasic taxonomic data, strain MJ-SS7T represents a novel species of a new genus within the family Roseobacteraceae, for which the name Ovoidimarina sediminis gen. nov., sp. nov. is proposed. The type strain is MJ-SS7T (=KEMB 21436T=KCTC 8329T=JCM 36750T).

[Pasteurella] langaaensis has been found to be polyphyletic in relation to the type species Pasteurella multocida, as endicated by 16S rRNA gene sequence comparisons and a number of other comparisons (enclosing the genus name in brackets). 16S rRNA gene sequence-based phylogeny confirmed that [P.] langaaensis is unrelated to other members of Pasteurellaceae at the genus level and may be a candidate for a new genus with 95% 16S rRNA gene sequence identity to the closest related sequence belonging to the type strain of [Actinobacillus] rossii. The highest digital DNA–DNA hybridization value predicted from the whole-genomic sequence of the type strain of [P.] langaaensis was to the type strain of Acinobacillus suis with 26%, confirming a separate taxonomic status at the species level. The phylogenetic comparison of concatenated conserved protein sequences determined in a previous study showed a unique position of the taxon investigated, which qualified for the status of a new genus since the highest conserved protein sequence identity was found to [A.] rossii with 86%. A new genus with one species, Alitibacter langaaensis gen. nov., comb. nov., is proposed. The genus can be separated from other genera in the family Pasteurellaceae by from 1 up to 12 phenotypic characters, and it is monotypic from other genera with respect to analysis of 16S rRNA gene sequences as well as of predicted core genomic proteins. The type strain of Alitibacter langaaensis is F73T (=NCTC 11411T=CCUG 15566T=DSM 22999T=CPI 102678T=ATCC 43328T).

A novel Gram-stain-negative, motile and thermo-halophilic rod-shaped bacterium SMD15-11T was isolated from Seokmodo hot spring in Incheon, Republic of Korea. The strain grew at concentrations of 0.5–7% (w/v) NaCl (optimum at 3%), at pH 5.0–9.0 (optimum at 7.0) and in a temperature range of 30–60 °C (optimum at 50 °C). Strain SMD15-11T shared the highest 16S rRNA gene sequence percentage with Hahella chejuensis 96CJ10356T (92.5%). Both the phylogenetic and phylogenomic analyses showed that strain SMD15-11T clustered with Hahellaceae members, demonstrating its close relatedness to the type species of the Hahellaceae family. The genome-relatedness indices between strain SMD15-11T and other type species of the family Hahellaceae were in the ranges of 67.2–69.1% for average nucleotide identity, 59.3–62.8% for average amino acid identity and 15.9–24.8% for digital DNA–DNA hybridization, which were significantly below the cut-off values for the genus delineation. The genome comprised 3,444,746 bp with a G+C content of 60.1 mol%. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, two unidentified aminophospholipids and two unidentified lipids. The predominant fatty acids are C16:1  ω9c, C16:0, C18:1  ω9c and summed feature 3, comprising C16:1  ω7c/C16: 1  ω6c. The polyphasic taxonomic properties indicate that the strain represents a novel genus and species in the family Hahellaceae for which the name Thermohahella caldifontis gen. nov., sp. nov. is proposed. The type strain is SMD15-11T (=KCTC 8289T=NBRC 116488T).

An anaerobic, thermophilic methanogen, designated strain LWZ-6T, was isolated from the Shengli oil field, China. The cells of strain LWZ-6T were non-motile cocci, with a diameter of 0.5–1.0 µm, and formed aggregates. They reduced methanol and monomethylamine into methane, using H2 as an electron donor. Dimethylamine, trimethylamine and methanethiol, H2/CO2, formate, acetate, pyruvate, lactate and glucose were not used as energy sources. Strain LWZ-6T required yeast extract, acetate or CO2 as carbon sources. Strain LWZ-6T grew at 35–65 °C (optimum 55 °C), pH 5.0–8.0 (optimum 6.0–6.5) and 0–60 g l−1 NaCl (optimum 9 g l−1). The genome was 1.54 Mbp with a G+C content of 54.42 mol%. Strain LWZ-6T shared 83.54% 16S rRNA gene sequence identity with Infirmifilum lucidum strain 3507LTT in the class Thermoprotei. Phylogenetic analysis based on the 16S rRNA gene, along with phylogenomic analysis, indicated that strain LWZ-6T belonged to the candidate class ‘Candidatus Methanomethylicia’, which lacks cultivated representatives. Based on these findings, a new species within a new genus, Methanosuratincola petrocarbonis gen. nov., sp. nov., is proposed for LWZ-6T (=CCAM 1872T=JCM 39528T). In addition, we propose the Methanosuratincolia class. nov. for candidate class ‘Ca. Methanomethylicia’ represented by Methanosuratincolaceae fam. nov. and Methanosuratincolales ord. nov. within the phylum Thermoproteota.