An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids

Streptomyces odontomachi sp. nov., a novel actinobacterium with antimicrobial potential isolated from ants (Odontomachus simillimus Smith, 1858)

A new actinomycete strain, ODS25T, exhibited antimicrobial activity against Bacillus subtilis, Kocuria rhizophila, Staphylococcus aureus, Staphylococcus epidermidis, Candida albicans, Candida tropicalis, was isolated from the ants, Odontomachus simillimus, collected from National Science Museum Thailand, Pathum Thani, Thailand. A polyphasic technique was used to characterize the taxonomic position. The morphological and chemotaxonomic properties of the strain are typical of members of the genus Streptomyces. Strain ODS25T contained ll-diaminopimelic and glucose in the whole-cell hydrolysate. The major cellular fatty acids were iso-C16:0, iso-C15:0, and anteiso-C15:0. The polar lipids were phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, three unidentified amino lipids and two unidentified lipids. The menaquinones were MK-9(H6), MK-9(H8), and MK-9(H4). The G + C content of the genomic DNA was 71.3%. The 16 S rRNA gene sequence analysis demonstrated that the strain had the highest similarity to Streptomyces lusitanus NBRC 13464T (98.07%) but shared the phylogenetic neighbour with Streptomyces sulfonofaciens JCM 5069T. Both digital DNA-DNA hybridization and average nucleotide identity values among strain ODS25T and its associated Streptomyces type strains fell within the values lower than the threshold for differentiate the strain to the same species. Based on the phenotypic characteristics and genotypic distinctiveness, strain ODS25T is considered a novel species within the genus Streptomyces, for which the name Streptomyces odontomachi sp. nov. is proposed. The type strain is ODS25T (=TBRC 16204T=NBRC 115862T).

Streptomyces yaizuensis sp. nov., a berninamycin C-producing actinomycete isolated from sponge

While screening for antibiotics in a marine sample, we discovered a berninamycin C-producing actinomycete, designated YSPA8T, isolated from a sponge. A polyphasic approach was used to determine the taxonomic position of the strain. Strain YSPA8T formed sympodially branched aerial mycelia that ultimately segment into chains of spores. Comparative and phylogenetic analyses of the 16S rRNA gene sequence showed that strain YSPA8T were closely related to Streptomyces clavuligerus ATCC 27064T (99.66%), Streptomyces amakusaensis NRRL B-3351T (98.69%), Streptomyces inusitatus NBRC 13601T (98.48%), and 'Streptomyces jumonjinensis' JCM 4947 (98.41%). The phylogenetic tree using the 16S rRNA gene sequences, and both phylogenomic trees suggested that the closest relative of strain YSPA8T was S. clavuligerus ATCC 27064T. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between strain YSPA8T and S. clavuligerus ATCC 27064T were 84.1%, 28.9%, and 82.5%, respectively, which were below the thresholds of 95%, 70%, and 95% for a prokaryotic conspecific assignment. The G + C of the strain YSPA8T was 72.6%. Whole-cell hydrolysates of strain YSPA8T contained LL-diaminopimelic acid. The predominant menaquinones were MK-9(H6) (49%) and MK-9(H8) (48%), and the major fatty acids were C16:0 (26.8%), C16:1 ω7c/ω6c (17.2%), iso-C16:0 (16.0%), and iso-C15:0 (12.5%). The major phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, and other unidentified phospholipids. Based on the phenotypic, phylogenetic, genomic, and chemotaxonomic data, strain YSPA8T represents a novel species of the genus Streptomyces, and the proposed name for this species is Streptomyces yaizuensis sp. nov. The type strain is YSPA8T (=NBRC 115866T = TBRC 17196T).

Comparative genomic analyses of the genus Robertmurraya and proposal of the novel species Robertmurraya mangrovi sp. nov., isolated from mangrove soil

A Gram-positive, aerobic, motile, rod-shaped bacterial strain, designated 31A1RT, was isolated from the mangrove soil of Xilian village, Zhanjiang, China. Strain 31A1RT thrives at temperatures ranging from 15 to 45 °C (optimum at 30 °C), pH 6.5-10 (optimum at 8.5), and in the presence of 0-5% (w/v) NaCl (optimum at 1.5%). The strain shares the highest 16S rRNA gene sequence similarity with Robertmurraya crescens (97.24%) and Robertmurraya dakarensis (97.18%). The complete genome of strain 31A1RT spans 4.71 Mbp with a genomic DNA G + C content of 35.9 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain 31A1RT and type strains of other species of the genus Robertmurraya were 71.24-72.11% and 19.90-21.40%, respectively. The amino acid identity values and percentage of conserved proteins ranged from 66.94 to 68.10% and from 58.34 to 61.62%, respectively, aligning with intrageneric cutoff values. The major fatty acids (≥ 5.0%) were iso-C14:0 (5.0%), iso-C15:0 (41.4%), iso-C16:0 (12.6%), C16:1ω7c alcohol (12.2%), and iso-C17:1 ω10c (6.5%). The polar lipids profile was mainly composed of diphosphatidyl glycerol, phosphatidyl glycerol, and phosphatidyl ethanolamine. We also profiled the pan-genome and metabolic features of genomic assemblies of strains belonging to the genus Robertmurraya, which indicated functional capacities and metabolic similarities. Consequently, we propose that strain 31A1RT represents a new species in the genus Robertmurraya, for which the name Robertmurraya mangrovi sp. nov. is proposed, with the type strain being 31A1RT (= GDMCC 1.4378T = JCM 36937T).

Investigation on taxonomy, secondary metabolites and antibacterial activity of Streptomyces sediminicola sp. nov., a novel marine sediment-derived Actinobacteria

BACKGROUND

Marine actinomycetes, especially Streptomyces, are recognized as excellent producers of diverse and bioactive secondary metabolites on account of the multiplicity of marine habitations and unique ecological conditions, which are yet to be explored in terms of taxonomy, ecology, and functional activity. Isolation, culture and genome analysis of novel species of Streptomyces to explore their potential for discovering bioactive compounds is an important approach in natural product research.

RESULTS

A marine actinobacteria, designated strain SCSIO 75703 T, was isolated, and the potential for bioactive natural product discovery was evaluated based on genome mining, compound detection, and antimicrobial activity assays. The phylogenetic, phenotypic and chemotaxonomic analyses indicate that strain SCSIO 75703 T represents a novel species in genus Streptomyces, for which the name Streptomyces sediminicola sp. nov. is proposed. Genome analysis revealed the presence of 25 secondary metabolite biosynthetic gene clusters. The screening for antibacterial activity reveals the potential to produce bioactive metabolites, highlighting its value for in-depth exploration of chemical constituents. Seven compounds (1-7) were separated from the fractions guided by antibacterial activities, including three indole alkaloids (1-3), three polyketide derivatives (4-6), and 4-(dimethylamino)benzoic acid (7). These primarily antibacterial components were identified as anthracimycin (4), 2-epi-anthracimycin (5) and β-rubromycin (6), presenting strong antibacterial activities against Gram-positive bacteria with the MIC value ranged from 0.125 to 16 μg/mL. Additionally,, monaprenylindole A (1) and 3-cyanomethyl-6-prenylindole (2) displayed moderate inhibitory activities against α-glucosidase with the IC50 values of 83.27 and 86.21 μg/mL, respectively.

CONCLUSION

Strain SCSIO 75703 T was isolated from marine sediment and identified as a novel species within the genus Streptomyces. Based on genomic analysis, compounds isolation and bioactivity studies, seven compounds were identified, with anthracimycin and β-rubromycin showing significant biological activity and promising potential for further applications.

Sporosarcina hypophthalmichthys sp. nov. Isolated From Gastrointestinal Tract of Fish Hypophthalmichthys molitrix (Valenciennes, 1844)

A rod-shaped, motile, Gram-stain-positive bacterial strain RKN2T, was isolated from gut of silver carp (Hypophthalmichthys molitrix) residing in Gobindsagar reservoir, Himachal Pradesh, India. Having the greatest sequence similarity to Sporosarcina koreensis F73T (98.51%), Sporosarcina luteola Y1T (98.4%) and Sporosarcina aquimarina SW28T (98.36%), the 16S rRNA gene phylogeny confirmed the belonging of strain RKN2T to genus Sporosarcina. Digital DNA-DNA hybridization values were 21.7%, 20.6%, and 19.2%, and average nucleotide identity values were 76.42%, 80.16%, 76.51%, of strain RKN2T with Sporosarcina koreensis F73T, Sporosarcina luteola Y1T, and Sporosarcina aquimarina SW28T, respectively. The genomic analysis of strain RKN2T showed various biological properties including nitrate reduction, genes responsible for carbohydrate-active enzymes production, antimicrobial compounds, as well as potential metabolism of aromatic compounds and heavy metals. G+C composition of RKN2T genome was 52.7%. This strain can grow in temperatures between 10°C and 40°C (optimum, 28°C-30°C), NaCl concentrations up to 6.0% (w/v), and 6.0-8.0 (optimum, 6.5-7.5) pH range. MK-7 was the dominant respiratory quinone, A-4 type cell wall peptidoglycan was present with anteiso-C15:0, iso-C15: 0, and anteiso-C17:0 being the major fatty acids and Lys-Glu being main amino acids. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the strain RKN2T's three main polar lipids. The strain is a novel species under genus Sporosarcina based on polyphasic approach and the name Sporosarcina hypophthalmichthys sp. nov. is given for strain RKN2T. RKN2T is a type strain (= MCC 4365T = JCM34522T = CCM9112T).

Isolation and characterization of two new species, Hymenobacter mellowenesis sp. nov. and Hymenobacter aranciens sp. nov., from soil

Strains M29T and ASUV-10-1T, which are aerobic, non-flagellated, and Gram-stain-negative, were isolated from soil samples collected in Inje (37°57'49.1"N 128°19'53.7"E) and Cheonan City (36°48'47.1"N 127°05'22.4"E), South Korea. Phylogenetic analyses based on rRNA gene sequences revealed that strains M29T and ASUV-10-1T form a distinct branch within the family Hymenobacter (order Cytophagales, class Cytophagia). Strain M29T is most closely related to Hymenobacter rubidus DG7BT with a 16 S rRNA gene sequence similarity of 97.05%. Strain ASUV-10-1T shows closest genetic similarity to Hymenobacter frigidus B1789T (96.42%), Hymenobacter jeongseonensis BT683T (95.97%), and Hymenobacter terricola 3F2TT (95.65%). The optimal growth conditions for these strains are pH 7.0, no NaCl, and a temperature of 25 °C. The dominant cellular fatty acids identified in these strains are iso-C15:0, anteiso-C15:0, and Summed Feature 3 (C16:1ω 7c / C16:1ω 6c). Both strains predominantly contain MK-7 as the respiratory quinone. The major polar lipids in strains M29T and ASUV-10-1T are phosphatidylethanolamine, aminophospholipid, and aminolipid. Based on biochemical, chemotaxonomic, and phylogenetic data, it is evident that M29T and ASUV-10-1T represent new species within the genus Hymenobacter. The new species were classified based on biochemical and chemotaxonomic characteristics. The taxonomic classification of these species was conducted following the guidelines and protocols outlined in Bergey's Manual of Systematic Bacteriology. We followed the methods for determining physiological and biochemical characteristics, as well as chemotaxonomic markers such as fatty acid profiles, quinone types, and polar lipid compositions. We also compared with the results of carbohydrate utilization and enzyme activities results [Bergey 1994]. Therefore, we propose the names Hymenobacter mellowenesis for strain M29T (= KCTC 102056T = NBRC 116578T) and Hymenobacter aranciens for strain ASUV-10-1T (= KCTC 92969T = NBRC 116575T).

Acinetobacter corruptisaponis sp. nov., Isolated from a Spoiled Bath Lotion

Strain DM2021935T representing a novel Acinetobacter species was isolated from a spoiled bath lotion in Guangdong, China. Based on 16S rRNA gene phylogenetic analysis, strain DM2021935T was closely related to 'Acinetobacter thutiue' VNH17T, Acinetobacter junii CIP 64.5 T, and Acinetobacter tibetensis Y-23 T. Cells of strain DM2021935T were Gram-stain-negative, non-spore-forming, strictly aerobic, catalase-positive, oxidase-negative, α-hemolytic, and non-motile. Strain DM2021935T exhibited growth in 1-3% (w/v) NaCl at temperatures ranging from 4 to 37 °C and tolerated pH levels from 6.0 to 8.0. The predominant fatty acids in strain DM2021935T are C12:0, C16:0, C18:1 ω9c, and summed feature 3. Polar lipid profiles included glycolipids, phospholipids, phosphatidylethanolamine, and phosphatidyl-N-methylethanolamine. The identified respiratory quinones were ubiquinone Q-8 and Q-9. The genomic size of DM2021935T comprised 4.15 Mb, consisting of one chromosome (3,827,633 bp) and two plasmids (241,357 and 83,010 bp). The G + C content was 41.8%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain DM2021935T and phylogenetically related type strains were below the species delineation thresholds (72.2-95.4, 53.1-87.0, and 20.4-66.4%, respectively). AntiSMASH analysis identified four gene clusters: non-ribosomal peptide synthetase, non-alpha poly-amino group acids, YcaO cyclodehydratase, and aryl polyene biosynthesis. Based on genotypic data, strain DM2021935T represents a novel species within the genus Acinetobacter. The proposed name for the novel species is Acinetobacter corruptisaponis sp. nov. (type strain DM2021935T = KCTC 92772 T = GDMCC 1.3703 T).

Phenotypic and Genomic Characterization of a Sulfate-Reducing Bacterium Pseudodesulfovibrio methanolicus sp. nov. Isolated from a Petroleum Reservoir in Russia

The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69T. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0-4.0% (w/v) NaCl, at pH 6.5, and at 23-28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H2 and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H2/CO2/acetate for sulfate reduction. The genome size of the type strain 5S69T was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69T ((VKM B-3653T = KCTC 25499T) to a new species within the genus Pseudodesulfovibrio, is suggested, with the proposed name Pseudodesulfovibrio methanolicus sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water.

Methylobacterium flocculans sp. nov., a Floc-Forming Bacterium Isolated from Aquaculture Ponds

Strain FF17T, a Gram-negative, obligate aerobic, motile, pink-pigmented, and methylotrophic bacterium, was selected for a polyphasic taxonomic investigation due to its capacity for aggregation, or floc formation. The predominant respiratory quinone observed was Q-10, accounting for 83.36% of the total, while the major fatty acids were summed feature 8 (18:1 w6c and/or 18:1 w7c). The major polar lipids included Diphosphatidylglycerol (DPG), phosphatidylglycerol, phosphatidylethanolamine (PE), phosphatidylinositol (PI), and one unknown polar lipid. Phylogenetic analysis showed that strain FF17T was hithermost related to Methylobacterium goesingense iEII3T (99.86%), M. gossipiicola Gh-105 T (99.22%), M. adhaesivum AR27T (98.92%), and M. iners 5317S-33 T (97.27%) based on 16S rRNA gene sequence similarity. A 5,735,273-bp chromosome and six plasmids make up the genome, making it larger than the genomes of the other four Methylobacterium species described above. The digital DNA-DNA hybridization and average nucleotide identity values between strain FF17T and the reference strains were 21.90-28.70 and 77.39-85.04%, respectively. Strain FF17T had a genome DNA G + C content of 68.5 mol%. The analysis of genomes indicated that cellulose apparently plays an important character in the aggregation of Methylobacterium species. Genome annotation revealed the presence of genes involved in assimilatory/dissimilatory nitrate reduction and ammonia assimilation. In conclusion, Strain FF17T is identified as a new species in the Methylobacterium genus, based on analyses of genomics, phylogeny, biochemistry, and fatty acids, and the name Methylobacterium flocculans sp. nov. is proposed. The type strain is FF17T (= MCCC 1K08738T = KCTC 8320 T).

Chromobacterium indicum sp. nov., a Pigment-Producing Bacterium Isolated from Soil

A purple colony, designated as TRC1.1.SA was isolated from a tea garden soil sample. It was a Gram-negative, rod-shaped, non-spore-forming and motile bacterium. The strain TRC1.1.SAT grew aerobically at temperatures 15-37 ℃ and pH levels 5.0-9.0. It showed both oxidase and catalase activity. The 16S rRNA gene sequence blast analysis revealed identity with the members of the genus Chromobacterium. The maximum identity was with the type strains of species Chromobacterium piscinae CCM 3329T (99.8%), C. vaccinii MWU205T (99.7%), and C. violaceum ATCC 12472T (98.7%). However, the average nucleotide identity (ANI) of the genome sequence showed less than 96% similarity with all species of the genus Chromobacterium. Further, digital DNA-DNA hybridization (dDDH) revealed the highest identity of 63.4% with its phylogenetic relative C. piscinae CCM 3329T. The G + C content of the strain was 63.9%. The major polar lipids identified were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphoglyceraldehyde (PG). Fatty acid analysis showed C16:0, C16:1ω7c, C17:0 cyclo, and C18:1ω7c as the major fatty acids. RAST and antiSMASH analyses of the genome revealed the presence of a biosynthetic gene cluster (BGC) involved in the production of violacein pigment, as observed for type species C. violaceum ATCC 12472T. Considering the phenotypic differences and genomic identity, strain TRC1.1.SAT is assigned as a novel species of the genus Chromobacterium, for which the name Chromobacterium indicum is proposed. The type strain of prospective species is designated as TRC1.1.SAT (= MTCC 13391T; JCM 36723T; = KCTC 8324T).

Sphingomonas rustica sp. nov. and Sphingomonas agrestis sp. nov., novel carotenoid-producing bacterial species isolated from farm soil

Two yellow-pigmented novel strains, designated HF-S3T and HF-S4T, were isolated from farm soil in Paju, Republic of Korea. Cells of the two strains are characteristically Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and rod-shaped. Strain HF-S3T grew at 10-37 °C, while HF-S4T grew at 15-35 °C. Both strains grew at pH 5.0-12.0 and in NaCl concentrations (w/v) of 0-2.0%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that HF-S3T and HF-S4T belong to the genus Sphingomonas, with HF-S3T exhibiting 97.7, 97.6 and 97.4% similarity to Sphingomonas cannabina DM2-R-LB4T, Sphingomonas leidyi DSM 4733T and Sphingomonas canadensis FWC47T, respectively. Strain HF-S4T displayed 97.9, 97.7 and 97.6% similarity to Sphingomonas psychrotolerans Cra20T, Sphingomonas gei ZFGT-11T and Sphingomonas naasensis KIS18-15T, respectively. The DNA G+C contents of HF-S3T and HF-S4T were 67.0 and 66.5 mol%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values among the novel and related type strains were 20.2-28.2% and 75.9-84.3%, respectively. They all contained C14:0 2-OH and C16:0, summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) as the major fatty acids and ubiquinone-10 as the predominant respiratory quinone. Strains HF-S3T and HF-S4T were found to produce carotenoid-type pigments. Based on polyphasic taxonomic analysis, the new isolates ostensibly represent two novel species of the genus Sphingomonas, with the proposed names Sphingomonas rustica sp. nov. and Sphingomonas agrestis sp. nov. for strains HF-S3T and HF-S4T, respectively. The S. rustica and S. agrestis type strains are HF-S3T (=KACC 23554T =TBRC 18352T) and HF-S4T (=KACC 23386T =TBRC 17899T), respectively.

Amycolatopsis melonis sp. nov., a novel protease-producing and cellulose-degrading actinobacterium isolated from soil

A novel protease-producing and cellulose-degrading actinobacterium, designated strain NEAU-NG30T, was isolated from a melon rhizosphere soil sample collected in Harbin, Heilongjiang Province, China, and established its status using a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NEAU-NG30T was closely related to Amycolatopsis bullii DSM 45802T (98.7%) and Amycolatopsis vancoresmycina DSM 44592T (98.3%). The phospholipid profile contained diphosphatidylglycerol, phosphatidyl methylethanolamine, phosphatidylethanolamine and phosphatidylinositol. The diagnostic sugars in cell hydrolysates were determined to be galactose and arabinose. Cell walls contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C15:0 and iso-C16:0. Meanwhile, genome analysis of sequences revealed a genome size of 9 338 250 bp and a DNA G+C content of 71.6%. In addition, the average nucleotide identity values and the level of digital DNA-DNA hybridization between strain NEAU-NG30T and its reference strains fall below the thresholds typically used for delineating prokaryote species. According to phenotypic, chemotaxonomic and genotypic studies, it is indicated that strain NEAU-NG30T is considered to be a novel species of the genus Amycolatopsis, for which the name Amycolatopsis melonis sp. nov. is proposed, with NEAU-NG30T (=MCCC 1K08677T=JCM 35654T) as the type strain.

Description of Rhodobacter flavimaris sp. nov. and proposal of the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter as synonyms of Rhodobacter

Two Gram-stain-negative, aerobic, ovoid to short rod-shaped bacterial strains, designated as WL0062T and WL0115, were isolated from coastal zone of the Yellow Sea, Jiangsu Province, PR China, respectively. Strain WL0062T grew optimally at 28 °C, pH 7.0-8.0 and with 1.0-3.0% (w/v) NaCl. Strain WL0115 grew optimally at 28 °C, pH 6.0-7.0 and with 1.0-3.0% (w/v) NaCl. In the bac120 tree, strains WL0062T and WL0115 clustered together with Sedimentimonas flavescens B57T. The respiratory quinone of both strains was ubiquinone-10. The major polar lipids of both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, glycolipid, phosphatidylmonomethylethanolamine, and one unidentified polar lipid. The major fatty acids of strain WL0062T were summed features 8 (C18 : 1  ω6c and/or C18 : 1  ω7c). The major fatty acids of strain WL0115 were summed features 8 (C18 : 1  ω6c and/or C18 : 1  ω7c), C18 : 0, iso-C17 : 1  ω5c and C20 : 4  ω6/9/12/15c (arachidonic acid). The G+C content of genomic DNA of strains WL0062T and WL0115 was 64.0 mol% in both of them. Combined with the analysis of average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization, strain WL0062T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter flavimaris sp. nov is proposed. The type strain is WL0062T (=MCCC 1K06014T=JCM 34676T=GDMCC 1.2427T). Strain WL0115 (=MCCC 1K07531=JCM 35568=GDMCC 1.3088) should belong to the same species as Sedimentimonas flavescens B57T. In addition, on the basis of phylogenomic relationship and phenotypical characteristics, the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter are proposed as synonyms of Rhodobacter.

Polymorphospora lycopeni sp. nov., a lycopene-producing actinomycetes isolated from lakeside soil sample of Baiyangdian

A novel actinomycetes producing lycopene, designated HBU208002T, was isolated from a lakeside soil sample collected in Baiyangdian, located in Xiong'an New Area of China, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the strain HBU208002T fell within the genus Polymorphospora and was closely related to Polymorphospora rubra JCM 14904T (99.73% identity). However, the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and average amino acid identity (AAI) values between the strain HBU208002T and P. rubra JCM 14904T were 91.78, 44.7 and 91.6%, respectively, which were lower than the ANI (95-96%), DDH (>70%) and AAI (>95%) thresholds of prokaryotic microbial defined species. The predominant fatty acids of the strain HBU208002T were iso-C16:0, C17:1 ω8c. The menaquinones of the strain HBU208002T were MK-8(H8) and MK9(H4), while those of P. rubra JCM 14904T were MK-10(H6), MK-10(H4), MK-9(H6) and MK-9(H4). Meanwhile, some phenotypic characterizations and antibacterial activities distinguished the strain HBU208002T from P. rubra JCM 14904T. The strain HBU208002T exhibited inhibitory effects on Fusarium graminearum, Fusarium verticillioides and Botrytis cinerea, but P. rubra JCM 14904T had no activity. Therefore, the strain HBU208002T should be assigned as representing a novel species of the genus Polymorphospora, for which the name Polymorphospora lycopeni was proposed. The type strain is HBU208002T (=KCTC49833T = GDMCC4.236T).

Paracoccus actinidiae sp.nov., a novel bacterium isolated from kiwi tree rhizosphere soil

Strain M09T was isolated from the rhizoshere of kiwi fruit trees from an orchard located in Fangshan, Beijing, PR China (39° 49' 25.1″ N, 116° 4' 44.5″ E,). It is a short rod-shaped, Gram-stain-negative, facultatively anaerobic bacterium that tests positive for both oxidase and catalase. The strain exhibited growth within the temperature range of 15-45 °C (optimal growth at 30 °C) and the pH range of 4.0-10.0 (optimal growth at pH 7.0) and without NaCl. It also grew in a sodium chloride-free nutrient agar (NA) medium. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that M09T represents a member of the genus Paracoccus and shares high similarity with Paracoccus everestensis S8-55T (98.46%) and Paracoccus aerius 011410T (97.58%). The average nucleotide identity values between M09T and P. everestensis S8-55T, P. aerius 011410T, Paracoccus marinaquae X HP0099T and Paracoccus fontiphilus MVW-1T were 95.56, 84.51, 79.83 and 83.68%, respectively. The digital DNA-DNA hybridisation values between between M09T and P. everestensis S8-55T, P. aerius 011410T, P. marinaquae X HP0099T and P. fontiphilus MVW-1T were 56.40, 29.30, 21.60 and 28.60%, respectively. The major fatty acids identified were C10 : 0 3-OH (51.8%) and C18 : 1ω7c (35.5%). The major respiratory quinone was Q-10, with Q-8 present as a minor component. Polar lipids were mainly comprised of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE). Genome sequencing revealed that the strain has a DNA G+C content of 64.31 mol%. On the basis of this comprehensive taxonomic characterisation data, M09T represents a novel species within the genus Paracoccus and has been named Paracoccus actinidiae sp. nov. The type strain is designated as M09T (=GDMCC 1.4157T=KCTC 8143T).

Halostreptopolyspora alba gen. nov., sp. nov., a halophilic actinobacterium isolated from saline soil of Xinjiang, Northwest of China

A Gram-stain-positive, aerobic, moderate halophilic actinobacterium, designated strain YIM 96095T, was isolated from a saline soil sample collected from Aiding Lake, Xinjiang, North-western China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate belonged to the family Nocardiopsidaceae, formed a distinct subclade, and was most closely related to Lipingzhangella halophila DSM 102030T and Allosalinactinospora lopnorensis DSM 45697T with sequence identity values of 95.8 and 95.1%, respectively. Optimal growth occurred at 37 °C, pH 7.0-8.0 and with 5-16% (w/v) NaCl, with well-developed, non-fragmented substrate mycelia and single-, double-, or triple-wrinkled spore(s) on the mature aerial hyphae. The chemical analysis presented meso-diaminopimelic acid as the diagnostic diamino acid of the cell-wall peptidoglycan, and glucose, galactose and rhamnose as the major whole-cell sugars, and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids and unidentified glycolipid. The menaquinones were MK-10(H8), MK-10(H6) and MK-9(H10). Its G+C content was 69.7 mol% in the determined genome sequence. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, a novel genus and species named Halostreptopolyspora alba gen. nov., sp. nov. is proposed for isolate YIM 96095T (=KCTC 49266T=CGMCC 4.7636T).

Actinoplanes kirromycinicus sp. nov., isolated from soil

A novel actinomycete, designated as TPMA0078T, was isolated from a soil sample collected in Shinjuku, Tokyo, Japan. 16S rRNA gene sequence analysis indicated that strain TPMA0078T belongs to the genus Actinoplanes and is closely related to Actinoplanes regularis IFO 12514T (99.86% 16S rRNA gene sequence similarity). The spores of strain TPMA0078T were motile, and the sporangia were cylindrical. The diamino acids in the cell wall peptidoglycan of strain TPMA0078T were meso-diaminopimelic acid and 3OH-meso-diaminopimelic acid. Whole-cell sugars were glucose and mannose, with galactose as a minor component. The major cellular fatty acids identified were iso-C15:0, iso-C16:0, and anteiso-C17:0. The predominant menaquinone was MK-9(H4), and the principal polar lipid was phosphatidylethanolamine. These chemotaxonomic properties of strain TPMA0078T were consistent with those of Actinoplanes. Meanwhile, digital DNA-DNA hybridization and average nucleotide identity values showed low relatedness between strain TPMA0078T and A. regularis NBRC 12514T. Furthermore, several phenotypic properties of strain TPMA0078T distinguished it from those of closely related species. Based on its genotypic and phenotypic characteristics, strain TPMA0078T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes kirromycinicus sp. nov. is proposed. The type strain is TPMA0078T (=NBRC 116422T = TBRC 18262T).

Flavobacterium capsici sp. nov., isolated from the rhizospheric soils of bell pepper (Capsicum annuum L.)

Two separate bacterial strains, PMTSA4T and PMR2A8, were isolated from the rhizospheric soils of bell pepper plants grown in a plant nursery. These strains are Gram-negative, non-motile and rod-shaped and grow in aerobic conditions. They exhibit a positive reaction for catalase activity but negative results for oxidase activity. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the strains PMTSA4T and PMR2A8 are closely related to Flavobacterium piscinae ICH-30T (95.6%, respectively), Flavobacterium ahnfeltiae 10Alg 130T (95.5%) and Flavobacterium maris KMM 9535T (95.3%), aligning them within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identities (ANIs) of the whole-genome sequences for the two strains and related Flavobacterium species were significantly below the established thresholds for prokaryotic species delineation (<70% for dDDH and <95% for ANI). The observed values were as follows: Flavobacterium aquatile LMG 4008T (dDDH: 19.8% and ANI: 75.5%), F. piscinae ICH-30T (dDDH: 18.6% and ANI: 73.3%) and F. stagni WWJ 16T (dDDH: 18.5% and ANI: 72.0%). The strains have genome sizes of 3 068 185 bp and 3 068 330 bp, with a G+C content of 32.5 mol%. In phenotypic characterization, the new strains grew at 10-35 °C and tolerated up to 4% NaCl at pH 5-9 (optimum pH 8). The predominant cellular fatty acids were observed to be iso-C15:0, iso-C17:0 3-OH and iso-C15:0 3-OH. Menaquinone-6 was the predominant quinone. Considering the results from phenotypic, chemotaxonomic, phylogenetic and genomic analyses, it is proposed that the strains PMTSA4T and PMR2A8 represent a novel species within the genus Flavobacterium.

Yoonia algicola sp. nov., Yoonia rhodophyticola sp. nov. and Yoonia phaeophyticola sp. nov., isolated from marine algae

Three Gram-stain-negative, strictly aerobic, non-motile, oxidase- and catalase-positive, short-rod-shaped bacteria, designated as strains G8-12T, SS1-5T and BS5-3T, were isolated from marine algae in South Korea. Strain G8-12T exhibited optimal growth at 20-25 °C, pH 8.0 and 2.0-2.5% (w/v) NaCl, while strains SS1-5T and BS5-3T grew optimally at 25 °C, pH 7.0 and 1.5% NaCl. All strains contained ubiquinone-10 as the sole respiratory quinone, with phosphatidylglycerol and phosphatidylcholine as major polar lipids, and C18 : 1  ω7c and C16 : 0 as major fatty acids (>5 %); C18 : 1  ω7c 11-methyl and C18 : 1 2-OH were additionally identified as major fatty acids in strain SS1-5T. The genomic DNA G+C contents were 57.0, 58.3 and 56.4% for strains G8-12T, SS1-5T and BS5-3T, respectively. Strains G8-12T, SS1-5T and BS5-3T exhibited less than 74.8% average nucleotide identity (ANI) and 19.7% digital DNA-DNA hybridization (dDDH) values with each other, indicating that they represent different species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains G8-12T, SS1-5T and BS5-3T form distinct phylogenetic lineages within the genus Yoonia. Relative to other closely related Yoonia species, these strains exhibited ANI and dDDH values below 83.5 and 26.9%, respectively, suggesting that they constitute novel species within the genus Yoonia. Based on their phenotypic, chemotaxonomic and phylogenetic characteristics, strains G8-12T, SS1-5T and BS5-3T represent three novel species of the genus Yoonia, for which the names Yoonia algicola sp. nov. (G8-12T=KACC 22753T=JCM 35790T), Yoonia rhodophyticola sp. nov. (SS1-5T=KACC 22649T=JCM 35753T) and Yoonia phaeophyticola sp. nov. (BS5-3T=KACC 22648T=JCM 35751T) are proposed, respectively.

Extensive genomic study characterizing three Paracoccaceae populations and revealing Pseudogemmobacter lacusdianii sp. nov. and Paracoccus broussonetiae sp. nov

Bacteria within the family Paracoccaceae show promising potential for applications in various fields, garnering significant research attention. Three Gram stain-negative bacteria, strains CPCC 101601T, CPCC 101403T, and CPCC 100767, were isolated from diverse environments: freshwater, rhizosphere soil of Broussonetia papyrifera, and the phycosphere, respectively. Analysis of their 16S rRNA gene sequences, compared with those in the GenBank database, indicated that they belong to the family Paracoccaceae, with nucleotide similarities of 92.5%-99.9% to all of the Paracoccaceae members with valid taxonomic names. Phylogenetic studies based on 16S rRNA gene and whole-genome sequences identified CPCC 101601T as a member of the genus Pseudogemmobacter, CPCC 101403T belonging to the genus Paracoccus, and CPCC 100767 as part of the genus Gemmobacter. Notably, genomic analysis using average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; <70%) with their closely related strains suggested that CPCC 101601T and CPCC 101403T represent new species within their respective genera. Conversely, CPCC 100767 exhibited high ANI (98.5%) and dDDH (87.4%) values with Gemmobacter fulvus con5T, indicating it belongs to this already recognized species. The in-depth genomic analysis revealed that strains CPCC 101601T, CPCC 101403T, and CPCC 100767 harbor key genes related to the pathways for denitrifying, MA utilization, and polyhydroxyalkanoate biosynthesis. Moreover, genotyping and phenotyping analysis confirmed that strain CPCC 100767 has the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid, whereas CPCC 101601T can only perform the former bioprocess.IMPORTANCEBased on polyphasic taxonomic study, two new species, Pseudogemmobacter lacusdianii and Paracoccus broussonetiae, affiliated with the family Paracoccaceae were identified. This expands our understanding of the family Paracoccaceae and provides new microbial materials for further studies. Modern genomic techniques such as average nucleotide identity and digital DNA-DNA hybridization were utilized to determine species affiliations. These methods offer more precise results than traditional classification mainly based on 16S rRNA gene analysis. Beyond classification of these strains, the research delved into their genomes and discovered key genes related to denitrification, MA utilization, and polyhydroxyalkanoate biosynthesis. The identification of these genes provides a molecular basis for understanding the environmental roles of these strains. Particularly, strain CPCC 100767 demonstrated the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid. These bioprocess capabilities are of significant practical value, such as in agricultural production for use as biofertilizers or biostimulants.

Flagellimonas algarum sp. nov., isolated from dense mats of filamentous algae

A novel Gram-stain-negative, strictly aerobic, rod-shaped, light-yellow-pigmented, and chemo-organoheterotrophic bacterium, designated DF-77T, was isolated from dense mats of filamentous algae collected in March 2004 at Okinawa in Japan. The microorganism grew at 0-2.0% NaCl concentrations (w/v), pH 6.0-9.0, and 20-30 °C. The 16S rRNA gene sequence-based phylogenetic tree demonstrated that the strain DF-77T is a novel member of the family Flavobacteriaceae and was greatly related to Flagellimonas nanhaiensis SM1704T with sequence similarity of 95.5%. The main fatty acids were iso-C15:1 G, iso-C15:0, and iso-C17:0 3-OH, and the only isoprenoid quinone was menaquinone-6. The dominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phosphoaminolipid, and four unidentified lipids. The genome size of strain DF-77T was 3.60 Mbp with a DNA G + C content of 47.5%. The average nucleotide identity (ANI) value between the genomes of strain DF-77T and its closely related species was 69.8-70.7%. The digital DNA - DNA hybridization (dDDH) value of strain DF-77T with the strain of F. nanhaiensis SM1704T was 16.8%. The genome of the strain DF-77T revealed that it encoded several genes involved in bio-macromolecule degradation, indicating a high potential for producing industrially useful enzymes. Consequently, the strain is described as a new species in the genus Flagellimonas, for which the name Flagellimonas algarum sp. nov., is proposed with the type strain DF-77T (= KCTC 72791T = NBRC 114251T).

Discovery of two new actinobacteria, Micromonospora palythoicola sp. nov. and Streptomyces poriticola sp. nov., isolated from marine invertebrates

Marine invertebrates represent an underexplored reservoir for actinobacteria, which are known to synthesize novel bioactive compounds. This study isolated 37 actinobacterial strains from five distinct marine invertebrate hosts, namely Chondrilla australiensis, Palythoa sp., Favia sp., Porites lutea, and Acropora cervicornis, while no strains were obtained from Lissoclinum sp. and Lithophyllon sp. These isolates were taxonomically classified into six genera: Gordonia, Microbacterium, Micromonospora, Nocardia, Rhodococcus, and Streptomyces, with Streptomyces and Micromonospora being notably predominant. Comparative genomic analysis facilitated the identification of two novel species: Micromonospora palythoicola sp. nov. (strain S2-005T = TBRC 18343T and NBRC 116545T) and Streptomyces poriticola sp. nov. (strain C6-003T, =TBRC 17807T and NBRC 116425T). Both species exhibited substantial genetic differences from their nearest known species as demonstrated by digital DNA-DNA hybridization and average nucleotide identity scores, which fell below the thresholds of 70% and 95%, respectively. Streptomyces poriticola C6-003T displayed significant antimicrobial activity and selective cytotoxicity against human breast cancer MCF-7 cells, with reduced toxicity towards human dermal papilla cells. Micromonospora palythoicola S2-005T manifested antimicrobial properties against Streptococcus mutans and Kocuria rhizophila. These findings highlight the considerable diversity of actinobacteria within marine invertebrates and underscore their potential as a source of new species with promising biological properties for therapeutic applications.

Florfenicol-resistant Brevundimonas sanguinis sp. nov., a novel bacterium isolated from patient blood in South Korea

An aerobic, Gram-stain-negative, non-motile, non-spore-forming, short rod-shaped bacterial strain, designated NCCP 15609 T, was isolated from the blood sample of a patient in the Republic of Korea. The strain was identified as Brevundimonas diminuta using MALDI-TOF. A phylogenetic tree constructed using 16S rRNA gene sequences revealed that the isolate was of the genus Brevundimonas with 99.8% similarity to B. naejangsanensis. The strain NCCP 15609T genome consisted of one contig with 3,063,090 bp, and had a G+C content of 67.4%. The genome contained 2,949 protein-coding sequences, 52 tRNAs, and 6 rRNAs. The DNA-DNA hybridisation between NCCP 15609T and B. naejangsanensis yielded 92.5% and 49.5% ± 2.6%, respectively, using the average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH). The predominant fatty acids of strain NCCP 15609T were summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C16:0. The isolate contained polar lipids and quinone, corresponding to phosphatidylglycerol, 1,2-di-O-acyl-3-O-[D-glycopyranosyl (1 → 4)-α-D-glucopyranuronosyl] glycerol, and ubiquinone-10, respectively. Based on its phylogenetic, physiological, and chemotaxonomic characteristics, we suggest that NCCP 15609T represents a novel pathogen resource of the genus Brevundimonas and propose to name it Brevundimonas sanguinis sp. nov. The type strain is NCCP 15609T (= DSM 116005T).

Acidisoma cladoniae sp. nov., an acidotolerant bacterium isolated from an Antarctic lichen

Gram-staining-negative, aerobic, white-cream-pearly colony, coccobacilli, and non-motile bacterial strain, PAMC 29798T was isolated from an Antarctic lichen. The strain was acidotolerant and psychrotolerant growing at pH 4.0-7.5 (optimally at pH 4.0-6.5) and 0-25 °C (optimally at 10-20 °C). The major fatty acids are Summed Feature 8, C18:1 2OH, and C19:0 cyclo ω8c. The major respiratory quinone was Q-10. Phylogenetic and phylogenomic analyses indicated that strain PAMC 29798T belonged to the genus Acidisoma and 16S rRNA gene sequences of PAMC 29798T were closely related to Acidisoma silvae (97.7% sequence similarity), Acidisoma cellulosilyticum (96.5%), Acidisoma tundrae (96.5%), and Acidisoma sibiricum (96.3%). Genomic relatedness analyses showed that strain PAMC 29798T was clearly distinguished from type strains of the genus Acidisoma based on values of average nucleotide identity (< 75%) and the digital DNA-DNA hybridization (< 19.6%). Genome analysis revealed that the genome size of PAMC 29798T is approximately 5.0 Mb with a G+C content of 63.4%. The complete genome comprises 5 contigs containing 4636 protein-coding genes, 46 tRNA genes, and 2 rRNA operons. The genome possesses genes for light-harvesting complexes, type-II photosynthetic reaction center, and C-P lyase to solubilize organic phosphates, while genes encoding nitrogenase iron protein involved in the nitrogen fixation were not present. Based on the results of phylogenetic, genome-based relatedness, and physiological and genomic analyses, strain PAMC 29798T is proposed to represent a novel species of the genus Acidisoma, with the name Acidisoma cladoniae. The type strain is PAMC 29798T (= KCTC 82159T = JCM 35634T).

Paracraurococcus lichenis sp. nov., isolated from lichen in Thailand

A novel bacterium, designated as strain LOR1-02T and isolated from a lichen sample collected from Kham Riang Subdistrict, Kantharawichai District, Maha Sarakham Province, Thailand, underwent thorough investigation utilizing a polyphasic taxonomic approach. Strain LOR1-02T demonstrated growth within a temperature range of 20-42 °C (optimal at 30 °C), pH range of 5.0-7.5 (optimal at pH 7.0), and tolerance to 4.0% (w/v) NaCl. Phylogenetic analysis revealed its close relation to Paracraurococcus ruber JCM 9931T, with a 16S rRNA gene sequence similarity of 97.16%, placing it within the genus Paracraurococcus. The approximate genome size of strain LOR1-02T was determined to be 8.6 Mb, with a G + C content of 70.9 mol%. Additionally, ANIb, ANIm, and AAI values between the whole genomes of strain LOR1-02T and type strains were calculated as 82.6-83.4%, 86.1-86.8%, and 81.4-82.2%, respectively, while the dDDH value was determined to be 26.3-28.5% (C.I. 24.0-31.0%). The predominant fatty acids detected were C18:1ω7c and/or C18:1ω6c, C16:0, and C18:12OH. The major ubiquinone identified was Q-10, and the polar lipids included phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, along with unidentified phosphoaminolipid, lipids, and an amino lipid. Based on comprehensive phenotypic, chemotaxonomic, and genotypic characterization, it is concluded that strain LOR1-02T represents a novel species within the genus Paracraurococcus, for which the name Paracraurococcus lichenis sp. nov. is proposed. The type strain designation is LOR1-02T (= JCM 33121T = NBRC 112776T = TISTR 2503T).

Novel isolates of hydrogen-oxidizing chemolithoautotrophic Sulfurospirillum provide insight to the functions and adaptation mechanisms of Campylobacteria in shallow-water hydrothermal vents

Enhancing the availability of representative isolates from hydrothermal vents (HTVs) is imperative for comprehending the microbial processes that propel the vent ecosystem. In recent years, Campylobacteria have emerged as the predominant and ubiquitous taxon across both shallow and deep-sea vent systems. Nevertheless, only a few isolates have been cultured, primarily originating from deep-sea HTVs. Presently, no cultivable isolates of Campylobacteria are accessible in shallow water vent systems (<200 m), which exhibit markedly distinct environmental conditions from their deep-sea counterparts. In this study, we enriched a novel isolate (genus Sulfurospirillum, Campylobacteria) from shallow-water HTVs of Kueishan Island. Genomic and physiological analysis revealed that this novel Campylobacteria species grows on a variety of substrate and carbon/energy sources. The pan-genome and phenotypic comparisons with 12 previously isolated Sulfurospirillum species from different environments supported the identification of functional features in Sulfurospirillum genomes crucial for adaptation to vent environments, such as sulfur oxidation, carbon fixation, biofilm formation, and benzoate/toluene degradation, as well as diverse genes related with signal transportation. To conclude, the metabolic characteristics of this novel Campylobacteria augment our understanding of Campylobacteria spanning from deep-sea to shallow-water vent systems.IMPORTANCECampylobacteria emerge as the dominant and ubiquitous taxa within vent systems, playing important roles in the vent ecosystems. However, isolated representatives of Campylobacteria have been mainly from the deep-sea hydrothermal fields, leaving a significant knowledge gap regarding the functions, activities, and adaptation strategies of the vent microorganisms in shallow-water hydrothermal vents (HTVs). This study bridges this gap by providing insights into the phenomics and genomic diversity of genus Sulfurospirillum (order Campylobacterales, class Campylobacteria) based on data derived from a novel isolate obtained from shallow-water HTVs. Our mesophilic isolate of Sulfurospirillum not only augments the genus diversity of Campylobacteria pure cultures derived from vent systems but also serves as the inaugural reference isolate for Campylobacteria in shallow-water environments.

Microbacterium rhizophilus sp. nov., an indole acetic acid-producing actinobacterium isolated from rhizosphere soil

A novel gram-stain-positive, short rod, aerobic, non-motile and non-spore-forming actinobacterial strain, designated GXG1230T was isolated from the rhizosphere soil of a coastal mangrove forest in Beihai city, Guangxi Zhuang Autonomous Region, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GXG1230T was affiliated with the genus Microbacterium. Additionally, it demonstrated a high degree of similarity to Microbacterium paludicola US15T (97.9%) and Microbacterium marinilacus YM11-607T (97.3%). Chemotaxonomic characteristics showed that the whole-cell sugars were glucose, xylose, rhamnose and galactose. Menaquinones MK-11 and MK-12 were detected as respiratory quinones. Lysine was found in the peptidoglycan hydrolysate and the polar lipids were diphosphatidylglycerol, one phospholipid and two unidentified glycolipid. The major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The strain GXG1230T exhibited a genomic DNA G + C content of 71.7%. Furthermore, the average nucleotide identity values of GXG1230T with the reference strains were 75.4% and 81.9%, respectively, while the digital DNA-DNA hybridization values were 20.1% and 25.0%. Based on physiological, chemotaxonomic and phylogenetic information, strain GXG1230T is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium rhizophilus sp.nov is proposed, with GXG1230T (= MCCC 1K09302T = KCTC 59252T) as the type strain.

Analysis of genomic and characterization features of Luteolibacter soli sp. nov., isolated from soil

The strain designated as Y139T is a novel Gram-stain-negative, aerobic, and non-motile bacterium, was isolated from a soil sample in McClain County, Oklahoma, United States. The cells of strain Y139T were a rod-shaped, with the width of 0.4-0.7 μm and the length of 1.5-2.0 μm . Growth occurred at 20-37°C (optimum, 30°C), pH 5.5-9.5 (optimum, pH 7.0), and 0-1.0% NaCl (w/v) (optimum, 0%). The polar lipid profiles included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, and an unidentified lipid. The major fatty acids included C16:0, iso-C14:0, and C16:1 ω9c. Menaquinone-9 (MK-9) was recognized as the only respiratory quinone. Strain Y139T showed the highest 16S rRNA gene sequence similarity to Luteolibacter flavescens MCCC 1K03193T (98.3%). Phylogenetic analysis positioned it within the genus Luteolibacter. The draft genome of strain Y139T consisted of 7,106,054 bp, and contained 5,715 open reading frames (ORFs), including 5,656 coding sequences (CDSs) and 59 RNA genes. The genomic DNA G + C content was found to be 62.5%. Comparing strain Y139T with L. flavescens MCCC 1K03193T and Luteolibacter arcticus CCTCC AB 2014275T, the average nucleotide identity (ANI) values were 80.6 and 82.1%, respectively. Following phylogenetic, physiological, biochemical, and chemotaxonomic analyses, a novel species within the genus Luteolibacter, designated as Luteolibacter soli sp. nov., was proposed for strain Y139T, which was also assigned as the type strain (=KCTC 92644T = MCCC 1H01451T). Further analysis of core genes across 9 Luteolibacter species uncovered significant genomic divergence, particularly in those related to cofactor, vitamin, and energy metabolism. Analysis of biogeographic distribution suggested that lake and soil were the main habitats for the genus Luteolibacter. Additionally, the genus Luteolibacter was sensitive to climate warming and precipitation.

Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring

Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066T and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066T carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066T might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".

Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter

Two Gram-stain-negative, aerobic, motile by means of flagella, short rod-shaped bacterial strains, designated IMCC43200T and IMCC45268T, were isolated from coastal seawater samples collected from the South Sea of Korea. Strains IMCC43200T and IMCC45268T shared 98.6% 16S rRNA gene sequence similarity and were closely related to Congregibacter litoralis KT71T (98.8% and 98.7%, respectively). Complete whole-genome sequences of IMCC43200T and IMCC45268T were 3.93 and 3.86 Mb in size with DNA G + C contents of 54.8% and 54.2%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 74.5% and 23.4%, respectively, revealing that they are independent species. The two strains showed ANI values of ≤ 75.8% and dDDH values of ≤ 23.0% to the type and only species of the genus Congregibacter (C. litoralis), indicating that each strain represents a novel species. Both strains contained summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and summed feature 8 (comprising C18:1 ω6c and/or C18:1 ω7c) as major fatty acid constituents. The predominant isoprenoid quinone detected in both strains was ubiquinone-8 (Q-8). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and aminolipids. Based on the phylogenetic, genomic, and phenotypic characterization, strains IMCC43200T and IMCC45268T were considered to represent two novel species within the genus Congregibacter, for which the names Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. are proposed with IMCC43200T (= KCTC 8133T = NBRC 116295T = CCTCC AB 2023139T) and IMCC45268T (= KCTC 92921T = NBRC 116135T) as the type strains, respectively.

Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov., isolated from marine sediment

Two bacterial strains, Y60-23T and HN-65T, were isolated from marine sediment samples collected from Xiaoshi Island, Weihai, and Dongzhai Harbour, Haikou, PR China, respectively. Based on the 16S rRNA gene sequences, strain Y60-23T exhibited 96.0% similarity to its most related type strain Hyphobacterium vulgare KCTC 52487T, while strain HN-65T exhibited 97.3% similarity to its most related type strain Hyphobacterium indicum 2ED5T. The 16S rRNA gene sequence similarity between the two strains was 95.8%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y60-23T and HN-65T belonged to the genus Hyphobacterium. Cells of strains Y60-23T and HN-65T were rod-shaped, Gram-stain-negative, aerobic, non-motile, prosthecate and multiplied by binary fission. The major cellular fatty acids (>10.0%) of strain Y60-23T were C18 : 1  ω7c and C17 : 0, while those of strain HN-65T were iso-C17 : 1  ω9c, iso-C17 : 0 and C18 : 1  ω7c. The major respiratory quinone in both strains was ubiquinone-10 (Q-10) and the major polar lipids were monoglycosyl diglyceride, sulfoquinovosyl diacylglycerol and glucuronopyranosyl diglyceride. The genomic DNA G+C contents of strains Y60-23T and HN-65T were 63.9 and 60.7 mol%, respectively. The average nucleotide identity value between the two strains was 72.1% and the DNA-DNA hybridization value was 18.4%, clearly distinguishing them from each other. According to the results of the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, the two strains represented two novel species within the genus Hyphobacterium, for which the names Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov. were proposed with the type strains Y60-23T (=MCCC 1H01433T=KCTC 8172T) and HN-65T (=MCCC 1H01434T=KCTC 8169T), respectively.

Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013

A Gram-stain-negative, yellow-pigmented, and strictly aerobic bacterium, designated as strain MSW5T, was isolated from seawater of the Yellow Sea in South Korea. The cells were non-motile rods exhibiting oxidase- and catalase-positive activities. Growth was observed at 15-25 °C (optimum, 25 °C) and pH 5.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 1.0-5.0% (w/v) NaCl (optimum, 2.0%). Menaquinone-6 was the sole respiratory quinone, and iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), iso-C15 : 0 3-OH, and C15 : 1  ω6c were the major cellular fatty acids. Major polar lipids included phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences and 92 concatenated core protein sequences revealed that strain MSW5T formed a distinct lineage within the genus Polaribacter. The genome of strain MSW5T was 3582 kb in size with a 29.1 mol% G+C content. Strain MSW5T exhibited the highest similarity to Polaribacter atrinae WP25T, with a 97.9% 16S rRNA gene sequence similarity. However, the average nucleotide identity and digital DNA-DNA hybridization values were 79.4 and 23.3%, respectively, indicating that strain MSW5T represents a novel species. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain MSW5T is proposed to represent a novel species, with the name Polaribacter ponticola sp. nov. The type strain is MSW5T (=KACC 22340T=NBRC 116025T). In addition, whole genome sequence comparisons and phenotypic features suggested that Polaribacter sejongensis and Polaribacter undariae belong to the same species, with P. undariae proposed as a later heterotypic synonym of P. sejongensis. An emended description of Polaribacter sejongensis is also proposed.

Dongia sedimenti sp. nov., isolated from river sediment

A Gram-stain-negative, non-spore-forming and strictly aerobic bacterial strain, designated R-7T, was isolated from river sediment in Wuxi, Jiangsu, PR China. Cells (1.6-3.8 µm long and 0.6-0.8 µm wide) were slightly curved to straight rods and motile by means of a polar flagellum. The strain grew optimally on Reasoner's 2A medium at 30 °C, pH 7.0 and with 1.0% (w/v) NaCl. Strain R-7T exhibited closest 16S rRNA gene sequence similarities to Dongia mobilis CGMCC 1.7660T (95.4%), D. rigui 04SU4-PT (94.6%) and D. soli D78T (93.8%). The phylogenetic trees based on genomic and 16S rRNA gene sequences showed that strain R-7T was clustered in the genus Dongia. The obtained average nucleotide identity and digital DNA-DNA hybridization values between R-7T and the three type strains of the genus Dongia were 73.4, 72.8 and 72.4% and 19.5, 19.0 and 18.7%, respectively. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, two unidentified aminophospholipids and nine unidentified polar lipids. The major cellular fatty acids (>5% of the total) were cyclo-C19 : 0  ω8c, C16 : 0 and C16 : 0 2-OH. The DNA G+C content was 65.5 mol%. On the basis of the evidence presented in this study, strain R-7T represents a novel species of the genus Dongia, for which the name Dongia sedimenti sp. nov. is proposed, with strain R-7T (=KCTC 8082T=MCCC 1K08805T) as the type strain.

Luteipulveratus flavus sp. nov. isolated from two lichen species

Two novel strains, YIM 133132T and YIM 133296, were isolated from lichen samples collected from Yunnan Province, Southwest PR China. YIM 133132T and YIM 133296 are aerobic, Gram-staining-positive, non-motile actinomycetes. They are also catalase-positive and oxidase-negative, and YIM 133132T formed flat yellowish colonies that were relatively dry on YIM38 agar medium. Flat yellowish colonies of YIM 133296 were also observed on YIM38 agar medium. YIM 133132T grew at 25-35 °C (optimum 25-30 °C), pH 6.0-9.0 (optimum pH 7.0) and in the presence of 0-8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains YIM 133132T and YIM 133296 represented members of the genus Luteipulveratus and exhibited high sequence similarity (96.93%) with Luteipulveratus halotolerans C296001T. The genomic DNA G+C content of both strains was 71.8%. The DNA-DNA hybridisation (dDDH) values between YIM 133132T and YIM 133296 were 85.1%, and the DNA-DNA hybridisation value between YIM 133132T and YIM 133296 and L. halotolerans C296001T was 23.4%. On the basis of the draft genome sequences, the average nucleotide identity (ANI) between strains YIM 133132T and YIM 133296 and L. halotolerans C296001T was 80.8%. The major menaquinones that were identified were MK-8(H4), MK-9 and MK-8(H2). The polar lipids were diphosphatidylglycerol and phosphatidylinositol. On the basis of the morphological, physiological, biochemical, genomic, phylogenetic and chemotaxonomic characteristics, strains YIM 133132T and YIM 133296 can be clearly distinguished from L. halotolerans C296001T, and the two strains represent a novel species for which the name L. flavus sp. nov. is proposed. The type strain is YIM 133132T (CGMCC= 1.61357T and KCTC= 49824T).

Microbulbifer spongiae sp. nov., isolated from marine sponge Diacarnus erythraeanus

A novel bacterium, designated as MI-GT, was isolated from marine sponge Diacarnus erythraeanus. Cells of strain MI-GT are Gram-stain-negative, aerobic, and rod or coccoid-ovoid in shape. MI-GT is able to grow at 10-40 °C (optimum, 28 °C), with 1.0-8.0% (w/v) NaCl (optimum, 4.0%), and at pH 5.5-9.0 (optimum, pH 8.0). The 16S rRNA gene sequence of strain MI-GT shows 98.35, 97.32 and 97.25% similarity to those of Microbulbifer variabilis Ni-2088T, Microbulbifer maritimus TF-17T and Microbulbifer echini AM134T, respectively. Phylogenetic analysis also exhibits that strain MI-GT falls within a clade comprising members of the genus Microbulbifer (class Gammaproteobacteria). The genome size of strain MI-GT is 4478124 bp with a G+C content of 54.51 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MI-GT and other type strains are 71.61-76.44% (ANIb), 83.27-84.36% (ANIm) and 13.4-18.7% (dDDH), respectively. These values are significantly lower than the recommended threshold values for bacterial species delineation. Percentage of conserved proteins and average amino acid identity values among the genomes of strain MI-GT and other closely related species are 52.04-59.13% and 67.47-77.21%, respectively. The major cellular fatty acids of MI-GT are composed of summed feature 8 (C18 : 1 ω7c or C18 : 1 ω6c), iso-C11 : 0 3-OH, iso-C15 : 0, C16 : 0, and summed feature 9 (C17 : 1 iso ω9c or C16 : 0 10-methyl). The polar lipids of MI-GT mainly consist of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and two glycolipids. The major respiratory quinone is Q-8. Based on differential phenotypic and phylogenetic data, strain MI-GT is considered to represent a novel species of genus Microbulbifer, for which the name Microbulbifer spongiae sp. nov. is proposed. The type strain is MI-GT (=MCCC 1K07826T=KCTC 8081T).

Paenibacillus gyeongsangnamensis sp. nov., Isolated from Soil

A Gram-stain-positive, aerobic, white-coloured, rod-shaped bacteria, designated as a strain dW9T, was isolated from soil. Strain dW9T was catalase-positive and oxidase-negative. Strain dW9T grew at temperature of 20-37°C and at pH of 5.0-7.0. Phylogenetic and 16S rRNA gene analysis indicated that strain dW9T belonged to the genus Paenibacillus with its closest relative being Paenibacillus filicis S4T (97.4% sequence similarity). The genome size of dW9T was 7,787,916 bp with DNA G+C content of 51.3%. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of dW9T with its closest relatives were found to be <22.0% and <74.0%, respectively. The only respiratory quinone was MK-7, and the major fatty acids were antiso-C15:0 and iso-C16:0. Overall, the comprehensive taxonomic analysis revealed that strain dW9T met all the fundamental criteria to be classified as a novel species within the genus Paenibacillus. Accordingly, we propose the name Paenibacillus gyeongsangnamensis sp. nov., with the type strain dW9T (=KCTC 43431T =NBRC 116022T).

Description of Aliirhizobium terrae sp. nov., A Plant Growth-Promoting Bacterium Isolated from a Maize-Rice Rotation Agriculture Field

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-CFT758T, isolated from a maize-rice rotation agriculture field in Taiwan. The cells are aerobic, Gram-stain-negative, rod-shaped, positive for catalase and oxidase, and grow at 20-30 °C (optimal 30 ℃), at pH 6.0-8.0 (optimal 8.0), and with 0-4% (w/v) NaCl (optimum, 2-3%). Phylogenetic analysis based on 16S rRNA gene sequencing, the strain CC-CFT758T belongs to the genus "Aliirhizobium" of the family Rhizobiaceae. The closest known relatives of this strain are "Aliirhizobium wenxiniae" 166T (with 98.7% similarity), "Aliirhizobium cellulosilyticum" SEMIA 448T (with 97.9% similarity), and "Aliirhizobium smilacinae" PTYR-5T (with 97.0% similarity). The genome size was 5.9 Mbp, with a G + C content of 60.6%. Values of digital DNA-DNA hybridization between the strain and closely related species were 29.5% for "Ali. cellulosilyticum", and 23.9% for "Ali. wenxiniae" and "Ali. smilacinae". Strain CC-CFT758T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the genus "Aliirhizobium", ranging from 80.4 to 81.6% (n = 3). Chemotaxonomical analysis indicated that strain CC-CFT758T contained C16:0, C16:0 3OH, C19:0 cyclo ω8c, C14:0 3OH/iso-C16:1 I, and C18:2 ω6,9c/ante C18:0 as dominant fatty acids, and the major polyamines were putrescine and spermidine. The polar lipids comprised diphosphatidylglycerol, phosphatidylcholin, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, seven unidentified aminolipids, three unidentified phospholipids, and two unidentified polar lipids. Strain CC-CFT758T exhibited distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, AAI, dDDH, and phylogenomic placement. Therefore, this strain represents a new species of the genus "Aliirhizobium", for which the name Aliirhizobium terrae sp. nov. is proposed, with the type strain is CC-CFT758T (= BCRC 81364T = JCM 35482T).

Rufibacter psychrotolerans sp. nov., a Cold-Tolerating Novel Species Isolated from Desert Soil

Strain SYSU D00308T, a short-rod-shaped bacterium, was isolated from a sandy soil collected from the Gurbantunggut Desert, Xinjiang, PR China. Strain SYSU D00308T was Gram-stain-negative, aerobic, pink-pigmented, non-motile, catalase- and oxidase-positive. The strain grew at 4-37 ℃, pH 5.0-8.0 and 0-1.5% (w/v) NaCl. 16S rRNA gene sequencing analyses demonstrated that strain SYSU D00308T belonged to the genus Rufibacter and exhibited the highest sequence similarity (97.4%) to Rufibacter glacialis MDT1-10-3T. Summed features 3, 4, and iso-C15:0 were the major fatty acids, and menaquinone 7 (MK-7) was the sole respiratory menaquinone. The polar lipid profiles comprised phosphatidylethanolamine, an unidentified glycolipid, an unidentified phospholipid, two unidentified aminophospholipids, and two unidentified lipids. The genome size and DNA G + C content of strain SYSU D00308T were 5,176,683 bp and 54.8%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU D00308T and members of the genus Rufibacter were 77.7-81.8% and 20.4-23.4% respectively, which were less than the corresponding thresholds (ANI: 95-96%; dDDH: 70%) for prokaryotic species definition. According to the genotypic, phenotypic and phylogenetic characteristics, strain SYSU D00308T represents a novel species of the genus Rufibacter. We propose the name, Rufibacter psychrotolerans sp. nov., with SYSU D00308T (= CGMCC 1.18621T = KCTC 82275T = MCCC 1K04970T) as the type strain.

Salmonirosea aquatica gen. nov., sp. nov., a Novel Genus within the Family Spirosomaceae, Was Isolated from Brackish Water in the Republic of Korea

A Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strain designated SJW1-29T was isolated from brackish water samples collected from the Seomjin River, Republic of Korea. The purpose of this study was to characterize strain SJW1-29T and determine its taxonomic position as a potential new genus within the family Spirosomaceae. The strain grew within the range of 10-30 °C (optimum, 25 °C), pH 5.0-10.0 (optimum, 7.0), and 1-4% NaCl (optimum, 3%). Phylogenetic analysis based on the 16S rRNA gene revealed that strain SJW1-29T belongs to the family Spirosomaceae and is closely related to Persicitalea jodogahamensis Shu-9-SY12-35CT (91.3% similarity), Rhabdobacter roseus R491T (90.6%), and Arundinibacter roseus DMA-K-7aT (90.0%), while the similarities to strains within the order Cytophagales were lower than 90.0%. The genome is 7.1 Mbp with a G+C content of 50.7 mol%. The use of genome-relatedness indices confirmed that this strain belongs to a new genus. The major polar lipid profile consisted of phosphatidylethanolamine, and MK-7 was the predominant menaquinone. The predominant fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0, iso-C17:0 3-OH, and C16:0, representing more than 80% of the total fatty acids. The phenotypic, chemotaxonomic, genetic, and phylogenetic properties suggest that strain SJW1-29T represents a novel species within a new genus in the family Spirosomaceae, for which the name Salmonirosea aquatica gen. nov., sp. nov., is proposed. The type strain of Salmonirosea aquatica is SJW1-29T (=KCTC 72493T = NBRC 114061T = FBCC-B16924T).

Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan

The strain designated NCCP-602T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602T within genus Brevibacterium and showed that it was closely related to Brevibacterium ammoniilyticum JCM 17537T. Strain NCCP-602 T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602T provided additional evidence supporting the classification of strain NCCP-602T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0, and anteiso-C17:0 were identified as the predominant cellular fatty acids (> 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602 T be classified as a distinct species Brevibacterium metallidurans sp. nov. within genus Brevibacterium with type strain NCCP-602T (JCM 18882T = CGMCC1.62055T).

Aquibium pacificus sp. nov., a Novel Mixotrophic Bacterium from Bathypelagic Seawater in the Western Pacific Ocean

A novel Gram-stain-negative, facultatively anaerobic, and mixotrophic bacterium, designated as strain LZ166T, was isolated from the bathypelagic seawater in the western Pacific Ocean. The cells were short rod-shaped, oxidase- and catalase-positive, and motile by means of lateral flagella. The growth of strain LZ166T was observed at 10-45 °C (optimum 34-37 °C), at pH 5-10 (optimum 6-8), and in the presence of 0-5% NaCl (optimum 1-3%). A phylogenetic analysis based on the 16S rRNA gene showed that strain LZ166T shared the highest similarity (98.58%) with Aquibium oceanicum B7T and formed a distinct branch within the Aquibium genus. The genomic characterization, including average nucleotide identity (ANI, 90.73-76.79%), average amino identity (AAI, 88.50-79.03%), and digital DNA-DNA hybridization (dDDH, 36.1-22.2%) values between LZ166T and other species within the Aquibium genus, further substantiated its novelty. The genome of strain LZ166T was 6,119,659 bp in size with a 64.7 mol% DNA G+C content. The predominant fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The major polar lipids identified were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), glycolipid (GL), and phosphatidylglycerol (PG), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The genomic annotation indicated the presence of genes for a diverse metabolic profile, including pathways for carbon fixation via the Calvin-Benson-Bassham cycle and inorganic sulfur oxidation. Based on the polyphasic taxonomic results, strain LZ166T represented a novel species of the genus Aquibium, for which the name Aquibium pacificus sp. nov. is proposed, with the type strain LZ166T (=MCCC M28807T = KACC 23148T = KCTC 82889T).

Reclassification of Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970 as a Later Heterotypic Synonym of Streptomyces violaceus (Rossi Doria 1891) Waksman 1953 using a Polyphasic Approach

The taxonomic relationship between Streptomyces violarus and Streptomyces violaceus was reevaluated using a polyphasic taxonomic approach in this work. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Streptomyces violarus JCM 4534 T was closely related to Streptomyces arenae ISP 5293 T. However, phylogenetic analysis based on five house-keeping gene (atpD, gyrB, recA, rpoB and trpB) showed that the evolutionary neighbor of Streptomyces violarus JCM 4534 T was Streptomyces violaceus CGMCC 4.1456 T, suggesting that there was a close genetic relationship between these two strains. The average nucleotide identity and digital DNA-DNA hybridization values between them were 97.0 and 72.9%, respectively, greater than the 96.7 and 70% cut-off points recommended for delineating a Streptomyces species. This result indicated that they belonged to the same genomic species which was also verified by a comprehensive comparison of phenotypic and chemotaxonomic characteristics between Streptomyces violarus JCM 4534 T and Streptomyces violaceus CGMCC 4.1456 T. According to all these data and the rule of priority in nomenclature, it is proposed the Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970 is a later heterotypic synonym of Streptomyces violaceus (Rossi Doria 1891) Waksman 1953. In addition, based on dDDH, Streptomyces violaceus and Streptomyces violarus are simultaneously designated as two different subspecies, i.e., Streptomyces violaceus subsp. violaceus and Streptomyces violaceus subsp. violarus.

Two new members of the genus Sphingobacterium: Sphingobacterium zhuxiongii sp. nov. and Sphingobacterium luzhongxinii sp. nov

Four strains, designated dk4302T, dk4209, xlx-73T, and xlx-183, were isolated from Tibetan gazelle and red swamp crawfish collected from the Qinghai-Tibet Plateau and Jiangxi Province, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, mucoid, and yellow-pigmented. Strains dk4302T and dk4209 grew at 10-40 °C and pH 6.0-9.0, while strains xlx-73T/xlx-183 grew at 15-40 °C and pH 6.0-10.0. Both strains exhibited growth in the presence of up to 3.5 % (w/v) NaCl. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene sequences and 652 core genes, respectively, revealed that the four strains formed two distinct clusters in the genus Sphingobacterium. Strains dk4302T and dk4209 formed a distinct clade with Sphingobacterium hotanense XH4T and Sphingobacterium humi D1T. The most closely related strains to xlx-73T and xlx-183 were Sphingobacterium nematocida M-SX103T. The DNA G+C contents were 38.9 and 39.8 mol%. The digital DNA-DNA hybridization (dDDH) values between dk4302T and S. humi D1T and S. hotanense XH4T were 19.2 and 21.8 % (19.0 and 21.6 % for strain dk4209), respectively. The corresponding average nucleotide identity (ANI) values were 74.3 and 78.1 % (74.4 and 78.3 % for strain dk4209), respectively. The dDDH values between xlx-73T (xlx-183) and S. nematocida M-SX103T was 24.6 % (25.7 %). The corresponding ANI value was 85.7 % (85.5 % for strain xlx-183). The major fatty acid and respiratory quinone of dk4302T and xlx-73T were iso-C15:0 and MK7. The polar lipids identified in all of the novel strains were phosphatidylethanolamine, phosphoglycolipids, aminophospholipids, and phospholipids. A total of 61/190 (32.1 %) and 82/190 (43.2 %) carbon substrates were metabolized by strains dk4302T and xlx-73T in the Biolog MicroPlates, respectively. Based on the results from this polyphasic taxonomic study, two novel species in the genus Sphingobacteruim are proposed, namely Sphingobacteruim zhuxiongii sp. nov. (type strain dk4302T=CGMCC 1.16795T=JCM 33600T) and Sphingobacteruimluzhongxinii sp. nov. (type strain xlx-73T=GDMCC 1.1712T=JCM 33886T).

Gilvirhabdus luticola gen. nov., sp. nov., a mesophilic and halophilic bacterium isolated from tidal flat sediment

Two novel bacteria, MJ-SS3T and MJ-SS4, were isolated from tidal flat sediment sampled in Gochang, Republic of Korea. The isolates were Gram-stain-negative, aerobic, non-motile, rod-shaped, yellow-coloured, oxidase-positive, and catalase-positive. Strains MJ-SS3T and MJ-SS4 grew at 20-37 °C (optimum, 30 °C), at pH 6-8 (optimum, pH 7.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 2.0 % NaCl). Strains MJ-SS3T and MJ-SS4 showed 99.9 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on genome and 16S rRNA gene sequences indicated that strains MJ-SS3T and MJ-SS4 were affiliated with the family Flavobacteriaceae and most closely related to Formosa maritima 1494T (95.3 %), Hanstruepera flava NBU2984T (95.2 %), Yeosuana marina JLT21T (95.2 %), Meridianimaribacter flavus NH57NT (95.1 %), and Geojedonia litorea YCS-16T (95.1 %). The major respiratory quinone was menaquinone-6. The major identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and amino lipids. The major cellular fatty acids of strain MJ-SS3T were iso-C15 : 1 G (24.6 %), iso-C15 : 0 (21.6 %), and iso-C17 : 0 3-OH (15.8 %). The genome length of strain MJ-SS3T is 3.1 Mbp (DNA G+C content, 32.5 mol%) and it has 2822 coding and 59 tRNA genes. The average amino acid identity and average nucleotide identity values, as well as biochemical, phylogenetic, and physiological characteristics, strongly supported the genotypic and phenotypic differentiation of strains MJ-SS3T and MJ-SS4 from other members of the family Flavobacteriaceae. Hence, strains MJ-SS3T and MJ-SS4 are considered to represent a novel species of a new genus in the family Flavobacteriaceae, for which the Gilvirhabdus luticola gen. nov., sp. nov. is proposed. The type strain is MJ-SS3T (=KCTC 102114T=KEMB 20189T=JCM 36595T), with reference strain MJ-SS4 (=KCTC 102115=KEMB 20190).

Discovery of a new bacterium, Microbacterium betulae sp. nov., in birch wood associated with hypersensitivity pneumonitis in woodworkers

A Gram-positive, aerobic, rod-shaped mesophilic bacterium was isolated from birch wood, referred to as the AB strain. Allergological tests suggest that this strain may cause allergic alveolitis in sawmill workers. Employing a polyphasic taxonomic approach, the AB strain's 16S rRNA gene sequence showed high similarity to Microbacterium barkeri and M. oryzae, with 97.25% and 96.91%, respectively, a finding supported by rpoB and gyrB sequence analysis. Further genome sequence comparison with the closely related M. barkeri type strain indicated a digital DNA-DNA hybridization value of 25.5% and an average nucleotide identity of 82.52%. The AB strain's cell wall peptidoglycan contains ornithine, and its polar lipids comprise diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Its major fatty acids include anteiso C15:0, anteiso C17:0, and iso C16:0, while MK-10 is its predominant respiratory quinone. Comprehensive analysis through 16S rRNA, whole-genome sequencing, phenotyping, chemotaxonomy, and MALDI-TOF MS profiling indicates that the AB strain represents a new species within the Microbacterium genus. It has been proposed to name this species Microbacterium betulae sp. nov., with ABT (PCM 3040T = CEST 30706T) designated as the type strain.

Microbacterium humicola sp. nov., Microbacterium terrisoli sp. nov., Paenibacillus pedocola sp. nov., Paenibacillus silviterrae sp. nov., Flavobacterium terrisoli sp. nov., and Aquabacterium humicola sp. nov., isolated from soil

Four Gram-stain-positive and two Gram-stain-negative bacterial strains, designated as W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T, were isolated from soil samples collected from the Republic of Korea. The 16S rRNA gene sequence analysis showed that strains W4T and FW7T belonged to the genus Microbacterium, strains TW48T and UW52T were affiliated to the genus Paenibacillus, strain PT-3T was related to the genus Flavobacterium, and strain RJY3T was associated with the genus Aquabacterium. The closest phylogenetic taxa to W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T were Microbacterium bovistercoris NEAU-LLET (97.7 %), Microbacterium protaetiae DFW100M-13T (97.9 %), Paenibacillus auburnensis JJ-7T (99.6 %), Paenibacillus allorhizosphaerae JJ-447T (95.7 %), Flavobacterium buctense T7T (97.1 %), and Aquabacterium terrae S2T (99.5 %), respectively. Average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and related reference type strains were <95.0 % and <70.0 %, respectively. The major cellular fatty acid in strains W4T, FW7T TW48T, and UW52T was antiso-C15 : 0. Similarly, strain PT-3T revealed iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH as its principal fatty acids. On the other hand, RJY3T exhibited summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), and C12 : 0 as its predominant fatty acids. Overall, the polyphasic taxonomic data indicated that strains W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T represent novel species within the genera Microbacterium, Paenibacillus, Flavobacterium, and Aquabacterium. Accordingly, we propose the names Microbacterium humicola sp. nov., with the type strain W4T (=KCTC 49888T=NBRC 116001T), Microbacterium terrisoli sp. nov., with the type strain FW7T (=KCTC 49859T=NBRC 116000T), Paenibacillus pedocola sp. nov., with the type strain TW48T (=KCTC 43470T=NBRC 116017T), Paenibacillus silviterrae sp. nov., with the type strain UW52T (=KCTC 43477T=NBRC 116018T), Flavobacterium terrisoli sp. nov., with the type strain PT-3T (=KCTC 92106T=NBRC 116012T), and Aquabacterium humicola sp. nov., with the type strain RJY3T (=KCTC 92105T=NBRC 115831T).

Psychrosphaera algicola sp. nov. and Paraglaciecola algarum sp. nov., and reclassification of Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi as later heterotypic synonyms of P. distincta, P. maricaloris, and P. gelatinilytica

Two Gram-negative, obligately aerobic, rod-shaped bacteria, strains G1-22T and G1-23T, were isolated from the phycosphere of a marine brown alga. Both strains exhibited catalase- and oxidase-positive activities. Strain G1-22T displayed optimal growth at 25 °C, pH 8.0, and 2.0-3.0% (w/v) NaCl, while strain G1-23T exhibited optimal growth at 25 °C, pH 8.0, and 4.0% NaCl. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. As major fatty acids (> 5%), strain G1-22T contained C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C12 : 1 3-OH, and C10 : 0 3-OH, while strain G1-23T contained C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and C14 : 0. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were major polar lipids in both strains. Strains G1-22T and G1-23T had DNA G+C contents of 40.2 and 38.9 mol%, respectively. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains G1-22T and G1-23T formed distinct phylogenetic lineages within the genera Psychrosphaera and Paraglaciecola, respectively. Strain G1-22T showed closest relatedness to Psychrosphaera ytuae MTZ26T with 97.8% 16S rRNA gene sequence similarity, 70.2% average nucleotide identity (ANI), and a 21.5% digital DNA-DNA hybridization (dDDH) value, while strain G1-23T was most closely related to Paraglaciecola aquimarina KCTC 32108T with 95.6% 16S rRNA gene sequence similarity, 74.6% ANI, and a 20.1% dDDH value. Based on phenotypic and molecular characteristics, strains G1-22T and G1-23T are proposed to represent two novel species, namely Psychrosphaera algicola sp. nov. (type strain G1-22T=KACC 22486T=JCM 34971T) and Paraglaciecola algarum sp. nov. (type strain G1-23T=KACC 22490T=JCM 34972T), respectively. Additionally, based on the comparison of whole genome sequences, it is proposed that Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi are reclassified as later heterotypic synonyms of Pseudoalteromonas distincta, Pseudoalteromonas maricaloris, and Pseudoalteromonas gelatinilytica, respectively.

Actinomycetospora aeridis sp. nov., Actinomycetospora flava sp. nov. and Actinomycetospora aurantiaca sp. nov., endophytic actinobacteria isolated from wild orchid (Aerides multiflora Roxb)

Three novel mycelium-forming actinobacteria, designated OC33-EN06T, OC33-EN07T, and OC33-EN08T, were isolated from wild orchid (Aerides multiflora Roxb), collected from a hill evergreen forest in Northern Thailand. Strains OC33-EN06T and OC33-EN07T showed the highest 16S rRNA gene similarity with Actinomycetospora lutea TT00-04T, 99.17 and 99.45%, respectively. Strain OC33-EN08T showed high similarity with four species, namely 'Actinomycetospora termitidis Odt1-22T' (99.37%), Actinomycetospora chiangmaiensis DSM 45062T (99.02%), Actinomycetospora corticicola 014-5T (99.02%), and Actinomycetospora soli SF1T (98.81%). Comparative genome analysis of OC33-EN06T, OC33-EN07T, and OC33-EN08T with the closely related type strains showed that average nucleotide identity (ANI) based on blast, ANI based on MUMmer, and average amino acid identity values were less than 95% and the digital DNA-DNA hybridization values were less than 70%, all below the thresholds for species demarcation. The digital G+C content of OC33-EN06T, OC33-EN07T, and OC33-EN08T were 74.5, 74, and 74 mol%, respectively. These three strains developed bud-like chains of non-motile cylindrical spores with a smooth surface. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained ribose, arabinose, and galactose. The predominant menaquinone was MK-8(H4). The phospholipid profile included phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. Based on comparative analysis of genotypic, phenotypic and chemotaxonomic data, strains OC33-EN06T (=TBRC 18349T=NBRC 116543T), OC33-EN07T (=TBRC 18350T=NBRC 116544T), and OC33-EN08T (=TBRC 18318T=NBRC 116542T) represent the type strains of three novel species of the genus Actinomycetospora for which the names Actinomycetospora aeridis sp. nov., Actinomycetospora flava sp. nov., and Actinomycetospora aurantiaca sp. nov., are proposed.

Ferviditalea candida gen. nov., sp. nov., a novel member of the family Paenibacillaceae isolated from a geothermal area

OBJECTIVE

The family Paenibacillaceae is linked to the order Caryophanales. Paenibacillaceae members residing in compost or soil play crucial roles in nutrient recycling and breaking down complex organic materials. However, our understanding of Paenibacillaceae remains limited.

METHODS

Strain SYSU GA230002T was conclusively identified using a polyphasic taxonomic approach frequently utilized in bacterial systematics. Standard microbiological techniques were employed to characterize the morphology and biochemistry of strain SYSU GA230002T.

RESULTS

An anaerobic and gram--negative bacterium, designated SYSU GA230002T, was isolated from geothermally heated soil of Tengchong, Yunnan Province, south-west China. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain SYSU GA230002T belongs to the family Paenibacillaceae. 16S rRNA gene sequence similarity (<94.0 %), ANI (<71.95 %) and AAI values (<58.67 %) between strain SYSU GA230002T with other members of the family were lower than the threshold values recommended for distinguishing novel species. Growth was observed at 30-45 °C (optimum, 37 °C), pH 7.0-8.0 (optimum, pH 7.5) and in 0-3.0 % (w/v) NaCl concentrations (optimum, 0 %). The major fatty acids detected were anteiso-C15:0, iso-C16:0 and iso-C17:0. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid, one unidentified aminolipid and two unidentified glycolipids. The respiratory quinone was MK-7. The DNA G + C content of strain SYSU GA230002T was 49.87 %.

CONCLUSION

Based on the results of morphological, physiological properties, and chemotaxonomic characteristics, this strain is proposed to represent a new species of a new genus Ferviditalea candida gen. nov., sp. nov. The type strain of the type species is SYSU GA230002T (=KCTC 25726T = GDMCC 1.4160T).

Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream

A Gram-strain-negative, aerobic, yellow-colored, non-motile, and rod-shaped bacterial strain, designated IMCC34852T, was isolated from a freshwater stream in the Republic of Korea. Cellular growth occurred at 10-37 °C, pH 6.0-9.0, and with 0-0.5% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that strain IMCC34852T belonged to the genus Flavobacterium and that the strain was most closely related to F. cheonhonense ARSA-15 T (97.6%), F. buctense T7T (96.7%), F. silvisoli RD-2-33 T (96.1%), and F. paronense KNUS1T (96.1%). The whole-genome sequence of strain IMCC34852T was 3.2 Mbp in size, with a DNA G + C content 37.3%. The average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values between strain IMCC34852T and its related species were all below 79.8% and 22.7%, respectively, which are significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The major respiratory quinone of strain IMCC34852T was menaquinone-6 (MK-6) and the predominant cellular fatty acids were iso-C15:0 (32.6%), iso-C16:0 (11.7%), iso-C15:1 G (10.3%), and iso-C14:0 (6.7%). The major polar lipids of the strain were phosphatidylethanolamine, two unidentified aminolipids and six unidentified lipids. Based on these results, it was concluded that strain IMCC34852T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium rivulicola sp. nov is proposed. The type strain of the proposed novel species is IMCC34852T (= KACC 23133 T = KCTC 82066 T = NBRC 114419 T).