Hong Ming

A novel Gram-stain-negative, non-motile, short rod-shaped and aerobic bacterial strain, designated as CFH 74456 ^T, was isolated from sediment of a hot spring, Tengchong, Yunnan Province, south-western China. Growth occurred at 20–53 ºC (optimum 45 ºC), pH 7.0–9.0 (optimum pH 8.0) and up to 2.0% (w/v) NaCl (optimum 0–1.0%, w/v). The predominant respiratory quinone was ubiquinone 10 (Q-10). The major fatty acids (> 10%) were C_17:1 ω6c (17.9%) and summed feature 8 (38.6%). The polar lipid profile of strain CFH 74456 ^T was identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, three unidentified glycolipids and three unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CFH 74456 ^T belongs to the genus Qipengyuania, and was most closely related to Qipengyuania sediminis CGMCC 1.12928 ^T (95.7%). The draft genome size of the isolate was 2.29 Mb with G + C content of 68.5%. The amino acid identity, average nucleotide identity and the digital DNA-DNA hybridization values between strain CFH 74456 ^T and the closest relatives ranged from 67.0 to 67.9%, 73.0 to 74.2% and 18.2–19.3%, respectively. On the basis of phenotypic, phylogenetic and genotypic analyses, it is concluded that strain CFH 74456 ^T represents a new species of the genus Qipengyuania, for which the name Qipengyuania thermophila sp. nov. is proposed. The type strain is CFH 74456 ^T (= KCTC 62921 ^T = CCTCC AB 2018237 ^T).

A novel actinobacterium, designated strain CFH 90414T, was isolated from sediment sampled at a saline lake in Yuncheng, Shanxi, PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of strain CFH 90414T were Gram-reaction-positive, aerobic and non-motile. Growth occured at 4−40 °C, pH 5.0−9.0 and in the presence of up to 0–3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CFH 90414T was a member of the genus Agromyces . The 16S rRNA gene sequence similarity analysis indicated that strain CFH 90414T was most closely related to Agromyces italicus JCM 14320T (98.07 %) and Agromyces lapidis JCM 14321T (97.18 %). The whole genome of CFH 90414T was 3.64 Mb, and showed a G+C content of 71.5 mol%. The average nucleotide identity (ANI) values and digital DNA–DNA hybridization (dDDH) values between CFH 90414T and the other species of the genus Agromyces were found to be low (ANI <78.99 % and dDDH <22.9 %). The whole-cell sugars were rhamnose, mannose, ribose, glucose and galactose. The isolate contained l-2,4-diaminobutyric acid, d-alanine, d-glutamic acid and glycine in the cell-wall peptidoglycan. The predominant menaquinone was MK-12. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. On the basis of phenotypic, genotypic and phylogenetic data, strain CFH 90414T is considered to represent a novel species of the genus Agromyces , for which the name Agromyces agglutinans sp. nov. is proposed. The type strain is CFH 90414T (=DSM 105966T=KCTC 49062T).

Strain CFH S0501^T, a novel Gram-stain-positive, aerobic, rod-shaped, endospore-forming and motile micro-organism with peritrichous flagella, was isolated from a sediment sample collected from the Yellow River in Henan Province, PR China. Optimum growth was observed at 28 °C, pH 7.0 and without NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain belonged to the genus Brevibacillus and was closely related to Brevibacillus centrosporus DSM 8445^T and Brevibacillus ginsengisoli Gsoil 3088^T (with 96.8 and 96.7 % sequence similarity, respectively). The predominant menaquinone was MK-7. Major cellular fatty acids were anteiso-C_15 : 0 and iso-C_15 : 0. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unidentified phospholipids and an unidentified polar lipid. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid. The genome size was 5.26 Mbp with a G+C content of 49.7 mol%. The average nucleotide identity (ANI) and in silico DNA–DNAhybridization (DDH) values between CFH S0501^T and the other species of the genus Brevibacillus were found to be low (ANIm T is considered to represent a novel species, for which the name Brevibacillus migulae sp. nov. is proposed. The type strain is CFH S0501^T (=DSM 29940^T=BCRC 80809^T).

A novel thermophilic bacterium, designated CFH 72773^T was isolated from the enrichment of a Jinze hot spring sample which was collected from Dientan town, Tengchong county, Yunnan province, south-western PR China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and non-sporulating. The taxonomic position of the strain was investigated by using a polyphasic approach. Growth occurred at 37–75 °C, pH 6.0–8.0 and with 0–2.0 % (w/v) NaCl. Comparison of the 16S rRNA gene sequences indicated the strain represented a member of the genus Thermus and showed close relationships to the type strains Thermus caliditerrae YIM 77925^T (96.3 % similarity) and Thermus igniterrae RF-4^T (96.2 % similarity). The whole genome of CFH 72773^T consisted of 2.25 Mbp and the DNA G+C content was 69.5 mol%. A total of 2262 genes, including a variety of enzymes for chemolithotrophy and anerobic respiration, were predicted. The strain had a unique negative oxidase activity and could hydrolyze starch at high temperature. Furthermore, various genes related to methane, sulfur, fumarate and nitrate metabolism were found, all these indicated that it is worth studying the novel strain. The predominant menaquinone is MK-8. The predominant cellular fatty acids included iso-C_15 : 0, iso-C_16 : 0 and iso-C_17 : 0. The major polar lipids were comprised of aminophospholipid, glycolipid and two phospholipids. On the basis of low ANI values, different phenotypic and chemotaxonomic characters and phylogenetic analysis, we made a proposal that strain CFH 72773^T represents a novel member of the genus Thermus , for which the name Thermus thermamylovorans sp. nov. is proposed. The type strain is CFH 72773^T (=CCTCC AB2018244^T=KCTC 43129^T).

A novel Gram-negative bacterium, designated CFH 10530T, was isolated from the intestine of grass carp. The sample was collected from the aquaculture training base at the College of Fisheries, Henan Normal University, Xinxiang, PR China. Cells of strain CFH 10530T were coccoid, ovoid or short-rod-shaped, aerobic, non-spore-forming and non-motile. 16S rRNA gene sequence analysis demonstrated that strain CFH 10530T was closely related to Paracoccus endophyticus SYSUP0003T (97.7 % sequence similarity), Paracoccus halophilus HN-182T (96.5 %) and Paracoccus panacisoli DCY94T (96.1 %). The strain grew optimally at 25–28 °C, at pH 7.0 and with 0–2 % (w/v) NaCl. Cells were positive for catalase and oxidase, nitrate was reduced and H2S was not produced. The isoprenoid quinone was Q-10. Major cellular fatty acids were summed feature 8, C18 : 0 and C18 : 03-OH. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and five unidentified polar lipids. The genome size was 3 331 229 bp with a G+C content of 69.6 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between CFH 10530T and the other species of the genus Paracoccus were found to be below the recommended levels for species delineation (ANIm <85, ANIb <80 and dDDH <24 %). Based on its physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain CFH 10530T is considered to represent a novel species for which the name Paracoccus luteus sp. nov., is proposed. The type strain is CFH 10530T (=KCTC 62919T=CGMCC 1.16597T).

A Gram-stain positive, aerobic, non-motile and short-rod-shaped strain, CFH S00084T, was isolated from a sediment sample of the Yellow River in Henan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CFH S00084T clustered within members of Microbacterium and was most closely related to the type strains Microbacterium yannicii JCM 18959T and Microbacterium arthrosphaerae DSM 22421T (98.97 % and 98.36 % similarity, respectively). The strain grew optimally at 25–37 °C, at pH 7.0 and in 0–3 % (w/v) NaCl. The major whole-cell sugars were rhamnose and glucose. The cell-wall peptidoglycan mainly contained glycine, alanine and ornithine. The menaquinones of strain CFH S00084T were MK-13, MK-12 and MK-11. The major fatty acids detected were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The genome of strain CFH S00084T was 4.03 Mbp with a G+C content of 70.5 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between CFH S00084T and the other species of the genus Microbacterium were found to be low (ANIm <85 %, ANIb <75 % and dDDH <24 %). The phylogenomic analysis provided evidence for clear phylogenetic divergence between strain CFH S00084T and its closely related type strains. On the basis of the differential physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain CFH S00084T is considered to represent a novel species for which the name Microbacterium ureisolvens sp. nov. is proposed. The type strain is CFH S00084T (=KCTC 39802T=DSM 103157T).

Objective: To clone a full-length cDNA sequence of xynB, encoding endo-1,4-β-xylanase of Aspergillus niger C71 and express in Escherichia coli BL21(DE3). Methods: The xynB was cloned using rapid amplification of cDNA ends (RACE) methods. The sequenced DNA was compared with the available sequences from GenBank using the BLASTX program, and the phylogenetic tree of the xylanases was then constructed using MEGA version 5.0. The amino acid sequences of XYNB were submitted to the ESyPred3D Web Server 1.0 for Homology modeling. The XYNB was purified by MonoQ an ion exchange chromatography and analyzed by SDS-PAGE. Results: The results showed that xynB is 678 bp in length, and encodes a 18 amino acid signal peptide as well as a 22 amino acid mature peptide with a calculated molecular weight of 24.127 kDa. Phylogenetic analysis of xynB, three-dimensional structure and overlap analysis of XYNB demonstrated that XYNB has a β-jelly-roll architecture, which is more conversation in the catalytic domain of GH11 xylanases, belonging to the family 11 of glycosyl hydrolases. A maximum enzyme activity of 62,242.33 U•ml ^-1 was obtained from XYNB. The XYNB with MW of 41 kDa demonstrated a broad pH stability from pH 3.0 to pH 12. 0.5 mM of Fe ²⁺ could greatly enhance activity of XYNB to 567.02%. The mainly hydrolysis products of beechwood xylan were xylobiose. The hydrolysis products of XYNB effecting on beechwood xylan were analysed by HPLC. Conclusion: The xynB had been successfully expressed in Escherichia coli BL21, with high enzyme activity and a broad pH stability, and it would be a very good application prospect as the feed enzyme.