Characterization of Bifidobacterium apousia sp. nov., Bifidobacterium choladohabitans sp. nov., and Bifidobacterium polysaccharolyticum sp. nov., three novel species of the genus Bifidobacterium from honey bee gut

Bifidobacterium is one of the dominating bacterial genera in the honey bee gut, and they are the key degrader of diet polysaccharides for the host. Previous genomic analysis shows that they belong to separate phylogenetic clusters and exhibited different functional potentials in hemicellulose digestion. Here, three novel strains from the genus Bifidobacterium were isolated from the guts of the honey bee (Apis mellifera). Phylogenomic analysis showed that the isolates could be grouped into four phylogenetic clusters. The average nucleotide identity values between strains from different clusters are <95%, while strains in Cluster IV belong to the characterized species Bifidobacterium asteroides. Carbohydrate-active enzyme annotation confirmed that the metabolic capacity for carbohydrates varied between clusters of strains. Cells are Gram-positive rods; they grew both anaerobically and in a CO₂-enriched atmosphere. All strains grew at a temperature range of 20–42 °C, with optimum growth at 35 °C. The pH range for growth was 5–9. Strains from different phylogenetic clusters varied in multiple phenotypic and chemotaxonomic characterizations. Thus, we propose three novel species Bifidobacterium apousia sp. nov. whose type strain is W8102^T (=CGMCC 1.18893 ^T = JCM 34587 ^T), Bifidobacterium choladohabitans sp. nov., whose type strain is B14384H11^T (=CGMCC 1.18892 ^T = JCM 34586 ^T), and Bifidobacterium polysaccharolyticum sp. nov. whose type strain is W8117^T (=CGMCC 1.18894 ^T = JCM 34588 ^T).     

Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov., two novel resistant bacteria isolated from pearl river estuary

Two novel species of the genus Deinococcus, designated SYSU M49105^T and SYSU M42101^T, were isolated from freshwater samples of the Pearl River estuary in Guangdong, China. Phylogenetic analysis using 16S rRNA gene sequence indicated that strains SYSU M49105^T and SYSU M42101^T showed the highest sequence similarities to Deinococcus aetherius JCM 11751 ^T (93.6%) and Deinococcus multiflagellatus NBRC 112888 ^T (97.3%), respectively. Cells of both strains were Gram-staining positive, aerobic, coccus-shaped, oxidase-negative and non-motile. The cell wall contained meso-diaminopimelic acid as their diagnostic diamino acid. MK-8 was the predominant respiratory quinone for both strains. The polar lipid profile of SYSU M49105^T contained two unidentified phosphoglycolipids, nine unidentified glycolipids, and five unidentified polar lipids. SYSU M42101^T had one unidentified phosphoglycolipid, nine unidentified glycolipids, one unidentified aminophospholipid and four unidentified polar lipids. The major fatty acids of strains SYSU M49105^T and SYSU M42101^T were summed feature 3 (C_16:1 ω7c and/ or C_16:1 ω6c) and C_16:0. The G?+?C contents of the novel isolates based on genomic DNAs were 69.6% and 67.4%, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU M49105^T and SYSU M42101^T should be considered to represent two novel species in the genus Deinococcus, for which the names Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov. were proposed with the type strains SYSU M49105^T (=?KCTC 43258 ^T?=?CGMCC 1.18609 ^T) and SYSU M42101^T (=?KCTC 43257 ^T?=?CGMCC 1.18614 ^T), respectively.

     

Nocardioides lacusdianchii sp. nov., an attached bacterium of Microcystis aeruginosa

Attached bacteria of Microcystis play important roles in the occurence, outbreak and decline of Microcystis water blooms. In this study, a novel actinobacterium, designated strain JXJ CY 38 ^T, was isolated from the culture mass of Microcystis aeruginosa FACHB-905 (MAF), collected from Lake Dianchi, south-west, China. The strain was found to be a Gram-stain positive, short rod, catalase positive and oxidase negative. The isolate was found to be able to grow at 5.0–38.0 °C (optimum, 28.0 °C), pH 4.0–11.0 (optimum, 7.0–8.0) and 0–3.0% (w/v, optimum, 0%) NaCl. Based on 16S rRNA gene sequences, strain JXJ CY 38 ^T shows high similarities to Nocardioides furvisabuli JCM 13813 ^T (99.0%) and Nocardioides alpinus JCM 18960 ^T (98.7%), and less than 98.2% similarities to other members of the genus. The major cellular fatty acids (>?10.0%) were identified as iso-C_16:0 (23.6%), C_18:1ω9c (18.2%) and C_17:1ω8c (16.4%), while the predominant menaquinone was found to be MK-8 (H₄). The diagnostic diamino acids in the cell wall peptidoglycan were identified as aspartic acid, glutamic acid, glycine and alanine, with mannose, ribose and arabinose as whole cell sugars. The polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, a phospholipid, phosphatidylcholine and an unidentified lipid. The DNA G?+?C content was determined to be 71.3%. The digital DNA-DNA hybridization and average nucleotide identity values between strain JXJ CY 38 ^T and the type strains N. furvisabuli JCM 13813 ^T and N. alpinus JCM 18960 ^T were 49.4% and 37.7%, and 92.0% and 83.4%, respectively. On the basis of the above taxonomic data and differences in physiological characteristics from the closely related type strains, strain JXJ CY 38 ^T was determined to represent a novel species of genus Nocardioides, for which the name Nocardioides lacusdianchii sp. nov. is proposed. The type strain is JXJ CY 38 ^T (=?KCTC 49381 ^T?=?CGMCC 4.7665 ^T). Strain JXJ CY 38 ^T apparently exhibits complex effects on the interactions between MAF and other attached bacteria, including the promotion or inhibition of the growth of MAF and bacteria, and the synthesis and release of microcystins by MAF.

     

Hyphomonas sediminis sp. nov., isolated from marine sediment

A Gram-staining-negative, aerobic and pear-shaped bacterial strain, designated WL0036^T, 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 WL0036^T was found to grow at 20–37 °C (optimum, 28 °C) with 0–9.0% NaCl (optimum, 2.5–4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0–10.0 (optimum, pH 7.0–8.0). The polar lipids profile of strain WL0036^T included phosphatidylcholine, phosphatidylethanolamine, glycolipid and an unidentified lipid. The major isoprenoid quinone was determined to be Q-11 and the major fatty acids were C_16:0, 11-methyl-C_18:1ω7c, and summed features 8 (C_18:1ω6c and/or C_18:1ω7c). The G?+?C content of genomic DNA was 61.8%. Phylogenetic trees constructed based on 16S rRNA gene sequence and bac120 gene set (a collection of 120 single-copy protein sequences prevalent in bacteria) indicted that strain WL0036^T clustered with strains Hyphomonas neptunium ATCC 15444^T and H. polymorpha PS728^T. The average nucleotide identities between strain WL0036^T and strains H. neptunium ATCC 15444^T and H. polymorpha PS728^T were 80.7% and 81.2%, respectively. Strain WL0036^T showed 22.8% and 23.2% of digital DNA-DNA hybridization identities with H. neptunium ATCC 15444^T and H. polymorpha PS728^T, respectively. As inferred from the phenotypic and genotypic characteristics and the phylogenetic trees, strain WL0036^T ought to be recognized as a novel species in genus Hyphomonas, for which the name Hyphomonas sediminis sp. nov. is proposed. The type strain is WL0036^T (=?MCCC 1K05843^T?=?JCM 34658^T?=?GDMCC 1.2413^T).

     

Halorubrum salinum sp. nov., isolated from a marine solar saltern

The halophilic archaeal strain GX71^T was isolated from the Gangxi marine solar saltern near the Weihai city of Shandong Province, China. Cells of the strain were pleomorphic and lysed in distilled water, stained Gram-negative and formed red-pigmented colonies. Strain GX71^T was able to grow at 25–45 °C (optimum 30 °C), in the presence of 1.7–4.8 M NaCl (optimum 2.6 M NaCl), with 0.005–0.7 M MgCl₂ (optimum 0.05 M MgCl₂) and at pH 5.5–9.5 (optimum pH 7.0–7.5). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 10 % (w/v). The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, one major glycolipid chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-3) and an unidentified lipid was also detected. The 16S rRNA gene sequence of strain GX71^T showed 94.0–97.0 % similarity to members of the genus Halorubrum of the family Halobacteriaceae. The rpoB′ gene sequence of strain GX71^T was 87.3–93.4 % similarity to current members of the genus Halorubrum. The DNA G+C content of GX71^T was 67.1 mol%. Strain GX71^T showed low DNA–DNA relatedness with Halorubrum lipolyticum CGMCC 1.5332^T, Halorubrum saccharovorum CGMCC 1.2147^T, Halorubrum kocurii CGMCC 1.7018^T and Halorubrum arcis CGMCC 1.5343^T, the most closely related members of the genus Halorubrum. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain GX71^T represents a novel species of the genus Halorubrum, for which the name Halorubrum salinum sp. nov. is proposed. The type strain is GX71^T (= CGMCC 1.10458^T = JCM 17093^T).     

Halohasta litorea gen. nov. sp. nov., and Halohasta litchfieldiae sp. nov., isolated from the Daliang aquaculture farm, China and from Deep Lake, Antarctica, respectively

Two halophilic archaeal strains, R30^T and tADL^T, were isolated from an aquaculture farm in Dailing, China, and from Deep Lake, Antarctica, respectively. Both have rod-shaped cells that lyse in distilled water, stain Gram-negative and form red-pigmented colonies. They are neutrophilic, require >120?g/l NaCl and 48–67?g/l MgCl₂ for growth but differ in their optimum growth temperatures (30?°C, tADL^T vs. 40?°C, R30^T). The major polar lipids were typical for members of the Archaea but also included a major glycolipid chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1). The 16S rRNA gene sequences of the two strains are 97.4?% identical, show most similarity to genes of the family Halobacteriaceae, and cluster together as a distinct clade in phylogenetic tree reconstructions. The rpoB′ gene similarity between strains R30^T and tADL^T is 92.9?% and less to other halobacteria. Their DNA G?+?C contents are 62.4–62.9?mol?% but DNA–DNA hybridization gives a relatedness of only 44?%. Based on phenotypic, chemotaxonomic and phylogenetic properties, we describe two new species of a novel genus, represented by strain R30^T (=?CGMCC 1.10593^T?=?JCM 17270^T) and strain tADL^T (=?JCM 15066^T?=?DSMZ 22187^T) for which we propose the names Halohasta litorea gen. nov., sp. nov. and Halohasta litchfieldiae sp. nov., respectively.     

Miltoncostaea marina gen. nov. sp. nov., and Miltoncostaea oceani sp. nov., a novel deep branching phylogenetic lineage within the class Thermoleophilia isolated from marine environments,and proposal of Miltoncostaeaceae fam. nov. and Miltoncostaeales ord. nov

Two novel marine actinobacteria, designated as SCSIO 60955^T and SCSIO 61214^T, were isolated from deep-sea sediment samples collected from the South China Sea. The cells of these organisms stained Gram-negative and were rod shaped. These strains were aerobic, and catalase- and oxidase-positive. Optimal growth occurred at 28 °C and pH 7 over 14 days of cultivation. Both strains possessed phospholipids and phosphoglycolipids. The main menaquinone was MK-7. The major fatty acid was C_16:0. The peptidoglycan structure was type A1γ′ (meso-Dpm). Analysis of genome sequences revealed that the genome size of SCSIO 60955^T was 3.37 Mbp with G + C content of 76.1%, while the genome size of SCSIO 61214^T was 3.67 Mbp with a G + C content of 74.8%. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains were 73.4% and 97.7% and that with other recognized Thermoleophilia species were less than 69.1% and 87.8%, respectively. Phylogenetic analysis of the 16S rRNA gene sequences showed that strains SCSIO 60955^T and SCSIO 61214^T were separately clustered together and formed a well-separated phylogenetic branch distinct from their most related neighbor Gaiella occulta. Based on the data presented here, these two strains are proposed to represent two novel species of a novel genus, for which the name Miltoncostaea marina gen. nov., sp. nov., with the type strain SCSIO 60955^T (=DSM 110281^T =CGMCC 1.18757^T), and Miltoncostaea oceani sp. nov., with the type strain SCSIO 61214^T (=KCTC 49527^T =CGMCC 1.18758^T) are proposed. We also propose that these organisms represent a novel family named Miltoncostaeaceae fam. nov. of a novel order Miltoncostaeales ord. nov.     

Oceanobacillus aidingensis sp. nov., a moderately halophilic bacterium

Two Gram-positive, rod-shaped moderately halophilic bacterial strains, designated AD7-25^T and AB-11, were isolated from Aiding and Manasi salt lakes in Xinjiang of China, respectively. The strains were found to be able to grow at NaCl concentrations of 0–21 % (w/v), with optimum growth occurring at 6–8 % (w/v) NaCl. The optimal temperature and pH for growth were determined to be 33–37 °C and pH 7.0–7.5. Cells of the strains are motile by means of polar flagella. Both strains can produce ellipsoidal spores. The major cellular fatty acids were identified as anteiso-C_15:0, iso-C_15:0, iso-C_14:0, anteiso-C_17:0 and iso-C_16:0. The diamino acid in the peptidoglycan and the major quinone system were determined to be meso-diaminopimelic acid (meso-DAP) and MK-7, respectively. The DNA G+C contents of stains AD7-25^T and AB-11 were 39.8 and 40.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that these two novel strains are closely related to the genus Oceanobacillus showing 90–99.5 % similarity with respect to type strains. These two novel strains were most closely related to Oceanobacillus oncorhynchi subsp. incaldanensis DSM 16557^T (99.1 and 99.5 %), followed by O. oncorhynchi subsp. oncorhynchi JCM 12661^T (99.1 and 99.4 %), Oceanobacillus neutriphilus CGMCC 1.7693^T (97.0 and 97.5 %), Oceanobacillus sojae JCM 15792^T (97.6 and 98.0 %) and Oceanobacillus locisalsi KCTC 13253^T (96.5 and 96.9 %). The DNA–DNA hybridization data indicated that DNA relatedness between strains AD7-25^T and AB-11 was 91.0 %, and the genomic homology of representative strain AD7-25^T with O. oncorhynchi subsp. incaldanensis DSM 16557^T, O. oncorhynchi subsp. oncorhynchi JCM 12661^T, O. neutriphilus CGMCC 1.7693^T, O. sojae JCM 15792^T and O. locisalsi KCTC 13253^T were 41, 39, 20, 23 and 17 %, respectively. On the basis of phenotypic and phylogenetic distinctiveness, strains AD7-25^T and AB-11 should be assigned to the genus Oceanobacillus as a new species, for which the name Oceanobacillus aidingensis sp. nov. was proposed. The type strain is AD7-25^T (=CGMCC 1.9106 ^T = NBRC 105904^T).     

Salinarubrum litoreum gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from Chinese marine solar salterns

Three halophilic archaeal strains, XD46^T, YJ-63-S1 and ZS-1-H, were isolated from three Chinese marine solar salterns. All were observed to have pleomorphic cells that lysed in distilled water, stained Gram-negative and formed red-pigmented colonies. They were found to grow optimally at 37 °C, at pH 7.0 and in the presence of 2.6 M NaCl and 0.05 M Mg²⁺. The major polar lipids were identified as those typical for members of the Halobacteriaceae but also included major glycolipids chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether (DGD-1) and two unidentified ones. The 16S rRNA gene sequences of the three strains were 99.8–100 % identical, showing most similarity to sequences of members of the family Halobacteriaceae, and clustering together as a distinct clade in phylogenetic tree reconstructions. The rpoB′ gene similarities between the three strains were 98.7–100 % and lower to the sequences of other halobacteria. Their DNA G+C contents were determined to be 65.1–65.5 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains XD46^T (=CGMCC 1.12237^T = JCM 18649^T), YJ-63-S1 (=CGMCC 1.12574) and ZS-1-H (=CGMCC 1.12544) represent a novel species in a new genus within the family Halobacteriaceae, for which the name Salinarubrum litoreum gen. nov., sp. nov. is proposed.     

Halorubrum rubrum sp. nov., an extremely halophilic archaeon from a Chinese salt lake

Two halophilic archaeal strains, YC87^T and YCA11, were isolated from Yuncheng salt lake in Shanxi, China. Cells of the two strains were observed to be pleomorphic rod-shaped, stained Gram-negative and produced red-pigmented colonies. Strain YC87^T was able to grow at 20–50 °C (optimum 37 °C), at 1.4–4.8 M NaCl (optimum 2.1 M NaCl), at 0.05–1.0 M MgCl₂ (optimum 0.3 M MgCl₂) and at pH 6.0–9.0 (optimum pH 7.0) while strain YCA11 was able to grow at 20–50 °C (optimum 37 °C), at 2.1–4.8 M NaCl (optimum 3.1 M NaCl), at 0.01–0.7 M MgCl₂ (optimum 0.1 M MgCl₂) and at pH 6.0–9.0 (optimum pH 7.5). The cells of both isolates were observed to lyse in distilled water. The minimum NaCl concentrations that prevented cell lysis were determined to be 8 % (w/v) for strain YC87^T and 12 % (w/v) for strain YCA11. The major polar lipids of the two strains were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one major glycolipid chromatographically identical to sulfated mannosyl glucosyl diether; another major glycolipid and trace amounts of several unidentified lipids were also detected. The 16S rRNA gene sequences of the two strains were 99.8 % identical, showing 93.2–98.2 % similarity to members of the genus Halorubrum of the family Halobacteriaceae. The rpoB′ gene similarity between strains YC87^T and YCA11 was 99.3 % and showed 87.5–95.2 % similarity to the closest relative members of the genus Halorubrum. The DNA G+C content of strains YC87^T and YCA11 were determined to be 64.9 and 64.5 mol%, respectively. The DNA–DNA hybridization value between strain YC20^T and strain YC77 was 87 % and the two strains showed low DNA–DNA relatedness with Halorubrum cibi JCM 15757^T and Halorubrum aquaticum CGMCC 1.6377^T, the most related members of the genus Halorubrum. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains YC87^T and YCA11 represent a novel species of the genus Halorubrum, for which the name Halorubrum rubrum sp. nov. is proposed. The type strain is YC87^T (=CGMCC 1.12124^T = JCM 18365^T).     

Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey

Four strains, designated as C-2, C-17^T, C-39^T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17^T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089^T while strains C-2, C-39^T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775^T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17^T, C-39^T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17^T and C-39^T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C_15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 – 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17^T and C-39^T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17^T (=JCM 34190^T = KCTC 82250^T) and C-39^T (=JCM 34191^T = KCTC 822251^T), respectively, are proposed.     

Two new Polyangium species,P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample

Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1^T, and two rose pink strains, designated SDU13 and SDU14^T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14^T formed solitary sporangioles under starvation conditions, while SDU3-1^T had no fruiting body structures. They showed 95.9–97.0% (SDU3-1^T) or 98.7–98.9% (SDU13 and SDU14^T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1^T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14^T) with the G + C content range of 68.3–69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C_18:1ω9c, C_16:0 and C_18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1^T (=CGMCC 1.16875^T = KCTC 72136^T) and SDU14^T (=CCTCC AB 2021123^T = KCTC 82625^T), respectively.     

Pseudomonas oryzae sp. nov. isolated from a paddy soil in South China

A Gram-staining-negative, rod-shaped and motile with several polar flagellums bacterium, designated WM-3^T, was isolated from a rice paddy soil in South China. Growth occurred with 0–3.0 % (w/v) NaCl (optimum 2.0 %), at pH 5.5–9.0 (optimum pH 7.0) and at 25–42 °C (optimum 30–37 °C) in liquid Reasoner’s 2A medium. Analysis of the 16S rRNA gene and gyrB gene sequences revealed that strain WM-3^T was most closely related to the type strains of the species Pseudomonas linyingensis and Pseudomonas sagittaria. Its sequence similarities with P. linyingensis CGMCC 1.10701^T and P. sagittaria JCM 18195^T were 97.4 and 97.3 %, respectively, for 16S rRNA gene, and were 94.1 and 94.2 %, respectively, for gyrB gene. DNA–DNA hybridization between strain WM-3^T and these two type strains showed relatedness of 35.6 and 30.9 %, respectively. G+C content of genomic DNA was 69.4 mol%. The whole-cell fatty acids mainly consisted of C_16:0 (30.0 %), C_16:1 ω6c and/or C_16:1 ω7c (19.3 %) and C_18:1 ω6c and/or C_18:1 ω7c (16.3 %). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain WM-3^T belongs to genus Pseudomonas but represents a novel species, for which the name Pseudomonas oryzae sp. nov. is proposed. The type strain is WM-3^T (=KCTC 32247^T =CGMCC 1.12417^T).     

Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza

Strains BSK12Z-3^T and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall peptidoglycan of strain BSK12Z-3^T was LL-diaminopimelic acid and MK-8(H₄) was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phospholipid (PL). The major fatty acids was iso-C_16:0. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Nocardioides, appearing most closely related to Nocardioides ginkgobilobae KCTC 39594^T (97.5–97.6 % sequence similarity) and Nocardioides marinus DSM 18248^T (97.4–97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3^T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus Nocardioides. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3^T, BSK12Z-4 with their most related species N. marinus DSM18248^T were within the ranges of 77.2–77.3 % and 21.3–21.4 %, respectively, clearly indicated that strains BSK12Z-3^T, BSK12Z-4 represented novel species. Strains BSK12Z-3^T and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3^T and BSK12Z-4 could be classified as a novel species of the genus Nocardioides, for which the name Nocardioides bruguierae sp. nov., is proposed. The type strain is BSK12Z-3^T (=CGMCC 4.7709^T = JCM 34554^T).     

Rubrimonas shengliensis sp. nov. and Polymorphum gilvum gen. nov., sp. nov., novel members of Alphaproteobacteria from crude oil contaminated saline soil

Four bacterial strains were isolated from a crude oil contaminated saline soil in Shengli Oilfield, China. Strains SL014B-28A2^T and SL014B-80A1 were most closely related to Rubrimonas cliftonensis OCh 317^T, while strains SL003B-26A1^T and SL003B-26A2 were most closely related to but readily different from the species in the Pannonibacter-Labrenzia-Roseibium-Stappia cluster. The major fatty acids were C_18:1ω7c, C_16:0, C_18:0 and 11-Methyl C_18:1ω7c, and C_18:1ω7c, 11-Methyl C_18:1ω7c and C_18:0, respectively, for these two groups of isolates. Q-10 was the predominant ubiquinone. The G + C contents of genomic DNA of the four isolates were 67.9, 69.7, 65.6 and 65.6 mol%. Based on the polyphasic taxonomic characteristics, strains SL014B-28A2^T and SL014B-80A1 represented a novel species of the genus Rubrimonas, for which the name Rubrimonas shengliensis sp. nov. is proposed, with strain SL014B-28A2^T (=LMG 26072^T = CGMCC 1.9170^T) as the type strain. Isolates SL003B-26A1^T and SL003B-26A2 represented a novel genus and species of the family Rhodobacteraceae, for which the name Polymorphum gilvum gen. nov., sp. nov. is proposed, with strain SL003B-26A1^T (=LMG 25793^T = CGMCC 1.9160^T) as the type strain.     

Pelagibacterium nitratireducens sp.nov., A Marine Alphaproteobacterium Isolated from the East China Sea

A Gram-negative, rod-shaped, non-spore-forming aerobic bacterium, motile with a single polar flagellum, strain JLT2005^T, was isolated from surface seawater collected from the East China Sea and formed ivory white colonies on a rich organic medium. The strain was positive for catalase, oxidase, and urease. It grew in the presence of 0–12 % (w/v) NaCl (optimum 5 %), at 20–35 °C (optimum 25 °C), or at pH 6–10 (optimum pH 9). The major fatty acids (>10 %) were C_18:1ω7c, C_19:0ω8c cyclo, C_16:0, and C_18:0. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and five unidentified glycolipids. Ubiquinone-10 and Ubiquinone-11 were present as the major quinones. The DNA G+C content was 74.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JLT2005^T belongs to the genus Pelagibacterium in the family Hyphomicrobiaceae, class Alphaproteobacteria. The closest neighbors were Pelagibacterium halotolerans B2^T (98.7 % similarity) and Pelagibacterium luteolum 1_C16_27^T (97.1 % similarity). DNA–DNA relatedness values of strain JLT2005^T with P. halotolerans B2^T and with P. luteolum 1_C16_27^T were 31.6 and 25 %. Evidence from genotypic, chemotaxonomic, and phenotypic data shows that strain JLT2005^T represents a novel species of the genus Pelagibacterium, for which the name Pelagibacterium nitratireducens sp. nov is proposed. The type strain is JLT2005^T (=CGMCC 1.10829^T =JCM 17767^T).     

Altererythrobacter oceanensis sp. nov., isolated from the Western Pacific

A Gram-stain negative, ovoid-rod shaped, strictly aerobic bacterium, strain Y2^T, was isolated from a deep-sea sediment of the Western Pacific. Phylogenetic and phenotypic properties of the organism indicated that it belongs to the genus Altererythrobacter. Strain Y2^T shares highest 16S rRNA gene sequence similarity of 96.6 % with Erythrobacter jejuensis CNU001^T, followed by the type strains of recognized members of the genus Altererythrobacter (94.8–96.5 %). Strain Y2^T forms a clade with E. jejuensis CNU001^T in the cluster of species of the genus Altererythrobacter. Growth of strain Y2^T was observed at 4–40 °C (optimum, 35–37 °C), at pH 6.0–10.0 (optimum, pH 7.0–8.0) and in the presence of 0–5 % (w/v) NaCl (optimum, 2–3 %). The major cellular fatty acids were found to be C_17:1 ω6c (41.5 %), summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c; 17.2 %), C_17:1 ω8c (11.0 %) and C_15:0 2OH (8.1 %). The major respiratory quinone was determine to be ubiquinone 10 (Q-10). The polar lipid analysis indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one sphingoglycolipid, three unidentified phospholipids, two unidentified glycolipids, two unidentified aminolipids and three unknown lipids. The DNA G + C content of the type strain is 60.0 mol %. On the basis of the data from the polyphasic characterization, strain Y2^T represents a novel species, for which the name Altererythrobacter oceanensis sp. nov. is proposed. The type strain is Y2^T (=CGMCC 1.12752^T =LMG 28109^T).     

Natronocalculus amylovorans gen. nov., sp. nov., and Natranaeroarchaeum aerophilus sp. nov., dominant culturable amylolytic natronoarchaea from hypersaline soda lakes in southwestern Siberia

Several pure cultures of alkaliphilic haloaloarchaea were enriched and isolated from hypersaline soda lakes in southwestern Siberia using amylopectin and fructans as substrates. Phylogenomic analysis placed the isolates into two distinct groups within the class Halobacteria. Four isolates forming group 1 were closely related to a recently described Natranaeroarchaeum sulfidigenes and the other three strains forming group 2 represent a novel genus-level phylogenetic lineage. All isolates are saccharolytic archaea growing with various starch-like alpha-glucans including soluble starch, amylopectin, dextrin, glycogen, pullulane and cyclodextrin. In addition, group 1 can use levan while group 2 – inulin (plant storage beta-fructans). Group 1 strains can also grow anaerobically with either glucose or maltose using elemental sulfur as the electron acceptor. Both groups are moderately alkaliphilic with a pH range for growth from 7.2 to 9.3 (optimum between 8.0–8.8) and low Mg-demanding extreme halophiles growing optimally at 4 M total Na⁺. The major respiratory menaquinone is MK-8:8 and the core biphytanyl lipids are dominated by archaeol (C₂₀-C₂₀) and a less abundant extended archaeol (C₂₀-C₂₅) with PG and PGP-Me as polar groups. The four isolates of group 1 are suggested to be classified into a new species as Natranaeroarchaeum aerophilus sp. nov. (type strain AArc-St1-1^T = JCM 32519^T). The three isolates of group 2 are proposed to form a new genus and species for which the name Natronocalculus amylovorans gen. nov., sp. nov. is suggested (type strain AArc-St2^T = JCM 32475^T).     

Pantoea endophytica sp. nov., novel endophytic bacteria isolated from maize planting in different geographic regions of northern China

Four endophytic bacterial strains were isolated from root, stem and leaf of maize planted in different regions of northern China. The four strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. Furthermore, the average nucleotide identity (ANI) values among them were higher than 95%, suggesting they all belong to one species. Based on 16S rRNA gene phylogeny, the four strains were clustered together with Pantoea rodasii LMG 26273^T and Pantoea rwandensis LMG 26275^T, but on a separate branch. Multilocus sequence analysis (MLSA) indicated that the four strains form a novel Pantoea species. Authenticity of the novel species was confirmed by ANI comparisons between strain 596^T and its closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. The genome size of 596^T was 5.1Mbp, comprising 4896 predicted genes with DNA G + C content of 57.8 mol%. The respiratory quinone was ubiquinone-8 (Q-8) and the polar lipid profile consisted of phosphatidylethanolamin, diphosphatidylglycerol, phosphatidylglycerol, unidentified aminophospholipid and unidentified phospholipid. The major fatty acids of strain 596^T were C_16:0, summed feature 2 (C_12:0 aldehyde), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, the four isolates are considered to represent a novel species of the genus Pantoea, for which the name Pantoea endophytica sp. nov., is proposed, with 596^T (= DSM 100,785^T = CGMCC 1.15280^T) as type strain.     

Halobacterium rubrum sp. nov., isolated from a marine solar saltern

Halophilic archaeal strain TGN-42-S1^T was isolated from the Tanggu marine solar saltern, China. Cells from strain TGN-42-S1^T were observed to be pleomorphic rods, stained Gram-negative, and formed red-pigmented colonies on solid media. Strain TGN-42-S1^T was found to be able to grow at 20–50 °C (optimum 35–37 °C), at 1.7–4.8 M NaCl (optimum 3.1 M), at 0–1.0 M MgCl₂ (optimum 0.1 M), and at pH 5.0–9.0 (optimum pH 7.0–7.5). The cells lysed in distilled water, and the minimal NaCl concentration to prevent cell-lysis was found to be 10 % (w/v). The major polar lipids of the strain were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, galactosyl mannosyl glucosyl diether (TGD-1), sulfated galactosyl mannosyl glucosyl diether (S-TGD-1), sulfated galactosyl mannosyl galactofuranosyl glucosyl diether (S-TeGD), and three unidentified glycolipids which were chromatographically identical to those of the Halobacterium species. The 16S rRNA gene and rpoB′ gene of strain TGN-42-S1^T were phylogenetically related to the corresponding genes of Halobacterium jilantaiense CGMCC 1.5337^T (98.8 and 93.5 % nucleotide identity, respectively), Halobacterium salinarum CGMCC 1.1958^T (98.4 and 91.9 %), and Halobacterium noricense JCM 15102^T (96.9 and 91.1 %). The DNA G + C content of strain TGN-42-S1^T was determined to be 69.2 mol %. Strain TGN-42-S1^T showed low DNA–DNA relatedness with Hbt. jilantaiense CGMCC 1.5337^T and Hbt. salinarum CGMCC 1.1958^T, the most closely related members of the genus Halobacterium. The phenotypic, chemotaxonomic, and phylogenetic properties suggested that strain TGN-42-S1^T (=CGMCC 1.12575^T =JCM 19908^T) represents a new species of Halobacterium, for which the name Halobacterium rubrum sp. nov. is proposed.