Proposal of Novosphingobium mangrovisedimenti as a replacement name for the illegitimate species name Novosphingobium mangrovi Huang et al. 2023.

Description and genomic characterization of Mesorhizobium marinum sp. nov., a bacterium isolated from sea sediment.

Three novel strains in the genus Shewanella, designated A3AT, C31T and C32, were isolated from mangrove sediment samples. They were facultative anaerobic, Gram-stain-negative, rod-shaped, flagellum-harbouring, oxidase- and catalase-positive, electrogenic and capable of using Fe(III) as an electron acceptor during anaerobic growth. Results of phylogenetic analysis based on 16S rRNA gene and genomic sequences revealed that the strains should be assigned to the genus Shewanella. The 16S rRNA gene similarity, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates and their closely related species were below the respective cut-off values for species differentiation. The 16S rRNA gene similarity, ANI and dDDH values between strains C31T and C32 were 99.7, 99.9 and 99.9 %, respectively, indicating that they should belong to the same genospecies. Based on polyphasic taxonomic approach, two novel species are proposed, Shewanella ferrihydritica sp. nov. with type strain A3AT (GDMCC 1.2732T=JCM 34899T) and Shewanella electrica sp. nov. with type strain C31T (GDMCC 1.2736T=JCM 34902T).

Members of the class Opitutae are widely distributed in various environments such as rice paddy soil, freshwater lakes, seawater, marine sediment, and invertebrate digestive tracts. The class currently consists of two orders, Opitutales and Puniceicoccales, represented by the families Opitutaceae and Puniceicoccaceae, respectively, which are primarily delineated on the basis of 16S rRNA gene sequences and limited phenotypic characterizations of a few type strains. The scarcity of 16S rRNA gene and genome sequences generated from the type strains of the class Opitutae constrained our understanding of the ecological distribution and adequate resolution of its taxonomy. Here, an Opitutae strain designated WMMB3T, isolated from a mangrove sediment, was subjected to taxonomic characterization. The 16S rRNA gene of strain WMMB3T shared high sequence similarities with Coraliomargarita akajimensis DSM 45221T and C. sinensis WN38T of 96.1 and 95.9%, respectively. Phylogenetic analysis suggested that strain WMMB3T formed a monophyletic branch affiliated to the genus Coraliomargarita. The average nucleotide identity (ANI) values, digital DNA-DNA hybridization (dDDH) values and average amino acid identity (AAI) values of strain WMMB3T compared between Coraliomargarita members were 71.8-72.5, 20.7, and 68.2-68.7%, respectively, indicating that strain WMMB3T represented a novel species of Coraliomargarita. The genome of strain WMMB3T was 4.5 Mbp with a DNA G + C content of 56.0%. The respiratory quinone was menaquinone-7. The major fatty acids were iso-C14:0, and C18:1ω9c. Based on genomic, phenotypic, and chemotaxonomic characterizations, strain WMMB3T represents a novel species, and Coraliomargarita parva sp. nov. is proposed. Additionally, the phylogenomic analysis of more than 500 genomes of the class Opitutae, encompassing a majority of uncultivated bacteria and a few type strains, was performed using the Genome Taxonomic Database toolkit (GTDB-Tk) to present adequate resolution of the taxonomy. Combined with 16S rRNA gene sequence phylogeny and genomic relatedness, five novel families retrieved mainly from marine habitats were proposed: Coraliomargaritaceae fam. nov., Pelagicoccaceae fam. nov., Cerasicoccaeae fam. nov., Oceanipulchritudinaceae fam. nov., and Alterococcaeae fam. nov. AAI values of 58-60% could be considered as the boundary to delineate families of the class Opitutae. This study provided a new taxonomic framework of the class Opitutae based on the genomic data.

A bacterial strain with chitin-degrading ability, designated FCG-7T, was isolated from a mangrove sediment in Guangxi, PR China, and characterized using a polyphasic taxonomy approach. Cells of strain FCG-7T were Gram-stain-negative, aerobic, rod-shaped and formed milky-white colonies. Growth occurred at 15-37 °C (optimum, 30 °C), at pH 7-9 (optimum, pH 7-8) and with 0-1% NaCl (optimum, 0.5%). The major isoprenoid quinone was ubiquinone-8 (Q-8). The predominant fatty acids were summed feature 3 (C16:1 ω6c and/or C16:1ω7c) and C16:0. The polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, five unidentified phospholipids and two unidentified aminophospholipids. The G + C content of the genomic DNA was 53.8%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FCG-7T belonged to the genus Chitinibacter and was closely related to Chitinibacter bivalviorum 2T18T (similarity 99.29%) and Chitinibacter fontanus STM-7T (similarity 98.85%). The average nucleotide identity (ANI) values of FCG-7T and the above two type strains were 81.4-83.1%, and the digital DNA-DNA hybridization (dDDH) values were 22.9-24.3%. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, strain FCG-7T represents a novel species of the genus Chitinibacter, for which the name Chitinibacter mangrovi sp. nov. is proposed. The type strain is FCG-7T (= KCTC 8742T = GDMCC 1.4868T).

Two Gram-stain-negative, obligately aerobic, non-motile, short rod-shaped bacteria, designated IMCC43871T and IMCC45206T, were isolated from coastal surface seawater collected from the Yellow Sea and the South Sea of Korea, respectively. The two strains shared 99.2% 16S rRNA gene sequence similarity with each other and exhibited ≤ 98.4% similarity to three described Rubrivirga species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between IMCC43871T and IMCC45206T were 88.5% and 36.3%, respectively, confirming that they represent two distinct species. Their ANI (≤ 77.7%) and dDDH (≤ 21.4%) values relative to the type strains of the genus Rubrivirga further supported the recognition of strains IMCC43871T and IMCC45206T as two novel species within the genus. The complete genomes of IMCC43871T (4.17 Mb, 71.8% G + C content) and IMCC45206T (4.17 Mb, 72.8% G + C content) fall within the known genomic range of the genus. Cellular fatty acid, quinone, and polar lipid profiles were consistent with the chemotaxonomic features of the genus Rubrivirga, supporting their affiliation with the genus. Based on phylogenetic, genomic, and phenotypic evidence, strains IMCC43871T and IMCC45206T are proposed as two novel species, Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., respectively. The type strains are IMCC43871T (= KCTC 102072T = NBRC 116463T) and IMCC45206T (= KCTC 92925T = NBRC 116172T = CCTCC AB 2023136T).

A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1 ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.

An aerobic phosphorus-recovering strain, designated WS-203T, was isolated from mangrove sediment. Strain WS-203T showed the highest 16S rRNA gene sequence similarity to the type strain of Pelagibacterium lacus (98.1%). A phylogenetic tree based on 16S rRNA gene sequences indicated that strain WS-203T clustered with members of the genus Pelagibacterium. Growth of strain WS-203T was observed at 20-37°C (optimum, 30°C), pH 6.0-9.5 (optimum, pH 7.5) and with 0-9.0% (w/v) NaCl (optimum, 3.0%). Strain WS-203T contained Q-10 as the respiratory quinone and C18:1 ω6c/C18:1 ω7c and C19:0 ω8c cyclo as the major fatty acids. The polar lipids detected in the strain were diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, two unidentified lipids and four unidentified glycolipids. The genomic DNA G + C content of strain WS-203T was 62.2%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain WS-203T and the closely related Pelagibacterium lacus were 78.6% and 21.7%, respectively, which were lower than the cut-off value (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. On the basis of these results, strain WS-203T represents a novel species of the genus Pelagibacterium, for which the name Pelagibacterium mangrovi sp. nov. is proposed. The type strain is WS-203T (= GDMCC 1.4694T = KCTC 8652T).

Four novel bacterial strains, designated RBB1W86T, RXD159T, RBB189T and RLT163T, were isolated from subtropical forest soil of the Nanling National Nature Reserve located in Guangdong Province, PR China. 16S rRNA gene phylogeny indicated their affiliation to the genus Dyella, among which strains RBB1W86T and RXD159T were closely related to Dyella halodurans CGMCC 1.15435T with 16S rRNA gene sequence similarities of 98.8 and 99.5 %, respectively, and strains RBB189T and RLT163T were closely related to Dyella tabacisoli CGMCC 1.16273T (98.8 %) and Dyella japonica JCM 21530T (99.4 %), respectively. Phylogenomic analysis based on 92 core genes showed consistent phylogeny with the 16S rRNA gene phylogeny for strains RBB1W86T, RBB189T and RLT163T, while strain RXD159T showed a closer relationship with D. tabacisoli CGMCC 1.16273T and strain RBB189T. The genome-derived average nucleotide identity (ANI) values between the newly isolated strains and their closely related species were 70.18‒90.20 %, and the corresponding digital DNA-DNA hybridization (dDDH) values were 20.80‒40.30 %. Meanwhile, the ANI and dDDH values between each pair of the newly isolated strains were 75.80‒79.77 % and 21.30‒23.30 %, respectively. They all took iso-C15 : 0 and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1 ω9c) as the major fatty acids. Moreover, C16 : 0, iso-C16 : 0, iso-C17 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) were also variously distributed as major components. They all took ubiquinone 8 as the only predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Phosphatidylmethylethanolamine was only present in strain RBB189T as another major component. Based on the results of phenotypic, genotypic and chemotaxonomic analyses, the newly isolated strains could be clearly distinguished from their closely related species and should represent four distinct novel species of the genus Dyella, for which the names Dyella humicola sp. nov. (type strain RBB1W86T=GDMCC 1.1901T=KACC 21988T), Dyella subtropica sp. nov. (type strain RXD159T=GDMCC 1.1902T=KACC 21989T), Dyella silvatica sp. nov. (type strain RBB189T=GDMCC 1.1900T=KACC 21990 T) and Dyella silvae sp. nov. (type strain RLT163T=GDMCC 1.1916T=KACC 21991T) are proposed.

An aerobic, non-motile, Gram-stain-positive bacterium, designated strain NEAU-Y5T, was isolated from a soil sample collected from Northeast Agricultural University, Heilongjiang province. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-Y5T belonged to the genus and showed high 16S rRNA sequence similarity to Isoptericola variabilis (98.9 %), Isoptericola nanjingensis (98.9 %), Isoptericola cucumis (98.5 %), Isoptericola hypogeus (98.5 %), Isoptericola dokdonensis (98.5 %), Isoptericola jiangsuensis (98.3 %), and Isoptericola halalbus (98.1 %), followed by other members of the genus Isoptericola (<98 %), and phylogenetically clustered with I. dokdonensis and I. jiangsuensis. Strain NEAU-Y5T was found to grow at 4-40 °C (optimum, 28 °C), pH 6.0-12.0 (optimum, pH 7.0), and tolerated 0-6 % NaCl (w/v). The cell-wall peptidoglycan type was l-Lys-d-Asp. The whole-cell hydrolysates contained glucose, galactose, and ribose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, and glucosamine unknown phospholipid. Major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The DNA G+C content was 73.4 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain NEAU-Y5T and the type strains of the genus Isoptericola ranged from 18.6 to 23.5 % and from 77.3 to 81.6 %, respectively. Based on morphological, physiological, chemotaxonomic, and phylogenetic data, as well as digital DNA-DNA hybridization and average nucleotide identity values, the novel strain NEAU-Y5T could be differentiated from its closest relatives. Therefore, the strain represents a novel species of the genus Isoptericola, for which the name Isoptericola luteus sp. nov. is proposed. The type strain is NEAU-Y5T (=CCTCC AA 2019087T=DSM 110637T).

A novel heterotrophic, cold-tolerant bacterium, designated Pseudomonas zhanjiangensis 25A3ET, was isolated from mangrove sediment and demonstrated excellent efficiency in cold wastewater treatment. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain 25A3ET within the genus Pseudomonas, showing the highest similarity (98.7%) with Pseudomonas kurunegalensis LMG 32023T. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were below the species delineation thresholds (70% for dDDH, 95% for ANI), indicating that strain 25A3ET represents a novel species. This strain demonstrated high efficiency in removing nitrogen (N) and organic pollutants under low-temperature conditions. Specifically, it achieved 72.9% removal of chemical oxygen demand (COD), 70.6% removal of ammoniacal nitrogen (NH4 +-N), and 69.1% removal of total nitrogen (TN) after 96 h at 10°C. Genomic analysis identified key genes associated with cold adaptation, nitrogen removal and organic matter degradation. These findings indicate that Pseudomonas zhanjiangensis 25A3ET holds significant potential for application in cold temperature wastewater treatment, offering a promising solution for environmental remediation in regions with low ambient temperatures.

Nine novel Gram-stain-positive bacteria were investigated by a polyphasic taxonomic approach. Based on the analysis of 16S rRNA gene sequences, these strains belonged to the Bacillus cereus group, sharing over 97 % similarity with the known species of this group, and less than 95 % similarity with other species of the genus Bacillus. Multilocus sequence typing analysis showed that they formed nine robust and well-separated branches from the known species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the nine strains were, respectively, below the 70 and 96 % threshold values for species definition, and between each strain and the known type strains of this group were also below the two threshold values. On the basis of the phenotypic and phylogenetic data, along with low dDDH and ANI values among these strains, these bacteria are assigned to the following nine novel species of the B. cereus group: Bacillus paranthracis sp. nov., type strain Mn5T (=MCCC 1A00395T=KCTC 33714T=LMG 28873T); Bacillus pacificus sp. nov., type strain EB422T (=MCCC 1A06182T=KCTC 33858T); Bacillus tropicus sp. nov., type strain N24T (=MCCC 1A01406T=KCTC 33711T=LMG 28874T); Bacillus albus sp. nov., type strain N35-10-2T (=MCCC 1A02146T=KCTC 33710T=LMG 28875T); Bacillus mobilis sp. nov., type strain 0711P9-1T (=MCCC 1A05942T=KCTC 33717T=LMG 28877T); Bacillus luti sp. nov., type strain TD41T (=MCCC 1A00359T=KCTC 33716T=LMG 28872T); Bacillus proteolyticus sp. nov., type strain TD42T (=MCCC 1A00365T=KCTC 33715T=LMG 28870T); Bacillus nitratireducens sp. nov., type strain 4049T (=MCCC 1A00732T=KCTC 33713T=LMG 28871T); and Bacillus paramycoides sp. nov., type strain NH24A2T (=MCCC 1A04098T=KCTC 33709T=LMG 28876T).

Lactic acid bacteria are commonly in the fermentation industry and pose potential positive effects on health. In this study, a new lactic acid bacterium was isolated from fermented vegetable extracts in Myoko, Niigata, Japan. This bacterium is fructophilic, acidophilic, and hard to grow on agar medium. The isolate is Gram-stain-positive, non-spore-forming, non-motile, rod-shaped, and catalase-negative. Growth occurred at pH 3.5-5.5, with optimal growth at pH 4.5-5.0. The cells formed colonies on a solid MRS medium with 20% (w/v) sucrose and 0.8% (w/v) gellan gum under anaerobic conditions. The bacterium was able to grow on up to 50% (w/v) sucrose but not on d-glucose. Moreover, 16S rRNA gene sequence analysis revealed that the strain was most closely related to Apilactobacillus ozensis (93.1% sequence similarity). The values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid sequence identity, and amino acid identity of conserved genes were calculated between the isolated strain (type strain is WR16-4T = NBRC 115064T = DSM 112857T) and its phylogenetically closest type strains. The average nucleotide identity values (73.36-78.28%) and DNA-DNA hybridization values (16.3-32.9%) were significantly lower than the threshold values for species boundaries. The average amino acid sequence identity values (53.96-60.88%) were significantly below the threshold boundary of genus demarcation (68%). The amino acid identity of conserved genes values compared to strain WR16-4T were the genera Apilactobacillus, Nicoliella spurrieriana SGEP1_A5T, Acetilactobacillus jinshanensis HSLZ-75T, and Fructilactobacillus were 62.51-63.79%, 62.87%, 62.03%, and 58.00-61.04%, respectively. The 16S rRNA gene and core genome phylogenetic trees suggested that this novel strain was most closely related to the type strain of A. jinshanensis HSLZ-75T. Based on the physiological, morphological, and phenotypical characteristics of strain WR16-4T, we propose its classification as a novel genus, Philodulcilactobacillus myokoensis gen. nov., sp. nov.

Two Gram-stain-negative, aerobic, rod-shaped, non-endospore-forming bacteria, designated as strain MH1T and MH2T, were isolated from branches of wilted pepper plants (Capsicum annuum) collected from a farmland in Machong town, Guangdong, China, and investigated using a polyphasic approach. MH1T grew at temperatures of 4-42 °C (optimum 28 °C), with 0-6.0 % (w/v) NaCl and at pH 4.0-10.0 (optimum pH 4.0). MH2T grew at temperatures of 4-42 °C (optimum 28 °C), with 0-6.0% (w/v) NaCl and at pH 4.0-10.0 (optimum pH 5.0). Analysis of the 16S rRNA gene sequence indicated that MH1T belongs to Stenotrophomonas and MH2T belongs to Pseudomonas. Genome-based phylogenetic analysis further established that MH1T shares the closest evolutionary relationships with Stenotrophomonas humi DSM 18929 and Stenotrophomonas terrae DSM 18941, and MH2T is sister to Pseudomonas wayambapalatensis RW3S1. Whole-genome comparisons between MH1T and known Stenotrophomonas species revealed average nucleotide identity (ANI) values up to 84.5%, as well as digital DNA-DNA hybridization (dDDH) values up to 28.3%, both substantially lower than the accepted thresholds for species delineation (ANI: 95%; dDDH: 70%). The ANI and dDDH values between MH2T and known Pseudomonas species were at most 94.6 and 59.2 %, respectively. Additional biochemical and physiological analyses further support that MH1T and MH2T represent a novel species in Stenotrophomonas and Pseudomonas, respectively. Notably, the differences in carbon source utilization could differentiate MH1T and its close relatives in Stenotrophomonas. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0 for MH1T and were C16 : 0, C18 : 1 ω7c/C18 : 1 ω6c (summed feature 8), C16 : 1 ω7c/C16 : 1 ω6c (summed feature 3) and C17 : 0 cyclo for MH2T. Therefore, we propose a new species Stenotrophomonas capsici sp. nov., with MH1T (=GDMCC 1.3749T=JCM 36317T) as the type strain, and a new species Pseudomonas machongensis sp. nov., with MH2T (=GDMCC 1.3750T=JCM 36318T) as the type strain. The MH1T genome has a size of 4.18 Mb and a GC-content of 67.19 mol%, while the MH2T genome has a size of 5.71 Mb and a GC-content of 63.12 mol%.

An aerobic bacterium, designated as PT-12T, was isolated from soil collected from agriculture field, and its taxonomic position was validated through a comprehensive polyphasic methodology. The strain was identified as Gram-stain-negative, non-motile, rod-shaped, and catalase- and oxidase-positive. The yellow-colored colonies showed growth ability at temperature range of 18-37°C, NaCl content of 0-1.0% (w/v), and at a pH of 6.0-8.0. The 16S rRNA gene and phylogenetic analysis showed that strain PT-12T affiliated with the genus Sphingomonas in the family Sphingomonadaceae, and displayed the highest 16S rRNA nucleotide sequence similarity with Sphingomonas limnosediminicola 03SUJ6T (98.4%). The genome size of strain PT-12T was 2,656,862bp and the DNA G + C content estimated from genome was 63.5%. The highest values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were observed between strain PT-12T and Sphingomonas segetis YJ09T, accounting to 76.2% and 20.2%, respectively. In addition, both ANI and dDDH values between strain PT-12T and other phylogenetically related neighbors ranged between 69.6% and 76.2% and 18.4% and 20.2%, respectively. Chemotaxonomic features exhibited Q-10 as the only ubiquinone; homospermidine as the major polyamine; summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and 10-methyl C18:0 as the notable fatty acids; and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and sphingoglycolipid as dominating polar lipids. Overall, the comprehensive polyphasic data supported that strain PT-12T represents a novel bacterial species within the genus Sphingomonas. Accordingly, we propose the name Sphingomonas flavescens sp. nov. The type strain is PT-12T (= KCTC 92114T = NBRC 115717T).

A novel species, Gulbenkiania indica, was reported from a sulfur spring. During the proposal of this species, it was reported that it shared 99.0% 16S rRNA gene sequence similarity with the type strain of Gulbenkiania mobilis. Despite its high 16S rRNA gene sequence similarity, a 30% DNA-DNA hybridization value was reported, which was below the threshold for species delineation (70%). Although DNA-DNA hybridization was considered the gold standard for species delineation, but often prone to errors. In the present study, the taxonomic position of Gulbenkiania indica was re-evaluated by genome relatedness, phylogenetic and phylogenomic analysis. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between Gulbenkiania mobilis DSM 18507T and Gulbenkiania indica DSM 17901T was 99.2 and 93.7%, respectively, which was above the cutoff value (95–96%, ANI; 70%, dDDH) for species delineation. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic (based on 71 bacterial single copy genes) trees, Gulbenkiania mobilis and Gulbenkiania indica clustered together. Based on the above results, we propose to reclassify Gulbenkiania indica Jyoti et al. 2010 as a later heterotypic synonym of Gulbenkiania mobilis Vaz-Moreira et al. 2007.