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Liu GH, Narsing Rao MP, Chen QQ, Che JM, Shi H, Liu B, Li WJ. Evansella halocellulosilytica sp. nov., an alkali-halotolerant and cellulose-dissolving bacterium isolated from bauxite residue. Extremophiles 2022; 26:19. [PMID: 35661272 DOI: 10.1007/s00792-022-01267-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/25/2022] [Indexed: 11/26/2022]
Abstract
An alkali and salt-tolerating strain FJAT-44876T was isolated from the bauxite residue sample. The 16S rRNA gene sequence and phylogenetic analysis suggest that strain FJAT-44876T was a member of the genus Evansella. It grew at 15-45 ℃ (optimum 20-25 ℃) and pH 6.5-11.0 (optimum pH 8.0-9.0) with 0-20% (w/v) NaCl (optimum 6-8%). The major fatty acids were anteiso-C15:0, iso-C15:0, anteiso-C17:0, iso-C17:0, and C16:0. The cell wall peptidoglycan contained meso-diaminopimelic acid and MK-7 as the menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G+C content was 38.2%. The average nucleotide identity values between strain FJAT-44876T and closely related members were below the cutoff level for species delineation. Thus, based on the above results, strain FJAT-44876T represents a novel species of the genus Evansella, for which the name Evansella halocellulosilytica sp. nov., is proposed. The type strain is FJAT-44876T (=CCTCC AB 2016264T = DSM 104633T).
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Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qian-Qian Chen
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Jian-Mei Che
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Huai Shi
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Bo Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Goto T, Ogami S, Yoshimume K, Yumoto I. Differences in Bioenergetic Metabolism of Obligately Alkaliphilic Bacillaceae Under High pH Depend on the Aeration Conditions. Front Microbiol 2022; 13:842785. [PMID: 35401478 PMCID: PMC8992544 DOI: 10.3389/fmicb.2022.842785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/22/2022] [Indexed: 11/26/2022] Open
Abstract
Alkaliphilic Bacillaceae appear to produce ATP based on the H+-based chemiosmotic theory. However, the bulk-based chemiosmotic theory cannot explain the ATP production in alkaliphilic bacteria because the H+ concentration required for driving ATP synthesis through the ATPase does not occur under the alkaline conditions. Alkaliphilic bacteria produce ATP in an H+-diluted environment by retaining scarce H+ extruded by the respiratory chain on the outer surface of the membrane and increasing the potential of the H+ for ATP production on the outer surface of the membrane using specific mechanisms of ATP production. Under high-aeration conditions, the high ΔΨ (ca. -170 mV) of the obligate alkaliphilic Evansella clarkii retains H+ at the outer surface of the membrane and increases the intensity of the protonmotive force (Δp) per H+ across the membrane. One of the reasons for the production of high ΔΨ is the Donnan potential, which arises owing to the induction of impermeable negative charges in the cytoplasm. The intensity of the potential is further enhanced in the alkaliphiles compared with neutralophiles because of the higher intracellular pH (ca. pH 8.1). However, the high ΔΨ observed under high-aeration conditions decreased (∼ -140 mV) under low-aeration conditions. E. clarkii produced 2.5–6.3-fold higher membrane bound cytochrome c in the content of the cell extract under low-aeration conditions than under high-aeration conditions. The predominant membrane-bound cytochrome c in the outer surface of the membrane possesses an extra Asn-rich segment between the membrane anchor and the main body of protein. This structure may influence the formation of an H+-bond network that accumulates H+ on the outer surface of the membrane. Following accumulation of the H+-bond network producing cytochrome c, E. clarkii constructs an H+ capacitor to overcome the energy limitation of low aeration at high pH conditions. E. clarkii produces more ATP than other neutralophilic bacteria by enhancing the efficacy per H+ in ATP synthesis. In low H+ environments, E. clarkii utilizes H+ efficiently by taking advantage of its high ΔΨ under high-aeration conditions, whereas under low-aeration conditions E. clarkii uses cytochrome c bound on its outer surface of the membrane as an H+ capacitor.
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Affiliation(s)
- Toshitaka Goto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shinichi Ogami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kazuaki Yoshimume
- College of Industrial Technology, Nihon University, Narashino, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- *Correspondence: Isao Yumoto,
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Narsing Rao MP, Xiao M, Liu D, Tang R, Liu GH, Li WJ. Genome-based reclassification of Evansella polygoni as a later heterotypic synonym of Evansella clarkii and transfer of Bacillus shivajii and Bacillus tamaricis to the genus Evansella as Evansella shivajii comb. nov. and Evansella tamaricis comb. nov. Arch Microbiol 2021; 204:47. [PMID: 34932158 DOI: 10.1007/s00203-021-02720-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/24/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022]
Abstract
In the present study, the taxonomic positions of Evansella polygoni, Evansella clarkii, Bacillus shivajii and Bacillus tamaricis were evaluated using phylogenetic and genome-based comparisons. In phylogenetic (based on 16S rRNA sequencing) and phylogenomic (based on concatenation of protein-marker genes) trees, Bacillus shivajii and Bacillus tamaricis were placed between genera Evansella and Alteribacter. The amino acid identity (AAI) values suggested that Bacillus shivajii and Bacillus tamaricis were members of the genus Evansella. The average nucleotide identity (ANI) value between Evansella polygoni and Evansella clarkii was higher than the threshold values for bacterial species delineation, indicating that they belong to the same species. Based on the results, we propose to reclassify Evansella polygoni as a later heterotypic synonym of Evansella clarkii and transfer Bacillus shivajii and Bacillus tamaricis to the genus Evansella as Evansella shivajii comb. nov. and Evansella tamaricis comb. nov.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dingqi Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753-5798. [PMID: 33112222 DOI: 10.1099/ijsem.0.004475] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.
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Key Words
- classification of Bacillus species
- conserved signature indels
- emendation of genus Bacillus
- genus Bacillus and the family Bacillaceae
- novel Bacillaceae genera Alteribacter, Ectobacillus, Evansella, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Niallia, Priestia, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sutcliffiella and Weizmannia
- phylogenomic and comparative genomic analyses
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
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Kumar S, Singh H, Kaur M, Kaur L, Tanuku NRS, Pinnaka AK. Bacillus shivajii sp. nov., isolated from a water sample of Sambhar salt lake, India. Int J Syst Evol Microbiol 2018; 68:3463-3470. [PMID: 30207517 DOI: 10.1099/ijsem.0.003008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, rod-shaped, motile, spore-forming, strictly aerobic, alkali- and halo- tolerant bacterium, designated strain AK72T, was isolated from a water sample collected from Sambhar salt lake, Rajasthan, India. The colony appears circular, shiny, smooth, translucent or slightly pale in colour and convex with an entire margin after 48 h incubation at 37 °C with pH 9. Growth of the bacterium occurred at 10-42 °C (optimum, 25-37 °C), at salinities of 0.5-10 % (w/v) NaCl (optimum 3-5 % NaCl) and pH of 6-10 (optimum pH 9). Strain AK72T was positive for oxidase, catalase, nitrate reductase, phenylalanine deaminase, ornithine decarboxylase, aesculinase, lipase and urease activities. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 and the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, three unidentified phospholipids and three unidentified lipids. The genomic DNA G+C content of the strain AK72T was 36.8 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain AK72T was closely related to Bacillus cellulosilyticus (96.5 %) and Bacillus vedderi (96.3 %), but the novel strain AK72T formed a separate clade with Bacillus aurantiacus whereas B. cellulosilyticus and B. vedderi were clustered in a separate clade. The above data in combination with the phenotypic characteristics and phylogenetic data inferred that strain AK72T represents a novel species of the genus Bacillus, for which the name Bacillusshivajii sp. nov. is proposed. The type strain is AK72T (=MTCC 12636T=KCTC 33981T=JCM 32183T).
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Affiliation(s)
- Shekhar Kumar
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Harjodh Singh
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India.,2Academy of Scientific and Innovative Research (AcSIR), CSIR Campus, Chennai, India.,3CSIR-Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Manpreet Kaur
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India.,2Academy of Scientific and Innovative Research (AcSIR), CSIR Campus, Chennai, India.,3CSIR-Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Lakhwinder Kaur
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Naga Radha Srinivas Tanuku
- 2Academy of Scientific and Innovative Research (AcSIR), CSIR Campus, Chennai, India.,4CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam 530017, India
| | - Anil Kumar Pinnaka
- 1MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India.,2Academy of Scientific and Innovative Research (AcSIR), CSIR Campus, Chennai, India
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Aliibacillus thermotolerans gen. nov., sp. nov.: a thermophilic and heterotrophic ammonia-oxidizing bacterium from compost. Arch Microbiol 2018; 200:1357-1363. [PMID: 29974158 DOI: 10.1007/s00203-018-1550-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/05/2018] [Accepted: 06/30/2018] [Indexed: 10/28/2022]
Abstract
A novel moderately thermophilic and heterotrophic ammonia-oxidizing bacterium, designated strain BM62T, was isolated from compost in the thermophilic stage in Harbin, China. Phylogenetic analysis based on the 16S rRNA gene indicated that strain BM62T belongs to the family Bacillaceae within the class Bacilli and was most closely related to Alteribacillus iranensis X5BT (only 94.6% sequence similarity). Cells of strain BM62T were Gram-positive, rod-shaped, motile by periflagella, catalase-positive and oxidase-negative. Growth of strain BM62T was observed at salinities of 0-4% (optimum 2-3%), temperatures of 35-65 °C (optimum 50 °C) and pH values of 5-9 (optimum pH 7). The major cellular fatty acid was iso-C16:0, and the predominant ubiquinone was MK-7. The peptidoglycan type is A1γ, and meso-diaminopimelic acid was the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The G + C content of its genomic DNA was 36.5 mol%. Data from this polyphasic taxonomy study suggested that strain BM62T should be classified as the type strain of the type species of a new genus within the family Bacillaceae for which the name Aliibacillus thermotolerans gen. nov., sp. nov. is proposed. The type strain of the species Aliibacillus thermotolerans sp. nov. is BM62T (= DSM 101851T = CGMCC 1.15790T). The respective DPD Taxon Number is GA00057.
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Singh H, Kaur M, Kaur L, Sharma S, Mishra S, Tanuku NRS, Pinnaka AK. Bacillus lacus sp. nov., isolated from a water sample of a salt lake in India. Int J Syst Evol Microbiol 2018; 68:801-809. [DOI: 10.1099/ijsem.0.002588] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Harjodh Singh
- Academy of Scientific and Innovative Research, (AcSIR), CSIR Campus, Chennai, India
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- Council of Scientific and Industrial Research (CSIR) Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Manpreet Kaur
- Academy of Scientific and Innovative Research, (AcSIR), CSIR Campus, Chennai, India
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- Council of Scientific and Industrial Research (CSIR) Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Lakhwinder Kaur
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Shivani Sharma
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Sunita Mishra
- Academy of Scientific and Innovative Research, (AcSIR), CSIR Campus, Chennai, India
- Council of Scientific and Industrial Research (CSIR) Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Naga Radha Srinivas Tanuku
- Academy of Scientific and Innovative Research, (AcSIR), CSIR Campus, Chennai, India
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam 530017, India
| | - Anil Kumar Pinnaka
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- Academy of Scientific and Innovative Research, (AcSIR), CSIR Campus, Chennai, India
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Liu B, Liu GH, Wang XY, Wang JP, Zhu YJ, Zhang HF, Sengonca C. Bacillus populi sp. nov. isolated from Populus euphratica rhizosphere soil of the Taklamakan desert. Int J Syst Evol Microbiol 2018; 68:155-159. [DOI: 10.1099/ijsem.0.002476] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo Liu
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Xiao-Ying Wang
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
- Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Jie-Ping Wang
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Yu-Jing Zhu
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Hai-Feng Zhang
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Sengonca
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A D-53115 Bonn, Germany
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Tidjani Alou M, Nguyen TT, Armstrong N, Rathored J, Khelaifia S, Raoult D, Fournier PE, Lagier JC. Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut. New Microbes New Infect 2016; 12:76-85. [PMID: 27354918 PMCID: PMC4910145 DOI: 10.1016/j.nmni.2016.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 12/20/2022] Open
Abstract
Numidum massiliense gen. nov., sp. nov., strain mt3(T) is the type strain of Numidum gen. nov., a new genus within the family Bacillaceae. This strain was isolated from the faecal flora of a Tuareg boy from Algeria. We describe this Gram-positive facultative anaerobic rod and provide its complete annotated genome sequence according to the taxonogenomics concept. Its genome is 3 755 739 bp long and contains 3453 protein-coding genes and 64 RNA genes, including eight rRNA genes.
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Affiliation(s)
- M. Tidjani Alou
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - T.-T. Nguyen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - N. Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - J. Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
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Zhang S, Li Z, Yan Y, Zhang C, Li J, Zhao B. Bacillus urumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:2305-2312. [DOI: 10.1099/ijsem.0.001028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaojun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanlun Zhang
- The School of Ocean and Earth Sciences, Tongji University, Shanghai 200092, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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11
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Kumar RM, Kaur G, Kumar A, Bala M, Singh NK, Kaur N, Kumar N, Mayilraj S. Taxonomic description and genome sequence of Bacillus campisalis sp. nov., a member of the genus Bacillus isolated from a solar saltern. Int J Syst Evol Microbiol 2016; 65:3235-3240. [PMID: 26296567 DOI: 10.1099/ijsem.0.000400] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a Gram-stain positive bacterium isolated from a solar saltern sample collected from Kanyakumari, coastal region of the Bay of Bengal, India, was analysed by using a polyphasic approach. The isolated strain, designated SA2-6T, had phenotypic characteristics that matched those of the genus Bacillus. The 16S rRNA gene sequence (1493 bases) of the novel strain was compared with those of previously studied Bacillus type strains and confirmed that the strain belongs to the genus Bacillus and was moderately closely related to the type strain of Bacillus foraminis at 97.5 % 16S rRNA gene sequence similarity, followed by those of Bacillus thioparans (96.9 %), Bacillus subterraneus (96.8 %), Bacillus jeotgali (96.6 %), Bacillus selenatarsenatis (96.6 %) and Bacillus boroniphilus (96.6 %). 16S rRNA gene sequence analysis indicated that strain SA2-6T differs from all other species of the genus Bacillus by at least 2.5 %. It contained MK-7 as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, and iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids. Major lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data from this polyphasic study, strain SA2-6T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus campisalis sp. nov. is proposed. The type strain is SA2-6T ( = MTCC 11848T = DSM 28801T). The draft genome of strain SA2-6T consisted of 5 183 363 bp with G+C content of 45.44 mol%, 5352 predicted coding sequences, 191 RNAs and 479 subsystems.
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Affiliation(s)
- Rajendran Mathan Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Gurwinder Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Anand Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Monu Bala
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Nitin Kumar Singh
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Navjot Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Narender Kumar
- Division of Protein Science & Engineering, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Shanmugam Mayilraj
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
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12
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Daroonpunt R, Itoh T, Kudo T, Ohkuma M, Tanasupawat S. Bacillus piscicola sp. nov., isolated from Thai fish sauce (Nam-pla). Int J Syst Evol Microbiol 2016; 66:1151-1155. [DOI: 10.1099/ijsem.0.000851] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rungsima Daroonpunt
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils. Antonie van Leeuwenhoek 2015; 109:149-58. [DOI: 10.1007/s10482-015-0616-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/30/2015] [Indexed: 10/22/2022]
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14
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Vishnuvardhan Reddy S, Thirumala M, Farooq M. Bacillus caseinilyticus sp. nov., an alkali- and thermotolerant bacterium isolated from a soda lake. Int J Syst Evol Microbiol 2015; 65:2441-2446. [DOI: 10.1099/ijs.0.000275] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, rod-shaped, motile, endospore-forming and proteolytic bacterial strain, SPT, was isolated from Lonar soda lake, in India. On the basis of 16S rRNA gene sequence analysis it was identified as belonging to the class Firmibacteria and was most closely related to Bacillus cellulosilyticus DSM 2522T (96.7 %) and other members of the genus Bacillus ( < 95.9 %). Strain SPT was catalase- and oxidase-positive. The cell-wall peptidoglycan of strain SPT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three phospholipids, two aminolipids and two unknown lipids. The predominant isoprenoid quinone was MK-7. Anteiso-C15 : 0 (26.8 %) was the predominant fatty acid and significant proportions (>5 %) of iso-C15 : 0 (20.9 %), C16 : 1ω7c alcohol (6.3 %), iso-C16 : 0 (6.3 %) and anteiso-C17 : 0 (5.3 %) were also detected in strain SPT. The DNA G+C content of strain SPT was 38.9 mol%. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain SPT from all other members of the genus Bacillus. Strain SPT represents a novel member of the genus Bacillus, for which the name Bacillus
caseinilyticus sp. nov. is proposed. The type strain is SPT ( = MCC 2612T = JCM 30246T).
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Affiliation(s)
- Sultanpuram Vishnuvardhan Reddy
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda- 508254, Telangana, India
| | - Mothe Thirumala
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda- 508254, Telangana, India
| | - Mohammed Farooq
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda- 508254, Telangana, India
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Abstract
ABSTRACT
The family
Bacillaceae
constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the
Bacillaceae
, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
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16
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Glaeser SP, McInroy JA, Busse HJ, Kämpfer P. Pseudogracilibacillus auburnensis gen. nov., sp. nov., isolated from the rhizosphere of Zea mays. Int J Syst Evol Microbiol 2014; 64:2442-2448. [DOI: 10.1099/ijs.0.064584-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive-staining, aerobic, endospore-forming bacterium, strain P-207T, was isolated from a rhizosphere soil sample in Auburn, AL, USA. On the basis of 16S rRNA gene sequence comparisons, strain P-207T was grouped in the vicinity of representatives of the genera
Virgibacillus
,
Ornithinibacillus
,
Cerasibacillus
,
Lentibacillus
and
Oceanobacillus
, but could not be assigned clearly to any of these genera. The highest similarity was found to the sequence of
Virgibacillus carmonensis
LMG 20964T (94.4 %); however, the 16S rRNA gene sequence similarity to the type strain of the type species of
Virgibacillus
,
Virgibacillus pantothenticus
, was only 92.9 %. The quinone system of strain P-207T consisted predominantly of menaquinone MK-7. The polar lipid profile exhibited the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and moderate to minor amounts of several unidentified phospholipids, glycolipids and phosphoglycolipids, an aminophospholipid and an aminolipid. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the polyamine pattern contained predominantly spermidine and spermine. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 34 mol%. Because of the low sequence similarity of strain P-207T to all representatives of
Virgibacillus
,
Ornithinibacillus
,
Cerasibacillus
,
Lentibacillus
and
Oceanobacillus
, which was always <95 %, and its unique lipid pattern, we propose that strain P-207T represents a novel species in a new genus, for which the name Pseudogracilibacillus auburnensis gen. nov., sp. nov. is proposed. The type strain of Pseudogracilibacillus auburnensis is P-207T ( = CCM 8509T = LMG 28212T = CIP 110797T).
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Affiliation(s)
- Stefanie P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A. McInroy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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17
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Zhai L, Ma Y, Xue Y, Ma Y. Bacillus alkalicola sp. nov., An Alkaliphilic, Gram-Positive Bacterium Isolated from Zhabuye Lake in Tibet, China. Curr Microbiol 2014; 69:311-6. [DOI: 10.1007/s00284-014-0576-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 02/15/2014] [Indexed: 10/25/2022]
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18
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Mead D, Drinkwater C, Brumm PJ. Genomic and enzymatic results show Bacillus cellulosilyticus uses a novel set of LPXTA carbohydrases to hydrolyze polysaccharides. PLoS One 2013; 8:e61131. [PMID: 23593409 PMCID: PMC3617157 DOI: 10.1371/journal.pone.0061131] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 03/08/2013] [Indexed: 11/19/2022] Open
Abstract
Background Alkaliphilic Bacillus species are intrinsically interesting due to the bioenergetic problems posed by growth at high pH and high salt. Three alkaline cellulases have been cloned, sequenced and expressed from Bacillus cellulosilyticus N-4 (Bcell) making it an excellent target for genomic sequencing and mining of biomass-degrading enzymes. Methodology/Principal Findings The genome of Bcell is a single chromosome of 4.7 Mb with no plasmids present and three large phage insertions. The most unusual feature of the genome is the presence of 23 LPXTA membrane anchor proteins; 17 of these are annotated as involved in polysaccharide degradation. These two values are significantly higher than seen in any other Bacillus species. This high number of membrane anchor proteins is seen only in pathogenic Gram-positive organisms such as Listeria monocytogenes or Staphylococcus aureus. Bcell also possesses four sortase D subfamily 4 enzymes that incorporate LPXTA-bearing proteins into the cell wall; three of these are closely related to each other and unique to Bcell. Cell fractionation and enzymatic assay of Bcell cultures show that the majority of polysaccharide degradation is associated with the cell wall LPXTA-enzymes, an unusual feature in Gram-positive aerobes. Genomic analysis and growth studies both strongly argue against Bcell being a truly cellulolytic organism, in spite of its name. Preliminary results suggest that fungal mycelia may be the natural substrate for this organism. Conclusions/Significance Bacillus cellulosilyticus N-4, in spite of its name, does not possess any of the genes necessary for crystalline cellulose degradation, demonstrating the risk of classifying microorganisms without the benefit of genomic analysis. Bcell is the first Gram-positive aerobic organism shown to use predominantly cell-bound, non-cellulosomal enzymes for polysaccharide degradation. The LPXTA-sortase system utilized by Bcell may have applications both in anchoring cellulases and other biomass-degrading enzymes to Bcell itself and in anchoring proteins other Gram-positive organisms.
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Affiliation(s)
- David Mead
- Lucigen Corporation, Middleton, Wisconsin, United States of America
- C5•6 Technologies, Middleton, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Colleen Drinkwater
- Lucigen Corporation, Middleton, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Phillip J. Brumm
- C5•6 Technologies, Middleton, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Glaeser SP, Dott W, Busse HJ, Kämpfer P. Fictibacillus phosphorivorans gen. nov., sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and Bacillus gelatini in the genus Fictibacillus. Int J Syst Evol Microbiol 2013; 63:2934-2944. [PMID: 23355698 DOI: 10.1099/ijs.0.049171-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive-staining, aerobic, endospore-forming bacterium (Ca7(T)) was isolated from a bioreactor showing extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strain Ca7(T) was grouped in the genus Bacillus, most closely related to Bacillus nanhaiensis JSM 082006(T) (100 %), Bacillus barbaricus V2-BIII-A2(T) (99.2 %) and Bacillus arsenicus Con a/3(T) (97.7 %). Moderate 16S rRNA gene sequence similarities were found to the type strains of the species Bacillus gelatini and Bacillus rigui (96.4 %), Bacillus macauensis (95.1 %) and Bacillus solisalsi (96.1 %). All these species were grouped into a monophyletic cluster and showed very low sequence similarities (<94 %) to the type species of the genus Bacillus, Bacillus subtilis. The quinone system of strain Ca7(T) consists predominantly of menaquinone MK-7. The polar lipid profile exhibited the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In addition, minor compounds of an unidentified phospholipid and an aminophospholipid were detected. No glycolipids were found in strain Ca7(T), which was consistent with the lipid profiles of B. nanhaiensis, B. barbaricus, B. arsenicus, B. rigui, B. solisalsi, B. macauensis and B. gelatini, but in contrast to B. subtilis. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the polyamine pattern contained predominantly spermidine and spermine. The major fatty acids, which were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0, supported the grouping of strain Ca7(T) in the family Bacillaceae. The strain showed DNA-DNA similarities of 48 % (reciprocal 47 %) to B. nanhaiensis DSM 23009(T), 31 % (reciprocal 36 %) to B. barbaricus V2-BIII-A2(T) and 29 % (reciprocal 39 %) to B. arsenicus DSM 15822(T), respectively. These results clearly demonstrate that strain Ca7(T) is a representative of a novel species, which can be differentiated from its closest relatives by physiological and biochemical tests. Because of the low sequence similarity of strain Ca7(T) to B. subtilis, which was shared by B. nanhaiensis, B. barbaricus, B. arsenicus, B. gelatini, B. rigui, B. solisalsi and B. macauensis, and their unique lipid patterns, we propose that strain Ca7(T) represents a novel species in a novel genus for which the name Fictibacillus phosphorivorans gen. nov., sp. nov. is proposed. The type strain is Ca7(T) (= CCM 8426(T) = LMG 27063(T)). In addition we propose the reclassification of B. nanhaiensis, B. barbaricus, B. arsenicus, B. rigui, B. macauensis, B. solisalsi and B. gelatini as Fictibacillus nanhaiensis comb. nov., Fictibacillus barbaricus comb. nov., Fictibacillus arsenicus comb. nov., Fictibacillus rigui comb. nov., Fictibacillus macauensis comb. nov., Fictibacillus solisalsi comb. nov. and Fictibacillus gelatini comb. nov., respectively [type strains JSM 082006(T) (= DSM 23009(T) = KCTC 13712(T)), V2-BIII-A2(T) ( = CCM 4982(T) = DSM 14730(T)), Con a/3(T) ( = MTCC 4380(T) = DSM 15822(T) = JCM 12167(T)), WPCB074(T) ( = KCTC 13278(T) = JCM 16348(T)), ZFHKF-1(T) ( = JCM 13285(T) = DSM 17262(T)), YC1(T) ( = KCTC 13181(T) = CGMCC 1.6854(T)) and LMG 21881(T) ( = DSM 15866(T)), respectively].
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Affiliation(s)
- Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Wolfgang Dott
- Institut für Hygiene und Umweltmedizin, RWTH Aachen, Germany
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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20
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Jang GI, Cho Y, Cho BC. Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern. Int J Syst Evol Microbiol 2012; 63:2124-2131. [PMID: 23104361 DOI: 10.1099/ijs.0.043661-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, non-motile, strictly aerobic, non-spore-forming, vibrio-shaped bacterial strain, CL-TW6(T), was isolated from a reservoir seawater sample from a solar saltern in Korea. Analysis of the 16S rRNA gene sequence of strain CL-TW6(T) revealed a clear affiliation with the family Microbacteriaceae. Strain CL-TW6(T) showed the closest phylogenetic relationships with the genera Yonghaparkia and Microcella, with 16S rRNA gene sequence similarity of 94.8-95.3%. The strain grew in the presence of 1-9% sea salts, at 15-35 °C and at pH 7.0-9.0. The major cellular fatty acids of strain CL-TW6(T) were anteiso-C15:0 (32.6%), iso-C16:0 (20.4%), iso-C15:0 (13.2%) and iso-C14:0 (11.8%) and the major menaquinones were MK-9 and MK-10. Cell-wall analysis showed that the peptidoglycan of strain CL-TW6(T) contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain CL-TW6(T) was 60.0 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed clearly that strain CL-TW6(T) could be distinguished from members of the family Microbacteriaceae with validly published names. Thus, strain CL-TW6(T) should be classified as representing a novel genus and species in the family Microbacteriaceae, for which the name Pontimonas salivibrio gen. nov., sp. nov. is proposed. The type strain of Pontimonas salivibrio is CL-TW6(T) (=KCCM 90105(T) =JCM 18206(T)).
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Affiliation(s)
- Gwang Il Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Yirang Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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Bacillus locisalis sp. nov., a new haloalkaliphilic species from hypersaline and alkaline lakes of China, Kenya and Tanzania. Syst Appl Microbiol 2011; 34:424-8. [DOI: 10.1016/j.syapm.2011.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 04/05/2011] [Accepted: 04/18/2011] [Indexed: 11/22/2022]
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Abstract
A novel Gram-stain-positive, slightly halophilic, facultatively alkaliphilic, catalase-positive, oxidase-negative, endospore-forming, motile, rod-shaped, aerobic bacterium, designated strain JSM 082006T, was isolated from an oyster collected from Naozhou Island in the South China Sea. The isolate grew in 0–18 % (w/v) NaCl (optimum, 0.5–4.0 %), at pH 6.0–10.5 (optimum, pH 8.0) and at 15–45 °C (optimum, 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Strain JSM 082006T contained MK-7 as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C content was 40.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 082006T should be assigned to the genus Bacillus and that it was most closely related to the type strains of Bacillus barbaricus (sequence similarity 99.1 %) and Bacillus arsenicus (97.5 %), followed by those of Bacillus rigui (96.6 %) and Bacillus solisalsi (96.1 %). Phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data support the view that strain JSM 082006T represents a novel species of the genus Bacillus, for which the name Bacillus nanhaiensis sp. nov. is proposed; the type strain is JSM 082006T ( = DSM 23009T = KCTC 13712T).
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Bioaugmentation with a novel alkali-tolerant Pseudomonas strain for alkaline phenol wastewater treatment in sequencing batch reactor. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0653-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sucharita K, Shiva Kumar E, Sasikala C, Panda BB, Takaichi S, Ramana CV. Marichromatium fluminis sp. nov., a slightly alkaliphilic, phototrophic gammaproteobacterium isolated from river sediment. Int J Syst Evol Microbiol 2010; 60:1103-1107. [DOI: 10.1099/ijs.0.013284-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anoxygenic, phototrophic gammaproteobacterium designated strain JA418T was isolated from a sediment sample collected from the Baitarani River, Orissa, India. The bacterium was a Gram-negative, motile rod with a single polar flagellum. Bacteriochlorophyll a and rhodopin were the major photosynthetic pigments. The organism grew best at slightly alkaline pH (8–8.5) and lacked chemotrophic growth. The major fatty acids were C16 : 0, C16 : 1
ω7c/C16 : 1
ω6c and C18 : 1
ω7c. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain JA418T clusters with species of the genus Marichromatium belonging to the class Gammaproteobacteria. The highest 16S rRNA gene sequence similarities of strain JA418T were found with the type strains of Marichromatium gracile (95.9 %), Marichromatium indicum (95.6 %), Marichromatium purpuratum (95.5 %) and Marichromatium bheemlicum (95.6 %). The DNA base composition of strain JA418T was 71.4 mol% G+C (by HPLC). Based on the 16S rRNA gene sequence analysis and physiological and chemotaxonomic characteristics, strain JA418T is sufficiently different from other Marichromatium species to merit the description of a novel species, Marichromatium fluminis sp. nov., to accommodate it. The type strain is JA418T (=KCTC 5717T =NBRC 105221T).
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Affiliation(s)
- K. Sucharita
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - E. Shiva Kumar
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - B. B. Panda
- Department of Botany, Bharampur University, Bharampur, Orissa, India
| | - S. Takaichi
- Department of Biology, Nippon Medical School, Kosugi-cho, Nakahara, Kawasaki 211-0063, Japan
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, PO Central University, Hyderabad 500 046, India
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Aizawa T, Urai M, Iwabuchi N, Nakajima M, Sunairi M. Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae (Trypoxylus dichotomus septentrionalis). Int J Syst Evol Microbiol 2010; 60:61-66. [DOI: 10.1099/ijs.0.005843-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three xylanase-producing alkaliphilic strains, SU1T, 36AC4 and 36AC6, were isolated from the guts of larvae of the Japanese horned beetle (Trypoxylus dichotomus septentrionalis). The isolates stained Gram-positive and were aerobic, spore-forming, non-motile and rod-shaped and grew optimally at 30 °C and pH 9. They contained MK-7 as the major isoprenoid quinone and iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C contents of the strains were 37.4–37.7 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Bacillus. Although their 16S rRNA gene sequence similarity to the type strains of the alkaliphilic species Bacillus pseudalcaliphilus and B. alcalophilus was 97 %, the novel isolates formed a distinct group in the phylogenetic trees and DNA–DNA relatedness values to the type strains of these species were less than 30 %. Results of physiological and biochemical tests, including salt preference, enabled these strains to be differentiated phenotypically from described Bacillus species. Therefore, strains SU1T, 36AC4 and 36AC6 represent a novel species for which the name Bacillus trypoxylicola sp. nov. is proposed; the type strain is SU1T (=NBRC 102646T =KCTC 13244T).
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Affiliation(s)
- Tomoko Aizawa
- Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan
| | - Makoto Urai
- Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan
| | - Noriyuki Iwabuchi
- Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan
| | - Mutsuyasu Nakajima
- Environmental Program, Nihon University Advanced Research Institute for the Sciences and Humanities, 12-5 Goban-cho Chiyoda, Tokyo 102-8251, Japan
- Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan
| | - Michio Sunairi
- Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan
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Chen YG, Zhang YQ, Wang YX, Liu ZX, Klenk HP, Xiao HD, Tang SK, Cui XL, Li WJ. Bacillus neizhouensis sp. nov., a halophilic marine bacterium isolated from a sea anemone. Int J Syst Evol Microbiol 2009; 59:3035-9. [DOI: 10.1099/ijs.0.009522-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Amoozegar MA, Sanchez-Porro C, Rohban R, Hajighasemi M, Ventosa A. Bacillus persepolensis sp. nov., a moderately halophilic bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2009; 59:2352-8. [DOI: 10.1099/ijs.0.010090-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Zhang L, Wang Y, Dai J, Tang Y, Yang Q, Luo X, Fang C. Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China. Int J Syst Evol Microbiol 2009; 59:1787-92. [DOI: 10.1099/ijs.0.004879-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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