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Joshi A, Thite S, Karodi P, Joseph N, Lodha T. Corrigendum: Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera. Front Microbiol 2022; 13:871596. [PMID: 35401476 PMCID: PMC8988803 DOI: 10.3389/fmicb.2022.871596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
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Joshi A, Thite S, Karodi P, Joseph N, Lodha T. Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera. Front Microbiol 2021; 12:722369. [PMID: 34707580 PMCID: PMC8543038 DOI: 10.3389/fmicb.2021.722369] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199T) was isolated from a sediment sample collected from Lonar Lake, India. The strain was oxidase and catalase positive. The strain grew optimally at pH 10, NaCl concentration of 3.5% at 37°C. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, and iso-C17:0. The peptidoglycan contained meso-diaminopimelic acid (meso-DAP). Phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol were the major polar lipids of MEB199T. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MEB199T belonged to the family Bacillaceae and exhibited a distinctive position among the members of the genus Alkalihalobacillus (Ahb.). Strain MEB199T shared the highest 16S rRNA gene sequence similarity with Alkalihalobacillus alkalinitrilicus ANL-iso4T (98.36%), whereas with type species Ahb. alcalophilus DSM 485T, it is 94.91%, indicating that strain MEB199T is distinctly related to the genus Alkalihalobacillus. The G + C content of genomic DNA was 36.47 mol%. The digital DNA-DNA hybridization (dDDH) (23.6%) and average nucleotide identity (ANI) (81%) values between strain MEB199T and Ahb. alkalinitrilicus ANL-iso4T confirmed the novelty of this new species. The pairwise identity based on the 16S rRNA gene sequence between the species of genus Alkalihalobacillus ranges from 87.4 to 99.81% indicating the heterogeneity in the genus. The different phylogenetic analysis based on the genome showed that the members of the genus Alkalihalobacillus separated into eight distinct clades. The intra-clade average amino acid identity (AAI) and percentage of conserved proteins (POCP) range from 52 to 68% and 37 to 59%, respectively, which are interspersed on the intra-genera cutoff values; therefore, we reassess the taxonomy of genus Alkalihalobacillus. The phenotypic analysis also corroborated the differentiation between these clades. Based on the phylogenetic analysis, genomic indices, and phenotypic traits, we propose the reclassification of the genus Alkalihalobacillus into seven new genera for which the names Alkalihalobacterium gen. nov., Halalkalibacterium gen. nov., Halalkalibacter gen. nov., Shouchella gen. nov., Pseudalkalibacillus gen. nov., Alkalicoccobacillus gen. nov., and Alkalihalophilus gen. nov. are proposed and provide an emended description of Alkalihalobacillus sensu stricto. Also, we propose the Ahb. okuhidensis as a heterotypic synonym of Alkalihalobacillus halodurans. Based on the polyphasic taxonomic analysis, strain MEB199T represents a novel species of newly proposed genus for which the name Alkalihalobacterium elongatum gen. nov. sp. nov. is proposed. The type strain is MEB199T (= MCC 2982T, = JCM 33704T, = NBRC 114256T, = CGMCC 1.17254T).
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Affiliation(s)
- Amaraja Joshi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Sonia Thite
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Prachi Karodi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Neetha Joseph
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
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Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406-438. [PMID: 31617837 DOI: 10.1099/ijsem.0.003775] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.
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Affiliation(s)
- Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
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Liu GH, Narsing Rao MP, Dong ZY, Wang JP, Chen Z, Liu B, Li WJ. Two novel alkaliphiles, Bacillus alkalisoli sp. nov., and Bacillus solitudinis sp. nov., isolated from saline-alkali soil. Extremophiles 2019; 23:759-764. [PMID: 31538256 DOI: 10.1007/s00792-019-01127-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Two alkaliphilic strains, designated FJAT-45086T and FJAT-45122T, were isolated from alkali soli in Nima County, Tibet, China. Both strains were Gram-positive, rod-shaped and shared low 16S rRNA gene sequence similarity with the members of the genus Bacillus. They contained meso-diaminopimelic acid as the cell-wall diamino acid and MK-7 as the menaquinone. The major fatty acids (>5%) of strain FJAT-45086T were anteiso-C15:0, C16:0, iso-C15:0, C16:1ω11c and anteiso-C17:0, whereas strain FJAT-45122T consisted of iso-C15:0, anteiso-C15:0, iso-C17:1ω10c, iso-C17:0, anteiso-C17:0, C16:0 and C16:1ω11c. The genome G + C content of strains FJAT-45086T and FJAT-45122T was 37.8 and 38.2 mol%, respectively. The polar lipids of strain FJAT-45086T were diphosphatidyl glycerol (DPG), phosphatidyl glycerol (PG), phosphatidyl ethanolamine (PE), and phosphatidyl choline (PC), whereas strain FJAT-45122T consisted of DPG, PG, phosphatidyl methyl ethanolamine (PME) and an unidentified aminophospholipids (UAPL). The average nucleotide identity values of strains FJAT-45086T and FJAT-45122T were below the cut-off level (95-96%) for species delineation. Based on the results, strains FJAT-45086T and FJAT-45122T represent two novel species of the genus Bacillus, for which the names Bacillus alkalisoli sp. nov., and Bacillus solitudinis sp. nov., are proposed. The type strain, FJAT-45122T (=DSM 104631T = CCTCC AB 2016254T), FJAT-45086T (=DSM 104056T = CCTCC AB 2016232T).
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Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jie-Ping Wang
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China
| | | | - Bo Liu
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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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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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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Hirota K, Nishita M, Matsuyama H, Yumoto I. Paralkalibacillus indicireducens gen., nov., sp. nov., an indigo-reducing obligate alkaliphile isolated from indigo fermentation liquor used for dyeing. Int J Syst Evol Microbiol 2017; 67:4050-4056. [DOI: 10.1099/ijsem.0.002248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8571, Japan
| | - Masatoshi Nishita
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan
| | - Hidetoshi Matsuyama
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan
| | - Isao Yumoto
- Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8571, Japan
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Borsodi AK, Tóth E, Aszalós JM, Bárány Á, Schumann P, Spröer C, Kovács AL, Márialigeti K, Szili-Kovács T. Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil. Int J Syst Evol Microbiol 2017; 67:3490-3495. [DOI: 10.1099/ijsem.0.002149] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrea K. Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Júlia M. Aszalós
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Ágnes Bárány
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Attila L. Kovács
- Department of Anatomy-, Cell- and Developmental Biology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, 1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Tibor Szili-Kovács
- Institute for Soil Sciences and Agricultural Chemistry, Agricultural Research Center, Hungarian Academy of Sciences, Herman Ottó út 15, H-1022 Budapest, Hungary
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Oren A, Garrity GM. Validation List No. 169. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2016; 66:2456-2458. [PMID: 27400683 DOI: 10.1099/ijsem.0.001181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, >published. Int J Syst Evol Microbiol 2016; 66:1913-1915. [PMID: 27142818 DOI: 10.1099/ijsem.0.001030] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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