Unidentified Lipids Research Articles

Defluviimonas sediminis sp. nov., isolated from mangrove sediment.

A Gram-stain-negative, facultatively aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT324T, was isolated from a surface mangrove sediment sample from Shenzhen, PR China. The taxonomic position of strain FT324T was determined by a combination of phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT324T grew at 20-40 °C (optimum, 30-37 °C), pH 5.0-9.0 (optimum, pH 8.0) and in the presence of 0-3 % (w/v) NaCl (optimum, 1 %). Its full-length 16S rRNA gene sequence was the most similar to Frigidibacter oleivorans XJ4T (97.4 %), followed by Defluviimonas denitrificans DSM 18921T (96.62 %), Pseudothioclava arenosa CAU 1312T (96.54 %) and Defluviimonas nitratireducens DL5-4T (96.47 %). The major fatty acids (>10 %) of FT324T were C19 : 0 cyclo ω8c (51.9 %) and summed feature 8(29.6 %). The predominant respiratory quinone was Q-10. Its polar lipid profile contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid, one unidentified lipid and two unidentified phospholipids. Its estimated genome size was 4 294 115 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT324T should represent a novel species of the genus Defluviimonas, for which the name Defluviimonas sediminis sp. nov. is proposed (=MCCC 1K07685T=KCTC 92477T).

Description and genome-wide analysis of Profundicola chukchiensis gen. nov., sp. nov., marine bacteria isolated from bottom sediments of the Chukchi Sea.

Two Gram-negative, aerobic halophilic non-motile strains designated KMM 9713 and KMM 9724T were isolated from the bottom sediments sampled from the Chukchi Sea in the Arctic Ocean, Russia. The novel strains grew in 0.5-5% NaCl, at 7-42°C, and pH 5.5-10.5. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences revealed that strains KMM 9713 and KMM 9724T were close to each other and shared the highest 16S rRNA gene sequence similarity of 91.28% with the type strain Ornithobacterium rhinotracheale DSM 15997T and 90.15-90.92% with the members of the genus Empedobacter in the family Weeksellaceae. Phylogenetic trees indicated that strains KMM 9713 and KMM 9724T formed a distinct line adjacent to their relative O. rhinotracheale DSM 15997T. The average nucleotide identity values between strain KMM 9724T and O. rhinotracheale DSM 15997T, Empedobacter brevis NBRC 14943T, and Moheibacter sediminis CGMCC 1.12708T were 76.73%, 75.78%, and 74.65%, respectively. The novel strains contained the predominant menaquinone MK-6 and the major fatty acids of iso-C17:0 3-OH, iso-C15:0 followed by iso-C17:1ω6. Polar lipids consisted of phosphatidylethanolamine, one an unidentified aminophospholipid, two unidentified aminolipids, and two or three unidentified lipids. The DNA G+C contents of 34.5% and 34.7% were calculated from genome sequence of the strains KMM 9713 and KMM 9724T, respectively. Based on the phylogenetic evidence and distinctive phenotypic characteristics, strains KMM 9713 and KMM 9724T are proposed to be classified as a novel genus and species Profundicola chukchiensis gen. nov., sp. nov. The type strain of Profundicola chukchiensis gen. nov., sp. nov. is strain KMM 9724T (= KACC 22806T).

Description of Flavimaribacter sediminis gen. nov., sp. nov., a New Member of the Family Rhizobiaceae Isolated from Marine Sediment.

A novel Gram-staining-negative, aerobic and rod-shaped bacterium, designated WL0058T, was isolated from coastal sediment sample collected in Nantong city, Jiangsu province of China (120° 51' 13″ E, 32° 6' 26″ N) in October 2020. Strain WL0058T was found to grow at 4-37°C (optimum, 28°C) with 1.5-4.0% NaCl (optimum, 4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0-10.0 (optimum, pH 6.0). Phylogenetic trees constructed based on 16S rRNA gene sequence indicated that strain WL0058T is a member of the family Rhizobiaceae, shared the highest similarity with "Hoeflea prorocentri" CCTCC AB 2016294T (97.7%) and constituted a sub-cluster within the family with it, while the similarity with others in the family Rhizobiaceae was lower than 97.0%. The G + C content of genomic DNA was 59.5mol%. Polar lipids profile of strain WL0058T included phosphatidylcholine (PC), phosphatidylethanolamine (PE), and glycolipid (GL), phosphatidylmonomethylethanolamine (PME) and two unidentified polar lipids (L). The major isoprenoid quinone was determined to be Q-10 and the major fatty acids were C16:0, C18:0, summed features 4 (iso-C17:1 and/or anteiso-C17:1), and summed features 8 (C18:1ω6c and/or C18:1ω7c). As inferred from the morphology, physiology, and biochemical analysis, genotypic characteristics, and the phylogenetic trees, strain WL0058T ought to be recognized as a novel genus in the family Rhizobiaceae, for which the name Flavimaribacter sediminis gen. nov., sp. nov. The type strain of Flavimaribacter sediminis gen. nov., sp. nov. is WL0058T (= MCCC 1K06063T = JCM 34659T = GDMCC 1.2448T).

Marinobacterium lacunae sp. nov. isolated from estuarine sediment.

A novel motile bacterium was isolated from a sediment sample collected in Kochi backwaters, Kerala, India. This bacterium is Gram negative, rod shaped, 1.0-1.5µm wide, and 2.0-3.0µm long. It was designated as strain AK27T. Colonies were grown on marine agar displayed circular, off-white, shiny, moist, translucent, flat, margin entire, 1-2mm in diameter. The major fatty acids identified in this strain were C18:1 ω7c, C16:0, and summed in feature 3. The composition of polar lipids in the strain AK27T included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified amino lipid, two unidentified aminophospholipids, two unidentified phospholipids, and six unidentified lipids. The genomic DNA of strain AK27T exhibited a G+C content of 56.4mol%. Based on the analysis of 16S rRNA gene sequence, strain AK27T showed sequence similarity to M. ramblicola D7T and M. zhoushanense WM3T as 98.99% and 98.58%, respectively. Compared to other type strains of the Marinobacterium genus, strain AK27T exhibited sequence similarities ranging from 91.7% to 96.4%. When compared to Marinobacterium zhoushanense WM3T and Marinobacterium ramblicola D7T, strain AK27T exhibited average nucleotide identity values of 80.25% and 79.97%, and dDDH values of 22.9% and 22.6%, respectively. The genome size of the strain AK27T was 4.55Mb, with 4,229 coding sequences. Based on the observed phenotypic and chemotaxonomic features, and the results of phylogenetic and phylogenomic analysis, this study proposes the classification of strain AK27T as a novel species within the genus Marinobacterium. The proposed name for this novel species is Marinobacterium lacunae sp. nov.

Description of Salinimicrobium tongyeongense sp. nov., isolated from seawater.

A Gram-stain-negative, non-motile by gliding and moderately halophilic rod-shaped bacterium HN-2-9-2T was isolated from seawater in Tongyeong, Republic of Korea. The strain grew at concentrations of 0.5‒7 % (w/v) NaCl, at pH 5.5‒8.5 and in a temperature range of 18‒45 °C. HN-2-9-2T shared the highest 16S rRNA gene sequence percentage with Salinimicrobium xinjiangense BH206T (98.2 %). The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) values between HN-2-9-2T and the S. xinjiangense BH206T were 76.0 %, 81.9 % and 19.7 %, respectively. The genome comprised 3 509 958 bp with a DNA G+C content of 43.0%. HN-2-9-2T contained MK-6 as the sole menaquinone. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH, iso-C16 : 0, iso-C15 : 1G and summed feature 9, comprising iso-C17 : 1ω6c/C16 : 1 10-methyl. The polar lipids contained phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids, an unidentified glycolipid and six unidentified lipids. The polyphasic taxonomic properties indicate that the strain represents a novel species within the genus Salinimicrobium, for which the name Salinimicrobium tongyeongense sp. nov. is proposed. The type strain is HN-2-9-2T (=KCTC 82934T=NBRC 115920T).

Parerythrobacter lacustris sp. nov., a novel member of the family Erythrobacteraceae isolated from an inland alpine lake.

A novel bacterium, designated as strain RS5-5T, was isolated from lake water in northwestern China. Cells of the isolate were observed to be rod shaped and Gram stain negative. Its growth occurred at 4-37℃, pH 6.5-9.0 and in the presence of 0-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RS5-5T was most closely related to Qipengyuania sediminis GDMCC 1.2497T (97.5%), followed by Erythrobacter dokdonensis DSW-74T (97.3%) and Qipengyuania algicida GDMCC 1.2535T (97.0%). Phylogenomic analysis revealed that strain RS5-5T formed a distinct branch with the genus Parerythrobacter. The sole quinone was ubiquinone-10, and the major fatty acids (≥ 10%) were unsaturated fatty acids including C17:1 ω6c, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified sphingoglycolipid, three unidentified glycolipids, one unidentified aminoglycolipid, one unidentified aminolipid, two unidentified phospholipids and four unidentified polar lipids. Chemotaxonomic characteristics of strain RS5-5T were coincident with those of the genus Parerythrobacter members. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain RS5-5T and two Parerythrobacter reference strains were in the ranges of 73.2-77.7%, 69.0-78.0% and 18.9-20.4%, respectively. The genomic DNA G + C content of strain RS5-5T was 64.1%. The results of phenotypic, phylogenetic and genomic analyses suggested that strain RS5-5T represents a novel species in the genus Parerythrobacter, for which the name Parerythrobacter lacustris sp. nov. is proposed. The type strain is RS5-5T (= GDMCC 1.3163T = KCTC 92277T).

Gimibacter soli gen. nov. sp. nov., isolated from mangrove soil and insight into its ecological distribution and metabolic potential.

A Gram-stain-negative, facultatively anaerobic, motile and rod-shaped bacterium, designated as 6D33T, was isolated from mangrove soil. Growth was found to occur at 15-32 °C (optimum, 28 °C), at pH 6-9 (optimum, pH 7) and in 0-3 % NaCl (optimum, 1 %, w/v). The results of 16S rRNA gene-based analysis showed that strain 6D33T belonged to the family Temperatibacteraceae, sharing 93.1-94.4 % identity with its close neighbours within the genus Kordiimonas. The phylogenomic results indicated that strain 6D33T formed an independent branch distinct from type strains of the genus Kordiimonas. The overall genome relatedness indices of digital DNA-DNA hybridization, average nucleotide identity and amino acid identity values showed that strain 6D33T represents a novel species of a novel genus. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of strain 6D33T were summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1 ω9c), summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C15 : 0; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids; the only respiratory quinone was ubiquinone-10. The genomic size and DNA G+C contents were 3.59 Mbp and 60.84 mol%, respectively. The 16S rRNA gene sequence reads abundance profiles revealed that the rare taxon is prevalent in marine environments, especially in sediments. Genome-scale metabolic reconstruction of strain 6D33T revealed a heterotrophic lifestyle and many pathways responsible for the degradation of aromatic compounds, suggesting application potential in aromatic hydrocarbon removal. Based on its genotypic and phenotypic characteristics, strain 6D33T is concluded to represent a novel species of the novel genus in the family Temperatibacteraceae, for which the name Gimibacter soli gen. nov. sp. nov. is proposed. The type strain of the type species is 6D33T (=GDMCC 1.1959T=KCTC 82335T).

Selenomonas caprae sp. nov., an obligately anaerobic and volatile fatty acid producing bacterium from ruminal fluid of domestic goat (Capra hircus L.).

A novel Gram-stain-negative, motile, obligately anaerobic bacterium strain mPRGC8T was isolated from the ruminal fluid of a domestic goat (Capra hircus L.) in Nakhon Pathom province, Thailand. The strain grew at 20-45 °C (optimum, 37 °C), pH 6.0-9.0 (optimum, pH 7.5) and 3 % (w/v) NaCl. It produced acetate, propionate, valerate, caproate and heptanoate from glucose. The 16S rRNA gene sequence analysis indicated that strain mPRGC8T belonged to the genus Selenomonas and was closely related to Selenomonas ruminantium subsp. ruminantium DSM 2150T (98.0 %) and Selenomonas ruminantium subsp. lactilytica JCM 6582T (97.9 %). The in silico DNA G+C content was 53.0 mol %. Strain mPRGC8T showed average nucleotide identity, digital DNA-DNA hybridization and average animo acid identity values with Selenomonas montiformis JCM 34373T, S. ruminantium subsp. lactilytica JCM 6582T and S. ruminantium subsp. ruminantium DSM 2150T ranging from 84.9 to 86.0 %, 21.3 to 21.8 % and 73.8 to 76.1 %, respectively. The predominant cellular fatty acids were C16 : 1 ω9c and C18 : 1 ω9c. Phosphatidylethanolamine, three unidentified aminophospholipids, two unidentified ninhydrin positive glycolipids, an unidentified phospholipid and an unidentified lipid were detected as polar lipids. The genomic and phenotypic characteristics of strain mPRGC8T strongly support its classification as representative of new species of the genus Selenomonas for which the name Selenomonas caprae sp. nov. is proposed. The type strain is mPRGC8T (=JCM 33725T=KCTC 25178T).

Larsenimonas rhizosphaerae sp. nov., isolated from a tidal mudflat.

A Gram-reaction-negative, aerobic, motile, rod-shaped bacterium, designated GH3-8T, was isolated from rhizosphere mudflats of halophytes on the seashore of Gangwha Island, Republic of Korea. Growth was observed at pH 4-10 (optimum, pH 7-8), at 4-40 °C (optimum, 37 °C) and in the presence of 0.5-20 % (w/v) NaCl (optimum, 4 %). The predominant respiratory quinone was Q-9. The major fatty acids were C18 : 1 ω7c, C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C12 : 0 3OH. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified phosphoglycoaminolipid, an unidentified glycoaminolipid, two unidentified phospholipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences exhibited that the isolate belonged to the family Halomonadaceae, with the most closely related species, Larsenimonas suaedae (98.1 % sequence similarity) and Larsenimonas salina (97.9 %). Sequence similarity values between the isolate and other representatives of the family Halomonadaceae were all below 95.3 %. The values of average nucleotide identity between strain GH3-8T and members of the genus Larsenimonas were 73.42 % with L. salina CCM 8464T and 72.38 % with L. suaedae DSM 22428T. Strain GH3-8T showed digital DNA-DNA hybridization values of 18.5-18.6 % with members of the genus Larsenimonas. Based on phenotypic and chemotaxonomic distinctiveness together with low overall genomic relatedness indices and phylogenetic data, the isolate is considered to represent a new species of the genus Larsenimonas, for which the name Larsenimonas rhizosphaerae sp. nov. is proposed, with the type strain GH3-8T (=KCTC 62127T=NBRC 113214T).

Habitat distribution of the genus Belliella in continental waters and the description of Belliella alkalica sp. nov., Belliella calami sp. nov. and Belliella filtrata sp. nov.

The genus Belliella belongs to the family Cyclobacteriaceae (order Cytophagales, phylum Bacteroidota) and harbours aerobic chemoheterotrophic bacteria. Members of this genus were isolated from various aquatic habitats, and our analysis based on global amplicon sequencing data revealed that their relative abundance can reach up to 5-10 % of the bacterioplankton in soda lakes and pans. Although a remarkable fraction of the most frequent genotypes that we identified from continental aquatic habitats is still uncultured, five new alkaliphilic Belliella strains were characterized in detail in this study, which were isolated from three different soda lakes and pans of the Carpathian Basin (Hungary). Cells of all strains were Gram-stain-negative, obligate aerobic, rod-shaped, non-motile and non-spore-forming. The isolates were oxidase- and catalase-positive, red-coloured, but did not contain flexirubin-type pigments; they formed bright red colonies that were circular, smooth and convex. Their major isoprenoid quinone was MK-7 and the predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 containing C16 : 1 ω6c and/or C16 : 1 ω7c. The polar lipid profiles contained phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, and several unidentified lipids and aminolipids. Based on whole-genome sequences, the DNA G+C content was 37.0, 37.1 and 37.8 mol % for strains R4-6T, DMA-N-10aT and U6F3T, respectively. The distinction of three new species was confirmed by in silico genomic comparison. Orthologous average nucleotide identity (<85.4 %) and digital DNA-DNA hybridization values (<38.9 %) supported phenotypic, chemotaxonomic and 16S rRNA gene sequence data and, therefore, the following three novel species are proposed: Belliella alkalica sp. nov. (represented by strains R4-6T=DSM 111903T=JCM 34281T=UCCCB122T and S4-10), Belliella calami sp. nov. (DMA-N-10aT=DSM 107340T=JCM 34280T=UCCCB121T) and Belliella filtrata sp. nov. (U6F3T=DSM 111904T=JCM 34282T=UCCCB123T and U6F1). Emended descriptions of species Belliella aquatica, Belliella baltica, Belliella buryatensis, Belliella kenyensis and Belliella pelovolcani are also presented.

Muricauda okinawensis sp. Nov. and Muricauda yonaguniensis sp. Nov., Two Marine Bacteria Isolated from the Sediment Core near Hydrothermal Fields of Southern Okinawa Trough.

Two strains, 81s02T and 334s03T, were isolated from the sediment core near the hydrothermal field of southern Okinawa Trough. The cells of both strains were observed to be rod-shaped, non-gliding, Gram-staining negative, yellow-pigmented, facultatively anaerobic, catalase and oxidase positive, and showing optimum growth at 30 °C and pH 7.5. The strains 81s02T and 334s03T were able to tolerate up to 10% and 9% (w/v) NaCl concentration, respectively. Based on phylogenomic analysis, the average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values between the two strains and the nearest phylogenetic neighbors of the genus Muricauda were in range of 78.0-86.3% and 21.5-33.9%, respectively. The strains 81s02T and 334s03T shared 98.1% 16S rRNA gene sequence similarity to each other but were identified as two distinct species based on 81.4-81.5% ANIb, 85.5-85.6% ANIm and 25.4% dDDH values calculated using whole genome sequences. The strains 81s02T and 334s03T shared the highest 16S rRNA gene sequence similarity to M. lutimaris SMK-108T (98.7%) and M. aurea BC31-1-A7T (98.8%), respectively. The major fatty acid of strains 81s02T and 334s03T were identified similarly as iso-C15:0, iso-C17:0 3-OH and iso-C15:1 G, and the major polar lipids of the both strains consisted of phosphatidylethanolamine and two unidentified lipids. The strains contained MK-6 as their predominant menaquinone. The genomic G+C contents of strains 81s02T and 334s03T were determined to be 41.6 and 41.9 mol%, respectively. Based on the phylogenetic and phenotypic characteristics, both strains are considered to represent two novel species of the genus Muricauda, and the names Muricauda okinawensis sp. nov. and Muricauda yonaguniensis sp. nov. are proposed for strains 81s02T (=KCTC 92889T = MCCC 1K08502T) and 334s03T (=KCTC 92890T = MCCC 1K08503T).

Sphingomonas lycopersici sp. nov., isolated from tomato rhizosphere soil.

Two aerobic, Gram-stain-negative, non-motile and non-spore-forming rods bacterial strains, designated MMSM20T and MMSM24, were isolated from tomato rhizosphere soil and could produce indole-3-acetic acid and siderophore. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that strains MMSM20T and MMSM24 belonged to the genus Sphingomonas and were most closely related to three validly published species Sphingomonas jeddahensis G39T, Sphingomonas mucosissima DSM 17494T and Sphingomonas dokdonensis DSM 21029T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains MMSM20T and MMSM24 were 97.6 and 81.0 %, respectively, demonstrating that they were conspecific. The ANI and dDDH values between the two strains and the three type strains above were below the threshold values for species delimitation. The genomic DNA G+C contents of strains MMSM20T and MMSM24 were 66.6 and 66.4 mol%, respectively. The major fatty acids of the two strains were identified as C14 : 0 2OH, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c); the predominant quinone was ubiquinone 10; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and unidentified lipids. Results of phenotypic and genotypic analyses supported that strains MMSM20T and MMSM24 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lycopersici sp. nov. is proposed. The type strain is MMSM20T (=GDMCC 1.3401T=JCM 35647T).

Thermomonas mangrovi sp. nov., isolated from soil of a mangrove nature reserve.

A Gram-stain-negative, non-motile, aerobic and ovoid-rod-shaped bacterial strain, designated as 2C3345T, was isolated from soil of a mangrove nature reserve in Shenzhen, PR China and its taxonomic position was investigated. The 16S rRNA gene sequence of strain 2C3345T exhibited the highest similarity value to that of the type strains Thermomonas aquatica NBRC 113114T (98.4 %), Thermomonas carbonis KCTC 42013T (98.1 %), Thermomonas brevis DSM 15422T (98.0 %) and Thermomonas haemolytica DSM 13605T (97.9 %). Strain 2C3345T grew optimally at 28-30 °C, pH 7.0 and without NaCl. The predominant ubiquinone in 2C3345T was identified as Q-8. The major fatty acids of 2C3345T were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (is0-C17:1ω9c and/or 10-methyl C16:0). The major polar lipids of 2C3345T were phosphatidylcholine (PC), phosphatidylglycerol (PG), diphosphatidglycerol (DPG), phosphatidylethanolamine (PE), an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. The DNA G+C content of strain 2C3345T was 69.9 %. The draft genome sequence of 2C3345T included 2 888 645 bp in total (N50=310 730 bp) with a medium read coverage of 388.6×and 21 scaffolds. In silico DNA-DNA hybridisation with type strains of species of the genus Thermomonas showed 24.4, 22.4, 24.1 and 23.2% relatedness to T. aquatica NBRC 113114T, T. carbonis KCTC 42013T, T. brevis DSM 15422T and T. haemolytica DSM 13605T, respectively. And the average nucleotide identity by blast (ANIb) values between 2C3345T and these four reference strains were 81.9, 80.0, 81.2 and 80.6 %, respectively, lower than the 95-96% threshold value for dividing prokaryotic species. On the basis of its phenotypic, chemotaxonomic, phylogenetic and phylogenomic properties, strain 2C3345T is considered to represent a novel species within the genus Thermomonas, for which the name Thermomonas mangrovi sp. nov. is proposed. The type strain is 2C3345T (=KCTC 92730T =MCCC 1K08335T).

Yinghuangia soli sp. nov., isolated from soil of weathering dolomite in a karst area.

A Gram-stain-positive, aerobic actinomycete strain, designated KLBMP 8922T, was isolated from a soil sample collected from weathering dolomite crust in Guizhou Province, PR China. KLBMP 8922T showed the 16S rRNA gene similarities to Yinghuangia seranimata CCTCC AA 206006T (98.7 %), Yinghuangia catbensis VN07A0015T (98.3 %) and Yinghuangia aomiensis M24DS4T (98.2 %). The taxonomic status of this strain was investigated by using a polyphasic approach. The aerial mycelia of KLBMP 8922T formed spore chains, and spores were cylindrical with smooth surfaces. The whole-cell sugars were ribose, mannose and galactose with traces of glucose and xylose. The diagnostic amino acids of the cell wall were ll-diaminopimelic acid, alanine and glutamic acid. The predominant menaquinones were MK-9(H6) and MK-9(H8). The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The major cellular fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0 and iso-C16 : 1H. The genomic DNA G+C content was 72.0 mol%. The digital DNA-DNA hybridization (dDDH) value between KLBMP 8922T and Y. seranimata CCTCC AA 206006T was 24.1 %, and the average nucleotide identity (ANI) value was 81.0 %. On the basis of a combination of morphological, chemotaxonomic and phylogenetic characteristics, strain KLBMP 8922T represents a novel species of the genus Yinghuangia for which the name Yinghuangia soli sp. nov. is proposed. The type strain was KLBMP 8922T (= CGMCC 1.19360T = NBRC 115572T).

Gracilimonas sediminicola sp. nov., a moderately halotolerant bacterium isolated from seaweed sediment collected in the East Sea, Republic of Korea.

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated as strain CAU 1638T, was isolated from seaweed sediment collected in the Republic of Korea. The cells of strain CAU 1638T grew at 25-37 °C (optimum, 30 °C), at pH 6.0-7.0 (optimum, pH 6.5) and in the presence of 0-10% NaCl (optimum, 2 %). The cells were positive for catalase and oxidase and did not hydrolyse starch and casein. Strain CAU 1638T was most closely related to Gracilimonas amylolytica KCTC 52885T (97.7 %), followed by Gracilimonas halophila KCTC 52042T (97.4 %), Gracilimonas rosea KCCM 90206T (97.2 %), Gracilimonas tropica KCCM 90063T and Gracilimonas mengyeensis DSM 21985T (97.1 %), as revealed by 16S rRNA gene sequencing. MK-7 was the major isoprenoid quinone, and iso-C15 : 0 and C15 : 1 ω6c were the major fatty acids. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids, two unidentified glycolipids and three unidentified phospholipids. The G+C content of the genome was 44.2 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain CAU 1638T and the reference strains were 73.1-73.9 % and 18.9-21.5 %, respectively. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CAU 1638T represents a novel species of the genus Gracilimonas, for which the name Gracilimonas sediminicola sp. nov. is proposed. The type strain is CAU 1638T (=KCTC 82454T=MCCC 1K06087T).

Description of Hymenobacter sediminicola sp. nov., isolated from contaminated sediment.

A polyphasic taxonomic study was conducted on two Gram-negative, non-sporulating, non-motile bacterial strains, S2-20-2T and S2-21-1, isolated from a contaminated freshwater sediment in China. Comparative 16S rRNA gene sequence studies revealed a clear affiliation of two strains with Bacteroidetes, which showed the highest pairwise sequence similarities with Hymenobacter duratus BT646T (99.3%), Hymenobacter psychrotolerans Tibet-IIU11T (99.3%), Hymenobacter kanuolensis T-3T (97.6%), Hymenobacter swuensis DY53T (96.9%), Hymenobacter tenuis POB6T (96.8%), Hymenobacter seoulensis 16F7GT (96.7%), and Hymenobacter rigui KCTC 12533T (96.5%). The phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Hymenobacter. Major fatty acids were identified as iso-C15:0, anteiso-C15:0, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c/t) and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). Major cellular polar lipids were identified as phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophosopholipid and an unidentified lipid. The respiratory quinone was detected as MK-7 and the genomic DNA G + C content was determined to be 57.9% (genome) for type strain S2-20-2T and 57.7mol% (HPLC) for strain S2-21-1. The observed ANI and dDDH values between strain S2-20-2T and its closely related strains were 75.7-91.4% and 21.2-43.9%, respectively. Based on physiological, biochemical, genetic and genomic characteristics, we propose that strains S2-20-2T and S2-21-1 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter sediminicola sp. nov. is proposed. The type strain is S2-20-2T (= CGMCC 1.18734T = JCM 35801T).

Georgenia halotolerans sp. nov., a halotolerant actinobacterium isolated from Taklamakan desert soil.

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and rod-shaped actinobacterium, designated strain 10Sc9-8T, was isolated from Taklamakan desert soil sampled in the Xinjiang Uygur Autonomous Region, China. Strain 10Sc9-8T grew at 8‒37 °C (optimum, 28‒30 °C), pH 6.0‒10.0 (optimum, pH 7.0-8.0) and in the presence of 0‒15 % (w/v) NaCl (optimum, 0-3 %). Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 10Sc9-8T was affiliated with members of the genus Georgenia and showed the highest 16S rRNA gene sequence similarity to Georgenia yuyongxinii Z443T (97.4 %). Phylogenomic analysis based on the whole genome sequences indicated that strain 10Sc9-8T should be assigned into the genus Georgenia. The average nucleotide identity and digital DNA-DNA hybridization values calculated from the whole genome sequences indicated that strain 10Sc9-8T was clearly separated from other closely related species of the genus Georgenia with values below the thresholds for species delineation. Chemotaxonomic analyses showed that the cell-wall peptidoglycan was in a variant of A4α type with an interpeptide bridge comprising l-Lys-l-Ala-Gly-l-Asp. The predominant menaquinone was MK-8(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, several unidentified phospholipids, glycolipids and one unidentified lipid. The major fatty acids were anteiso-C15 : 0, anteiso-C15 : 1 A and C16 : 0. The genomic DNA G+C content was 72.7 mol%. On the basis of phenotypic, phylogenetic and phylogenomic data, strain 10Sc9-8T represents a novel species of the genus Georgenia, for which the name Georgenia halotolerans sp. nov. is proposed. The type strain is 10Sc9-8T (=JCM 33946T=CPCC 206219T).

Paracoccus onchidii sp. nov., a moderately halophilic bacterium isolated from a marine invertebrate from the South China Sea.

A novel moderately halophilic bacterial strain, designated Z330T, was isolated from the egg of a marine invertebrate of the genus Onchidium collected in the South China Sea. The 16S rRNA gene sequence of strain Z330T exhibited the highest similarity value to that of the type strain Paracoccus fistulariae KCTC 22803T (97.6%), Paracoccus seriniphilus NBRC 100798T (97.6%) and Paracoccus aestuarii DSM 19484T (97.6%). Phylogenomic and 16S rRNA phylogenetic analysis showed that strain Z330T was most closely related to P. seriniphilus NBRC 100798T and P. fistulariae KCTC 22803T. Strain Z330T grew optimally at 28-30°C, pH 7.0-8.0 with the presence of 5.0-7.0% (w/v) NaCl. In addition, growth of strain Z330T occurred at 0.5-16% NaCl, indicated strain Z330T was a moderately halophilic and halotolerant bacterium of genus Paracoccus. The predominant respiratory quinone in strain Z330T was identified as ubiquinone-10. The major polar lipids of strain Z330T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, glycolipid and six unidentified polar lipids. The major fatty acids of strain Z330T was summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The draft genome sequence of strain Z330T includes 4,084,570bp in total (N50 = 174,985bp) with a medium read coverage of 463.6 × and 83 scaffolds. The DNA G + C content of strain Z330T was 60.5%. In silico DNA-DNA hybridization with the four type strains showed 20.5, 22.3, 20.1 and 20.1% relatedness to Paracoccus fistulariae KCTC 22803T, Paracoccus seriniphilus NBRC 100798T, Paracoccus aestuarii DSM 19484T and Paracoccus denitrificans 1A10901T, respectively. And the average nucleotide identity (ANIb) values between strain Z330T and these four type strains were 76.2, 80.0, 75.8 and 73.8%, respectively, lower than the 95-96% threshold value for dividing prokaryotic species. On the basis of the phenotypic, phylogenetic, phylogenomic and chemotaxonomic properties, a novel species of the genus Paracoccus, Paracoccus onchidii sp. nov. is proposed with the type strain Z330T (= KCTC 92727T = MCCC 1K08325T).

Polyphase taxonomy and genome analysis reveal the adaptability of Luteolibacter rhizosphaerae sp. nov. to the rhizosphere soil of Ulmus pumila L.

A Gram-stain-negative, rod-shaped, non-flagellated, pale-yellow bacterium, designated GHJ8T, was isolated from the rhizosphere soil of Ulmus pumila L., Shanxi Province, China. Growth occurred at 20-37°C (optimum, 28°C), pH 6.0-11.0 (optimum, pH 8.0), and 0-1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GHJ8T was related to members of the genus Luteolibacter, and close to Luteolibacter flavescens GKXT (98.5%), Luteolibacter luteus G-1-1-1T (97.3%), Luteolibacter arcticus MC 3726T (97.2%), and Luteolibacter marinus NBU1238T (96.0%). The genome size of strain GHJ8T was 6.2 Mbp, with a G + C content of 62.5%. Genomic mining revealed that the strain contained antibiotic resistance genes and secondary metabolic gene clusters, indicating that it had adaptation mechanisms to environmental stress. Comparative genomic analyses clearly separated strain GHJ8T from the recognized species of the genus Luteolibacter based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. The major cellular fatty acids were iso-C14:0 (30.8%), C16:1 ω9c (23.0%), C16:0 (17.3%), and C14:0 (13.4%). The quinone system was composed of the major menaquinones MK-8, MK-9, and MK-10, and the principal polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified glycolipid, two unidentified phospholipids, and three unidentified lipids. Based on its phenotypic and genotypic properties and phylogenetic inference, strain GHJ8T is a novel species of the genus Luteolibacter, for which the name Luteolibacter rhizosphaerae sp. nov. is proposed. The type strain is GHJ8T (= GDMCC 1.2160T = KCTC 82452T = JCM 34400T).

Chondrinema litorale gen. nov., sp. nov., of the phylum Bacteroidota, carrying multiple megaplasmids isolated from a tidal flat in the West Sea, Korea

A Gram-stain-negative, long rod, oxidase and catalase-positive strain WSW3-B12T was isolated from red algae on tidal flats in the West Sea, Korea. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain WSW3-B12T had the highest sequence similarity, 92.7%, to Flexithrix dorotheae DSM 6795T, followed by Rapidithrix thailandica TISTR 1750T at 90.8% in the family Flammeovirgaceae of the phylum Bacteroidota. The whole genome sequence determined using both the Nanopore and Illumina platforms revealed that the complete genome consists of 29 contigs, among which contig 1 was a circular chromosome, while the remaining 28 contigs were plasmids. The size of the genome was 10.1 Mbp and the G+C content was 34.1%. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), average amino acid identity (AAI), and percentage of conserved proteins (POCP), phylogenomic-related indexes between the strain WSW3-B12T and the closest strain Flexithrix dorotheae DSM 6795T, were 76.6%, 19.9%, 57.2%, and 55.6%, respectively, which were all lower than the threshold values to support the creation of a novel genus. A comprehensive genome analysis revealed that the strain WSW3-B12T harbored many of the key genes involved in central metabolism in the main chromosome and also carried important genes for the production of vitamins, quinone, and antimicrobial resistance on the plasmids. The strain also carried genes that are involved in the metabolism of heavy metals such as arsenic, cobalt, copper, and iron on both the chromosome and plasmids. Furthermore, the genome of the strain was highly enriched with carbohydrate-active enzymes (CAZymes), carrying a total of 241 CAZymes. Moreover, a complete CRISPR/Cas system was detected on plasmid 20. The major fatty acids of the strain were iso-C15:0 and C16:1 ω5. The polar lipids contained phosphatidylethanolamine, four unidentified lipids, and four glycolipids. The respiratory quinone was menaquinone 7. Based on the phenotypic, chemotaxonomic, and genomic analyses, the strain WSW3-B12T could be assigned to a novel species and novel genus within the family Flammeovirgaceae, for which the name Chondrinema litorale gen. nov., sp. nov. (type strain WSW3-B12T = KCTC 82707T = GDMCC 1.3198T) is proposed.