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1. Discovery of a novel geminivirus associated with camellia chlorotic dwarf disease

Author:
Tian, Xin,   et al.   ; Zhang, Song; Shen, Pan; Li, Min; Zhou, Changyong; Cao, Mengji;     Show all 6 Authors
Source:
Archives of virology 2018 v.163 no.6 pp. 1709-1712
ISSN:
0304-8608
Subject:
Citrus; Geminiviridae; RNA; genome; high-throughput nucleotide sequencing; molecular cloning; mulberries; new genus; nucleotides; open reading frames; phylogeny; polymerase chain reaction; proteins; viruses
Abstract:
... Next-generation sequencing of small RNAs and PCR amplification with two pairs of back-to-back primers, followed by cloning and sequencing, allowed identification of a novel geminivirus isolate provisionally named camellia chlorotic dwarf-associated virus (CaCDaV). The complete genome sequence of CaCDaV comprises 3,687 nucleotides (nts) and six open reading frames (ORFs). The genome and putative pr ...
DOI:
10.1007/s00705-018-3780-3

2. Molecular characterization of a novel luteovirus infecting apple by next-generation sequencing

Author:
Tian, Xin,   et al.   ; Shen, Pan; Zhang, Song; Ren, Fang; Li, Ping; Yu, Yun-qi; Li, Ruhui; Zhou, Changyong; Cao, Mengji;     Show all 9 Authors
Source:
Archives of virology 2018 v.163 no.3 pp. 761-765
ISSN:
0304-8608
Subject:
Luteovirus; RNA-directed RNA polymerase; amino acids; apples; high-throughput nucleotide sequencing; open reading frames; phylogeny; plant diseases and disorders; plant viruses; Czech Republic
Abstract:
... A new single-stranded positive-sense RNA virus, which shares the highest nucleotide (nt) sequence identity of 53.4% with the genome sequence of cherry-associated luteovirus South Korean isolate (ChALV-SK, genus Luteovirus), was discovered in this work. It is provisionally named apple-associated luteovirus (AaLV). The complete genome sequence of AaLV comprises 5,890 nt and contains eight open readi ...
DOI:
10.1007/s00705-017-3633-5

3. A new species in the lichen genus Peltigera from northern China based on morphology and DNA sequence data

Author:
Zheng, Tian-Xin,   et al.   ; Han, Liu-Fu; Guo, Shou-Yu;     Show all 3 Authors
Source:
The Bryologist 2015 v.118 no.1 pp. 46-53
ISSN:
0007-2745
Subject:
DNA; Peltigera; internal transcribed spacers; lichens; metabolites; models; montane forests; new species; phylogeny; solvents; taxonomic keys; terpenoids; thin layer chromatography; China
Abstract:
... In an investigation of Peltigera species in montane forests of northern China, a new species, P. isidiophora was identified based on morphological characteristics and DNA sequence data. It differs morphologically from other members of the P. canina-group by its laminal clustered isidia occurring in pits, shiny upper surface, and its slender, scattered and simple rhizines. It also differs chemicall ...
DOI:
10.1639/0007-2745-118.1.046

4. Deep sequencing reveals high bacterial diversity and phylogenetic novelty in pit mud from Luzhou Laojiao cellars for Chinese strong-flavor Baijiu

Author:
Tian, Xin-Hui,   et al.   ; Liu, Mao-Ke; Tang, Yu-Ming; Guo, Xiao-Jiao; Zhao, Ke; Liu, Ying; Yao, Wan-Chun; Deng, Bo; Ren, Dao-Qun; Zhang, Xiao-Ping;     Show all 10 Authors
Source:
Food research international 2017 v.102 pp. 68-76
ISSN:
0963-9969
Subject:
Clostridia; bacteria; bacterial communities; brewing; ecosystems; fermentation; high-throughput nucleotide sequencing; hosts; phylogeny
Abstract:
... The pit mud (PM) in fermentation cellar is a complex ecosystem that hosts diverse microbial communities that contribute to the production of Chinese strong-flavor Baijiu (CSFB). However, the microbial ecology of PM, particularly the extent of their phylogenetic novelty remains poorly understood. Here we conducted Illumina MiSeq sequencing to explore the diversity and novelty patterns of PM bacteri ...
DOI:
10.1016/j.foodres.2017.09.075

5. Gene loss in plants: Evidence from genome‐wide phylogenetic analysis of thiamine pyrophosphate‐dependent enzymes

Author:
Tian, Xin‐Min,   et al.   ; Wang, Peng; Hu, Wen‐Bin; Gao, Da‐Hai; Li, Qiong;     Show all 5 Authors
Source:
Journal of systematics and evolution 2015 v.53 no.3 pp. 221-227
ISSN:
1674-4918
Subject:
pyruvate dehydrogenase (lipoamide); phylogeny; acetolactate synthase; genes; gene deletion; Spermatophytina; thiamin
Abstract:
... Thiamine pyrophosphate (TPP)‐dependent enzymes are present in all domains of life, which share a cofactor with TPP. However, a comprehensive analysis of TPP‐dependent enzymes from sequenced genomes has not been reported and little is known about the evolutionary dynamics of this gene family in plants. In this study, the evolutionary relationships of the TPP‐dependent enzymes were investigated by u ...
DOI:
10.1111/jse.12129

6. Abyssicoccus albus gen. nov., sp. nov., a novel member of the family Staphylococcaceae isolated from marine sediment of the Indian Ocean

Author:
Tian, Xin-Peng,   et al.   ; Jiang, Zhao; Yuan, Chang-Guo; Xiao, Min; Khan, Inam-Ullah; Kim, Chang-Jin; Zhi, Xiao-Yang; Li, Wen-Jun;     Show all 8 Authors
Source:
Antonie van Leeuwenhoek 2016 v.109 no.8 pp. 1153-1160
ISSN:
0003-6072
Subject:
DNA; Macrococcus; amino acids; bacteria; cell walls; chemotaxonomy; fatty acids; galactose; glucose; mannose; marine sediments; menaquinones; new genus; new species; nucleotide sequences; pH; phenotype; phylogeny; rhamnose; ribose; ribosomal RNA; sequence homology; sodium chloride; temperature; xylose; Indian Ocean
Abstract:
... A Gram-stain positive, aerobic, non-motile, asporogenous, coccoid shaped bacterium, designated YIM M12140ᵀ, was isolated from a marine sediment sample collected from the Indian Ocean. Phylogenetic analysis showed that strain YIM M12140ᵀ forms a separate clade within the family Staphylococcaceae. Strain YIM M12140ᵀ shares high 16S rRNA gene sequence similarity with Macrococcus brunensis DSM 19358ᵀ ...
DOI:
10.1007/s10482-016-0717-2

7. Paenibacillus abyssi sp. nov., isolated from an abyssal sediment sample from the Indian Ocean

Author:
Tian, Xin-Peng,   et al.   ; Huang, Xiao-Fang; Wang, Fa-Zuo; Zhang, Wei; Li, Jie; Ling, Juan; Yang, Jian; Dong, Jun-De;     Show all 8 Authors
Source:
Antonie van Leeuwenhoek 2014 v.106 no.6 pp. 1089-1095
ISSN:
0003-6072
Subject:
DNA; Paenibacillus; bacteria; chemotaxonomy; correlation; fatty acids; new species; nucleotide sequences; pH; phylogeny; ribosomal RNA; sediments; sequence homology; sodium chloride; Indian Ocean
Abstract:
... A Gram-positive, rod-shaped bacterium, designated strain SCSIO N0306ᵀ, was isolated from an abyssal sediment sample collected from the Indian Ocean. The isolate was found to grow optimally at 0–2 % (w/v) NaCl, pH 7.0 and 30 °C. Comparative analysis of the 16S rRNA gene sequence showed that the isolate SCSIO N0306ᵀ belongs phylogenetically to the genus Paenibacillus, and to be most closely related ...
DOI:
10.1007/s10482-014-0277-2
PubMed:
25249446

8. Georgenia sediminis sp. nov., a moderately thermophilic actinobacterium isolated from sediment

Author:
Tian, Xin-Peng,   et al.   ; You, Zhi-Qing; Li, Jie; Qin, Sheng; Wang, Fa-Zuo; Zhang, Si;     Show all 6 Authors
Source:
International journal of systematic and evolutionary microbiology 2013 v.63 no.Pt 11 pp. 4243-4247
ISSN:
1466-5034
Subject:
DNA; Georgenia muralis; fatty acids; menaquinones; microbiology; nucleotide sequences; pH; peptidoglycans; phylogeny; ribosomal RNA; sediments; sodium chloride; temperature; South China Sea
Abstract:
... A Gram-stain-positive actinobacterium, designated strain SCSIO 15020T, was isolated from sediment of the South China Sea, and characterized by using a polyphasic approach. The temperature range for growth was 24–60 °C, with optimal growth occurring at 50 °C. The pH range for growth was 6–10 (optimum pH 8–9). The NaCl concentration range for growth was 0–5 % (w/v). The peptidoglycan type was A4α. P ...
DOI:
10.1099/ijs.0.051714-0

9. Bacillus abyssalis sp. nov., isolated from a sediment of the South China Sea

Author:
Tian, Xin-Peng,   et al.   ; You, Zhi-Qing; Li, Jie; Qin, Sheng; Wang, Fa-Zuo; Zhang, Si; Li, Wen-Jun;     Show all 7 Authors
Source:
Antonie van Leeuwenhoek 2013 v.103 no.5 pp. 963-969
ISSN:
0003-6072
Subject:
DNA; Gram-positive bacteria; fatty acids; nucleotide sequences; pH; phylogeny; ribosomal RNA; sediments; sodium chloride; South China Sea
Abstract:
... A Gram-positive bacterium, designated SCSIO 15042ᵀ, was isolated from a sediment of the South China Sea and was subjected to a polyphasic taxonomic study. The isolate grew at 20–60 °C, pH 6.0–10.0 and it could grow with up to 10 % (w/v) NaCl. The cell-wall diamino acid was found to be meso-diaminopimelic acid. Polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and phosphati ...
DOI:
10.1007/s10482-013-9875-7
PubMed:
23314911

10. Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment

Author:
Tian, Xin-Peng,   et al.   ; Xu, Ying; Liu, Yu-Juan; Li, Jie; Kim, Chang-Jin; Yin, Hao; Li, Wen-Jun; Zhang, Si;     Show all 8 Authors
Source:
International journal of systematic and evolutionary microbiology 2013 v.63 no.Pt 3 pp. 1045-1050
ISSN:
1466-5034
Subject:
DNA; Flavobacteriaceae; agar; bacteria; chemotaxonomy; fatty acids; islands; marine sediments; new genus; nucleotide sequences; pH; phosphatidylethanolamines; phylogeny; ribosomal RNA; sequence homology; sodium chloride; temperature; South China Sea
Abstract:
... A marine bacterium, designated SCSIO 03483T, was isolated from a marine sediment sample collected from the Nansha Islands in the South China Sea. The strain produced roundish colonies with diffusible yellow-coloured pigment on nutrient agar medium or marine agar 2216. Optimal growth occurred in the presence of 0–4 % (w/v) NaCl, at pH 7.0 and a temperature range of 28–37 °C. 16S rRNA gene sequence ...
DOI:
10.1099/ijs.0.041889-0

11. Actinophytocola sediminis sp. nov., an actinomycete isolated from a marine sediment

Author:
Tian, Xin-Peng,   et al.   ; Zhang, Dao-Feng; Jiang, Zhao; Zhang, Xiao-Mei; Yang, Ling-Ling; Long, Li-Juan; Zhang, Si; Li, Wen-Jun;     Show all 8 Authors
Source:
International journal of systematic and evolutionary microbiology 2014 v.64 no.Pt 8 pp. 2834-2840
ISSN:
1466-5034
Subject:
DNA; aerobes; fatty acids; galactose; glucose; hydrolysates; hyphae; marine sediments; menaquinones; microbiology; mycelium; nucleic acid hybridization; nucleotide sequences; phosphatidylethanolamines; phylogeny; rhamnose; ribose; ribosomal RNA; spores; South China Sea
Abstract:
... A novel actinomycete strain, designated YIM M13705T, was isolated from a marine sediment sample of the South China Sea and its characteristics were determined by a polyphasic approach. The slowly growing, Gram-stain-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, and no diffusible pigment was produced on the media tested. At maturity, spore chains were formed on ae ...
DOI:
10.1099/ijs.0.062638-0

12. Nocardioides nanhaiensis sp. nov., an actinobacterium isolated from a marine sediment sample

Author:
Tian, Xin-Peng,   et al.   ; Zhang, Dao-Feng; Zhong, Jing-Mei; Zhang, Xiao-Mei; Jiang, Zhao; Zhou, En-Min; Zhang, Si; Li, Wen-Jun;     Show all 8 Authors
Source:
International journal of systematic and evolutionary microbiology 2014 v.64 no.Pt 8 pp. 2718-2722
ISSN:
1466-5034
Subject:
DNA; Nocardioides kribbensis; fatty acids; hydrolysates; hyphae; marine sediments; menaquinones; microbiology; mycelium; nucleotide sequences; pH; phosphatidylcholines; phylogeny; pigments; ribosomal RNA; sequence homology; sodium chloride; South China Sea
Abstract:
... A rod- to coccus-shaped, non-spore-forming actinobacterium, strain YIM M13091T, was isolated from a marine sediment sample collected from the South China Sea and examined by a polyphasic approach to clarify its taxonomic position. This Gram-staining-positive, aerobic actinobacterium did not produce substrate mycelium and aerial hyphae, and no diffusible pigments were produced on the media tested. ...
DOI:
10.1099/ijs.0.062851-0

13. Bacillus tianshenii sp. nov., isolated from a marine sediment sample

Author:
Tian, Xin-Peng,   et al.   ; Jiang, Zhao; Zhang, Dao-Feng; Khieu, Thi-Nhan; Son, Chu Ky; Zhang, Xiao-Mei; Cheng, Juan; Zhang, Si; Li, Wen-Jun;     Show all 9 Authors
Source:
International journal of systematic and evolutionary microbiology 2014 v.64 no.Pt 6 pp. 1998-2002
ISSN:
1466-5034
Subject:
Bacillus halmapalus; Bacillus horikoshii; DNA; bacteria; fatty acids; marine sediments; menaquinones; nucleotide sequences; pH; peptidoglycans; phosphatidylethanolamines; phylogeny; ribosomal RNA; sodium chloride; South China Sea
Abstract:
... A novel Gram-stain-positive, motile, catalase- and oxidase-positive, aerobic, endospore-forming, peritrichous, rod-shaped bacterium, designated YIM M13235T, was isolated from a marine sediment sample collected from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M13235T belonged to the genus Bacillus. The strain grew optimally at 30 °C, pH 7.0 and ...
DOI:
10.1099/ijs.0.062224-0

14. Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov.

Author:
Tian, Xin-Peng,   et al.   ; Huang, Xiao-Fang; Liu, Yu Juan; Dong, Jun-De; Qu, Ling-Yun; Zhang, Yan-Ying; Wang, Fa-Zuo; Zhang, Si;     Show all 8 Authors
Source:
International journal of systematic and evolutionary microbiology 2014 v.64 no.Pt 3 pp. 875-881
ISSN:
1466-5034
Subject:
chemotaxonomy; fatty acids; genes; nitrogen fixation; nitrogen-fixing bacteria; nucleotide sequences; phospholipids; phylogeny; ribosomal RNA; sediments; sequence analysis
Abstract:
... A nitrogen-fixing bacterium, designated strain SCSIO N0430T, was isolated from a mangrove sediment sample. Analysis of the sequence of the nifH gene responsible for nitrogen fixation in this strain indicated a close relationship to an uncultured bacterium ZNZ-D11 (GenBank accession no. JF896696). 16S rRNA gene sequence analysis revealed that this isolate had less than 93 % similarity to its closes ...
DOI:
10.1099/ijs.0.052779-0

15. Mariniluteicoccus flavus gen. nov., sp. nov., a new member of the family Propionibacteriaceae, isolated from a deep-sea sediment

Author:
Tian, Xin-Peng,   et al.   ; Zhang, Dao-Feng; Wang, Hong-Fei; Xiong, Zi-Jun; Liu, Lan; Zhang, Xiao-Mei; Jiang, Zhao; Zhang, Si; Li, Wen-Jun;     Show all 9 Authors
Source:
International journal of systematic and evolutionary microbiology 2014 v.64 no.Pt 3 pp. 1051-1056
ISSN:
1466-5034
Subject:
DNA; Propioniferax; agar; alanine; chemotaxonomy; fatty acids; glutamic acid; glycolipids; menaquinones; microbiology; new genus; nucleotide sequences; pH; peptidoglycans; phosphatidylcholines; phylogeny; ribosomal RNA; sediments; sequence analysis; sodium chloride; South China Sea
Abstract:
... A Gram-staining-positive, aerobic, non-motile, irregular coccus, designated strain YIM M13146T, was isolated from a sediment sample collected from the South China Sea at a depth of 2439 m, and its taxonomic position was determined by a polyphasic approach. Optimal growth of the strain was observed at 30 °C (range 5–40 °C), pH 7.0 (pH 6.0–9.0) and 0–1 % NaCl (0–6 %, w/v) on/in tryptic soy agar/brot ...
DOI:
10.1099/ijs.0.058404-0

16. Pseudonocardia sediminis sp. nov., isolated from marine sediment

Author:
Tian, Xin-Peng,   et al.   ; Zhang, Dao-Feng; Jiang, Zhao; Li, Li; Liu, Bing-Bing; Zhang, Xiao-Mei; Zhang, Si; Li, Wen-Jun;     Show all 8 Authors
Source:
International journal of systematic and evolutionary microbiology 2014 v.64 no.Pt 3 pp. 745-750
ISSN:
1466-5034
Subject:
DNA; Pseudonocardia; arabinose; fatty acids; galactose; glucose; glycolipids; hydrolysates; hyphae; mannose; marine sediments; menaquinones; microbiology; mycelium; nucleotide sequences; pH; phosphatidylcholines; phosphatidylethanolamines; phylogeny; pigments; ribosomal RNA; sodium chloride; spores; South China Sea
Abstract:
... A Gram-stain-positive, aerobic actinomycete, designated strain YIM M13141T, was isolated from a marine sediment sample from the South China Sea, and its taxonomic position was determined using a polyphasic approach. The strain produced branched substrate mycelium and aerial hyphae, but no diffusible pigments were produced on the media tested. At maturity, substrate mycelium was fragmented and spor ...
DOI:
10.1099/ijs.0.057844-0

17. Streptomyces fildesensis sp. nov., a novel streptomycete isolated from Antarctic soil

Author:
Tian, Xin-Peng,   et al.   ; Li, Jing; Zhu, Tian-Jiao; Yang, Ling-Ling; Li, Wen-Jun;     Show all 5 Authors
Source:
Antonie van Leeuwenhoek 2011 v.100 no.4 pp. 537-543
ISSN:
0003-6072
Subject:
DNA; Streptomyces beijiangensis; Streptomyces purpureus; cell walls; fatty acids; galactose; glucose; islands; mannose; menaquinones; mycelium; nucleotide sequences; phospholipids; phylogeny; ribosomal RNA; soil; soil sampling; spores; Antarctic region; Antarctica
Abstract:
... A novel actinomycete strain, GW25-5T, was isolated from a soil sample collected from the Fildes Peninsula, King George Island, West Antarctica. The strain was characterized by white to grey aerial mycelia, which were differentiated to straight to flexuous spore chains, with rod-shaped smooth spores. The cell wall of strain GW25-5T contained LL-diaminopimelic acid (A2pm) and traces of meso-A2pm. Wh ...
DOI:
10.1007/s10482-011-9609-7
PubMed:
21691776

18. Rhodococcus nanhaiensis sp. nov., an actinobacterium isolated from marine sediment

Author:
Tian, Xin-Peng,   et al.   ; Li, Jie; Zhao, Guo-Zhen; Long, Li-Juan; Wang, Fa-Zuo; Zhang, Si; Li, Wen-Jun;     Show all 7 Authors
Source:
International journal of systematic and evolutionary microbiology 2012 v.62 no.Pt 10 pp. 2517-2521
ISSN:
1466-5034
Subject:
Actinobacteria; DNA; fatty acids; genes; marine sediments; menaquinones; microbiology; new species; nucleotide sequences; pH; phosphatidylethanolamines; phylogeny; ribosomal RNA; sequence analysis; South China Sea
Abstract:
... In this study, two strains (SCSIO 10187T and SCSIO 10197) were isolated from a sediment sample collected from the South China Sea and characterized by using a polyphasic approach. Growth was observed at 15–35 °C (optimum 28 °C) and pH 5.0–8.0 (optimum pH 6.0). Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Rhodococcus. Phylogenetic analysis showed tha ...
DOI:
10.1099/ijs.0.038067-0

19. Nocardiopsis coralliicola sp. nov., isolated from the gorgonian coral, Menella praelonga

Author:
Tian, Xin-Peng,   et al.   ; Li, Jie; Yang, Jian; Zhu, Wen-Yong; He, Jie; Xie, Qiong; Zhang, Si; Li, Wen-Jun;     Show all 8 Authors
Source:
International journal of systematic and evolutionary microbiology 2012 v.62 no.Pt 7 pp. 1653-1658
ISSN:
1466-5034
Subject:
Nocardiopsis; corals; genes; microbiology; new species; nucleotide sequences; phylogeny; ribosomal RNA; sequence homology; China
Abstract:
... An actinobacterial strain, SCSIO 10427T, was isolated from a gorgonian coral sample collected from Weizhou Island, Guangxi province, China, and its taxonomic position was investigated using a polyphasic approach. The organism was found to have a range of chemical and morphological properties consistent with its classification in the genus Nocardiopsis. Phylogenetic analysis indicated that 16S rRNA ...
DOI:
10.1099/ijs.0.035402-0

20. Bacillus oceani sp. nov., a new slightly halophilic bacterium, isolated from a deep sea sediment environment

Author:
Tian, Xin-Peng,   et al.   ; Liu, Yu-Juan; Long, Li-Juan; Huang, Xiao-Fang; You, Zhi-Qing; Wang, Fa-Zuo; Li, Jie; Kim, Chang-Jin; Zhang, Si;     Show all 9 Authors
Source:
Antonie van Leeuwenhoek 2013 v.104 no.5 pp. 829-836
ISSN:
0003-6072
Subject:
Bacillus carboniphilus; Bacillus endophyticus; bacteria; carbon; fatty acids; new species; nitrogen; nucleotide sequences; phylogeny; ribosomal RNA; sediments; sequence analysis; sodium chloride; South China Sea
Abstract:
... A strictly aerobic, Gram-stain positive, slightly halophilic strain, designated SCSIO 04524(T), was isolated from a deep sea sediment sample collected from the northern South China Sea at a depth of 3415 m. The isolate slightly embedded into the medium after 72 h incubation at 30 °C. Growth was found to occur on media with 0-10 % NaCl but extremely weak growth occurred without supplying NaCl. The ...
DOI:
10.1007/s10482-013-9995-0
PubMed:
23934481