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Yadav A, Teware R, Bhatt A, Bhavsar Y, Maurya A, Thorat V, Vemuluri VR, Kirdat K. Ureibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. Nov. Arch Microbiol 2024; 206:242. [PMID: 38698177 DOI: 10.1007/s00203-024-03970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/19/2024] [Indexed: 05/05/2024]
Abstract
A Gram-stain-positive aerobic, rod-shaped, spore-producing bacterium forming colonies with convex elevation and a smooth, intact margin was isolated from a freshwater sample collected from a well situated in an agricultural field. The 16S rRNA gene sequence of the isolated strain BA0131T showed the highest sequence similarity to Lysinibacillus yapensis ylb-03T (99.25%) followed by Ureibacillus chungkukjangi 2RL3-2T (98.91%) and U. sinduriensis BLB-1T (98.65%). The strain BA0131T was oxidase and catalase positive and urease negative. It also tested positive for esculin hydrolysis and reduction of potassium nitrate, unlike its phylogenetically closest relatives. The predominant fatty acids in strain BA0131T included were anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 and the major polar lipids comprised were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The respiratory quinones identified in strain BA0131T were MK8 (H2) (major) and MK8 (minor). The strain BA0131T shared the lowest dDDH values with L. yapensis ylb-03T (21%) followed by U. chungkukjangi 2RL3-2T (24.2%) and U. sinduriensis BLB-1T (26.4%) suggesting a closer genetic relationship U. sinduriensis BLB-1T. The ANI percentage supported the close relatedness with U. sinduriensis BLB-1T (83.61%) followed by U. chungkukjangi 2RL3-2T (82.03%) and U. yapensis ylb-03T (79.57%). The core genome-based phylogeny constructed using over 13,704 amino acid positions and 92 core genes revealed the distinct phylogenetic position of strain BA0131T among the genus Ureibacillus. The distinct physiological, biochemical characteristics and genotypic relatedness data indicate the strain BA0131T represents a novel species of the genus Ureibacillus for which the name Ureibacillus aquaedulcis sp. nov. (Type strain, BA0131T = MCC 5284 = JCM 36475) is proposed. Additionally, based on extensive genomic and phylogenetic analyses, we propose reclassification of two species, L. yapensis and L. antri, as U. yapensis comb. nov. (Type strain, ylb-03T = JCM 32871T = MCCC 1A12698T) and U. antri (Type strain, SYSU K30002T = CGMCC 1.13504T = KCTC 33955T).
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Affiliation(s)
- Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India.
| | - Ruchi Teware
- Department of Microbiology, Fergusson College, Shivajinagar, Pune, 411 004, India
| | - Agrima Bhatt
- Department of Biosciences and Technology, School of Science and Environmental Studies, Dr. Vishwanath Karad MIT World Peace University, Pune, 411 038, India
| | - Yash Bhavsar
- Department of Microbiology, Fergusson College, Shivajinagar, Pune, 411 004, India
| | - Akanksha Maurya
- Khwaja Moinuddin Chishti Language University, Sitapur Hardoi Road, Lucknow, 226 013, India
| | - Vipool Thorat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India
| | - Venkata Ramana Vemuluri
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, 160 003, India
| | - Kiran Kirdat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India.
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Jo JH, Lee SY, Rhee MS, Lee KH, Chun SY, Im WT. Solibacillus palustris sp. nov., isolated from wetland soil of ecology park. Int J Syst Evol Microbiol 2024; 74. [PMID: 38323635 DOI: 10.1099/ijsem.0.006065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
A Gram-staining-positive, motile, aerobic and rod-shaped bacterium, designated strain MA9T was isolated from wetland soil of ecology park, in Seoul, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using the polyphasic approach. Strain MA9T grew at 10-37 °C and at pH 6.0-9.5 on TSB. Menaquinone MK-7 was the predominant respiratory quinone and iso-C15 : 0, iso-C16 : 0 and C16 : 1 ω7c alcohol were the major fatty acids. The main polar lipids were phosphatidylethanolamine (PE), phosphatidylserine (PS), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The peptidoglycan type of the cell wall was A4α l-Lys-d-Glu. Based on 16S rRNA gene sequencing, strain MA9T clustered with species of the genus Solibacillus and appeared closely related to S. silvestris DSM 12223T (97.8 % sequence similarity), S. cecembensis DSM 21993T (97.6 %), S. isronensis DSM 21046T (97.6 %) and S. kalamii DSM 101595T (96.6 %). The G+C content of the genomic DNA was 37.0 mol%. Digital DNA-DNA hybridization between strain MA9T and type strains of S. silvestris, S. isronensis, S. cecembensis and S. kalamii resulted in values below 70 %. Strain MA9T could be differentiated genotypically and phenotypically from the recognized species of the genus Solibacillus. The isolate therefore represents a novel species, for which the name Solibacillus palustris sp. nov. is proposed, with the type strain MA9T (=KACC 22212T = LMG 32188T).
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Affiliation(s)
- Jung-Hun Jo
- Major in Applied Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do 17579, Republic of Korea
- AceEMzyme Co. Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Gyeonggi-do 17579, Republic of Korea
| | - Soon-Youl Lee
- Major in Applied Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do 17579, Republic of Korea
| | - Moon-Soo Rhee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Kang-Hyun Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Se-Yoon Chun
- Major in Applied Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do 17579, Republic of Korea
- AceEMzyme Co. Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Gyeonggi-do 17579, Republic of Korea
| | - Wan-Taek Im
- Major in Applied Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do 17579, Republic of Korea
- AceEMzyme Co. Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, 327 Chungang-no Anseong-si, Gyeonggi-do 17579, Republic of Korea
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Liang Y, Shi W, Wu LH, Zhang XJ, Chai LJ, Liu GQ, Zheng L, Wang ST, Zhang SY, Chen FW, Shen CH, Xu ZH, Lu ZM. Solibacillus daqui sp. nov., isolated from high-temperature Daqu. Int J Syst Evol Microbiol 2023; 73. [PMID: 37916708 DOI: 10.1099/ijsem.0.006109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterial strain, designated ZS111008T, was isolated from high-temperature Daqu, a starter for production of Chinese Jiang-flavour Baijiu, and was characterized by polyphasic taxonomy. This novel isolate grew in the presence of 0-5 % (w/v) NaCl, at pH 6.0-9.0 and 25-45 °C; optimum growth was observed with 1 % (w/v) NaCl, at pH 8.0 and 30 °C. A comparative analysis of the 16S rRNA gene sequence (1461 bp) of strain ZS111008T showed highest similarity to Solibacillus silvestris DSM12223T (96.7%), followed by Solibacillus cecembensis PN5T (96.6%) and Solibacillus isronensis AMCK01000046 (96.5%). The DNA G+C content of strain ZS111008T was 37.21 mol%. The respiratory quinone was identified as menaquinone-7 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and one unknown phospholipid. Lys was detected as the diagnostic diamino acid in the cell wall. Based on morphological characteristics, chemotaxonomic characteristics and physiological properties, strain ZS111008T represents a novel species of the genus Solibacillus, for which the name Solibacillus daqui sp. nov. is proposed. The type strain for this proposed species is ZS111008T (=CGMCC 1.19455T=JCM 35214T).
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Affiliation(s)
- Yuan Liang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
| | - Wei Shi
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
| | - Lin-Huan Wu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiao-Juan Zhang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
| | - Li-Juan Chai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
| | - Guang-Qian Liu
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Lei Zheng
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Song-Tao Wang
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Su-Yi Zhang
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Fu-Wei Chen
- Guizhou Zhongjian Wine Industry Group Co. LTD, Zunyi 564500, PR China
| | - Cai-Hong Shen
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Zheng-Hong Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Zhen-Ming Lu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
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An Updated review on production of food derived bioactive peptides; focus on the psychrotrophic bacterial proteases. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Akinwole P, Kaplan L, Findlay R. Elucidating stream bacteria utilizing terrestrial dissolved organic matter. World J Microbiol Biotechnol 2021; 37:32. [DOI: 10.1007/s11274-021-02997-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022]
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Gupta RS, Patel S. Robust Demarcation of the Family Caryophanaceae ( Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures. Front Microbiol 2020; 10:2821. [PMID: 32010063 PMCID: PMC6971209 DOI: 10.3389/fmicb.2019.02821] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
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Abstract
The cholesterol-dependent cytolysin (CDC) genes are present in bacterial species that span terrestrial, vertebrate, and invertebrate niches, which suggests that they have evolved to function under widely different environmental conditions. Using a combination of biophysical and crystallographic approaches, we reveal that the relative stability of an intramolecular interface in the archetype CDC perfringolysin O (PFO) plays a central role in regulating its pore-forming properties. The disruption of this interface allows the formation of the membrane spanning β-barrel pore in all CDCs. We show here that the relative strength of the stabilizing forces at this interface directly impacts the energy barrier posed by the transition state for pore formation, as reflected in the Arrhenius activation energy (Ea) for pore formation. This change directly impacts the kinetics and temperature dependence of pore formation. We further show that the interface structure in a CDC from a terrestrial species enables it to function efficiently across a wide range of temperatures by minimizing changes in the strength of the transition state barrier to pore formation. These studies establish a paradigm that CDCs, and possibly other β-barrel pore-forming proteins/toxins, can evolve significantly different pore-forming properties by altering the stability of this transitional interface, which impacts the kinetic parameters and temperature dependence of pore formation.IMPORTANCE The cholesterol-dependent cytolysins (CDCs) are the archetype for the superfamily of oligomeric pore-forming proteins that includes the membrane attack complex/perforin (MACPF) family of immune defense proteins and the stonefish venom toxins (SNTX). The CDC/MACPF/SNTX family exhibits a common protein fold, which forms a membrane-spanning β-barrel pore. We show that changing the relative stability of an extensive intramolecular interface within this fold, which is necessarily disrupted to form the large β-barrel pore, dramatically alters the kinetic and temperature-dependent properties of CDC pore formation. These studies show that the CDCs and other members of the CDC/MACPF/SNTX superfamily have the capacity to significantly alter their pore-forming properties to function under widely different environmental conditions encountered by these species.
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Sandalova T, Lee M, Henriques-Normark B, Hesek D, Mobashery S, Mellroth P, Achour A. The crystal structure of the major pneumococcal autolysin LytA in complex with a large peptidoglycan fragment reveals the pivotal role of glycans for lytic activity. Mol Microbiol 2016; 101:954-67. [PMID: 27273793 DOI: 10.1111/mmi.13435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 12/18/2022]
Abstract
The pneumococcal autolysin LytA is a key virulence factor involved in several important functions including DNA competence, immune evasion and biofilm formation. Here, we present the 1.05 Å crystal structure of the catalytic domain of LytA in complex with a synthetic cell-wall-based peptidoglycan (PG) ligand that occupies the entire Y-shaped substrate-binding crevice. As many as twenty-one amino-acid residues are engaged in ligand interactions with a majority of these interactions directed towards the glycan strand. All saccharides are intimately bound through hydrogen bond, van der Waals and CH-π interactions. Importantly, the structure of LytA is not altered upon ligand binding, whereas the bound ligand assumes a different conformation compared to the unbound NMR-based solution structure of the same PG-fragment. Mutational study reveals that several non-catalytic glycan-interacting residues, structurally conserved in other amidases from Gram-positive Firmicutes, are pivotal for enzymatic activity. The three-dimensional structure of the LytA/PG complex provides a novel structural basis for ligand restriction by the pneumococcal autolysin, revealing for the first time an importance of the multivalent binding to PG saccharides.
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Affiliation(s)
- Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Department of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, SE, 17176, Sweden
| | - Mijoon Lee
- Departments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, 17176, Sweden
| | - Dusan Hesek
- Departments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Shahriar Mobashery
- Departments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Peter Mellroth
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden. .,Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, 17176, Sweden.
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Department of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, SE, 17176, Sweden.
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Mual P, Singh NK, Verma A, Schumann P, Krishnamurthi S, Dastager S, Mayilraj S. Reclassification of Bacillus isronensis Shivaji et al. 2009 as Solibacillus isronensis comb. nov. and emended description of genus Solibacillus Krishnamurthi et al. 2009. Int J Syst Evol Microbiol 2016; 66:2113-2120. [DOI: 10.1099/ijsem.0.000982] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Poonam Mual
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
| | - Nitin Kumar Singh
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
| | - Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
| | - Peter Schumann
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen,Inhoffenstrasse 7b, D-38124, Braunschweig,Germany
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
| | - Syed Dastager
- NCIM Resource Center, CSIR – National Chemical Laboratory,Pune 411 008, Maharashtra,India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
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Draft Genome Sequence of Bacillus cecembensis PN5T (DSM 21993), a Psychrotolerant Bacterium Isolated from Soil Samples near the Pindari Glacier. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01687-15. [PMID: 26847893 PMCID: PMC4742690 DOI: 10.1128/genomea.01687-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacillus cecembensis PN5T is a Gram-positive, aerobic, and spore-forming bacterium with very high intrinsic heat resistance. Here, we report the 4.72-Mb draft genome sequence of B. cecembensis PN5T, the first genome sequence of this species, which will promote its fundamental research.
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Soil development and bacterial community shifts along the chronosequence of the Midtre Lovénbreen glacier foreland in Svalbard. ACTA ACUST UNITED AC 2015. [DOI: 10.5141/ecoenv.2015.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Yadav AN, Sachan SG, Verma P, Kaushik R, Saxena AK. Cold active hydrolytic enzymes production by psychrotrophic Bacilli isolated from three sub-glacial lakes of NW Indian Himalayas. J Basic Microbiol 2015; 56:294-307. [PMID: 26933936 DOI: 10.1002/jobm.201500230] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/29/2015] [Indexed: 11/08/2022]
Abstract
The diversity of culturable, cold-active enzymes producing Bacilli was investigated from three sub-glacial lakes of north western Indian Himalayas. Amplified ribosomal DNA restriction analysis (ARDRA) using three restriction enzymes Alu I, Msp I, and Hae III led to the clustering of 136 Bacilli into 26, 23, and 22 clusters at 75% similarity index from Chandratal Lake, Dashair Lake, and Pangong Lake, respectively. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 35 Bacilli that could be grouped in seven families viz.: Bacillaceae (48%), Staphylococcaceae (14%), Bacillales incertae sedis (13%), Planococcaceae (12%), Paenibacillaceae (9%), Sporolactobacillaceae (3%), and Carnobacteriaceae (1%), which included twelve different genera Bacillus, Desemzia, Exiguobacterium, Jeotgalicoccus, Lysinibacillus, Paenibacillus, Planococcus, Pontibacillus, Sinobaca, Sporosarcina, Staphylococcus, and Virgibacillus. Based on their optimal temperature for growth, 35 Bacilli were grouped as psychrophilic (11 strains), psychrotrophic (17 strains), or psychrotolerant (7 strains), respectively. The representative isolates from each cluster were screened for cold-active enzyme activities. Amylase, β-glucosidase, pectinase, and protease activities at 4 °C were detected in more than 80% of the strains while approximately 40, 31, 23, 14, 11, and 9% of strains possessed cellulase, xylanase, β-galactosidase, laccase, chitinase, and lipase activity, respectively. Among 35 Bacilli, Bacillus amyloliquefaciens, Bacillus marisflavi, Exiguobacterium indicum, Paenibacillus terrae, Pontibacillus sp., Sporosarcina globispora, and Sporosarcina psychrophila were efficient producers of different cold-active enzymes. These cold-adapted Bacilli could play an important role in industrial and agricultural processes.
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Affiliation(s)
- Ajar Nath Yadav
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India.,Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, India
| | | | - Priyanka Verma
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
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Diomandé SE, Nguyen-The C, Guinebretière MH, Broussolle V, Brillard J. Role of fatty acids in Bacillus environmental adaptation. Front Microbiol 2015; 6:813. [PMID: 26300876 PMCID: PMC4525379 DOI: 10.3389/fmicb.2015.00813] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/23/2015] [Indexed: 11/23/2022] Open
Abstract
The large bacterial genus Bacillus is widely distributed in the environment and is able to colonize highly diverse niches. Some Bacillus species harbor pathogenic characteristics. The fatty acid (FA) composition is among the essential criteria used to define Bacillus species. Some elements of the FA pattern composition are common to Bacillus species, whereas others are specific and can be categorized in relation to the ecological niches of the species. Bacillus species are able to modify their FA patterns to adapt to a wide range of environmental changes, including changes in the growth medium, temperature, food processing conditions, and pH. Like many other Gram-positive bacteria, Bacillus strains display a well-defined FA synthesis II system that is equilibrated with a FA degradation pathway and regulated to efficiently respond to the needs of the cell. Like endogenous FAs, exogenous FAs may positively or negatively affect the survival of Bacillus vegetative cells and the spore germination ability in a given environment. Some of these exogenous FAs may provide a powerful strategy for preserving food against contamination by the Bacillus pathogenic strains responsible for foodborne illness.
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Affiliation(s)
- Sara E Diomandé
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
| | - Christophe Nguyen-The
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
| | - Marie-Hélène Guinebretière
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
| | - Véronique Broussolle
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
| | - Julien Brillard
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; UMR 1333 DGIMI, INRA, Université de Montpellier Montpellier, France
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14
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Venkatachalam S, Gowdaman V, Prabagaran SR. Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal. MICROBIAL ECOLOGY 2015; 69:472-91. [PMID: 25204748 DOI: 10.1007/s00248-014-0476-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 07/28/2014] [Indexed: 05/18/2023]
Abstract
Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills.
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Affiliation(s)
- Siddarthan Venkatachalam
- Molecular Microbiology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
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15
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Description of Thalassospira lohafexi sp. nov., isolated from Southern Ocean, Antarctica. Arch Microbiol 2015; 197:627-37. [DOI: 10.1007/s00203-015-1092-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
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16
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Prospecting cold deserts of north western Himalayas for microbial diversity and plant growth promoting attributes. J Biosci Bioeng 2015; 119:683-93. [PMID: 25575970 DOI: 10.1016/j.jbiosc.2014.11.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/01/2014] [Accepted: 11/07/2014] [Indexed: 11/23/2022]
Abstract
Microbial communities in different samples collected from cold deserts of north western Himalayas, India, were analyzed using 16S rRNA gene sequencing and phospholipid fatty acids (PLFA) analysis. A total of 232 bacterial isolates were characterized employing 16S rDNA-Amplified Ribosomal DNA Restriction Analysis with the three restriction endonucleases Alu I, Msp I and Hae III, which led to formation of 29-54 groups for the different sites, adding up to169 groups. 16S rRNA gene based phylogenetic analysis, revealed that 82 distinct species of 31 different genera, belonged to four phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. PLFA profiling was performed for concerned samples which gave an estimate of microbial communities without cultivating the microorganisms. PLFA analysis led to characterization of diverse group of microbes in different samples such as gram-negative, gram-positive bacteria, actinomycetes, cyanobacteria, anaerobic bacteria, sulphate reducing bacteria and fungi. The representative strains were screened for their plant growth promoting attributes, which included production of ammonia, HCN, gibberellic acid, IAA and siderophore; solubilization of phosphorus and activity of ACC deaminase. In vitro antifungal activity assay was performed against Rhizoctonia solani and Macrophomina phaseolina. Cold adapted microorganisms may serve as inoculants for crops growing under cold climatic conditions. To our knowledge, this is the first report for the presence of Arthrobacter nicotianae, Brevundimonas terrae, Paenibacillus tylopili and Pseudomonas cedrina in cold deserts and exhibit multifunctional PGP attributes at low temperatures.
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17
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Culturable diversity and functional annotation of psychrotrophic bacteria from cold desert of Leh Ladakh (India). World J Microbiol Biotechnol 2014; 31:95-108. [DOI: 10.1007/s11274-014-1768-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/28/2014] [Indexed: 10/24/2022]
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18
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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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19
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Shivaji S, Reddy GS. Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov., isolated from the Southern Ocean. Int J Syst Evol Microbiol 2014; 64:3264-3275. [PMID: 24981324 DOI: 10.1099/ijs.0.065409-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analyses of the genus Glaciecola were performed using the sequences of the 16S rRNA gene and the GyrB protein to establish its taxonomic status. The results indicated a consistent clustering of the genus Glaciecola into two clades, with significant bootstrap values, with all the phylogenetic methods employed. Clade 1 was represented by seven species, Glaciecola agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. mesophila, G. polaris and G. psychrophila, while clade 2 consisted of only three species, Glaciecola nitratireducens, G. pallidula and G. punicea. Evolutionary distances between species of clades 1 and 2, based on 16S rRNA gene and GyrB protein sequences, ranged from 93.0 to 95.0 % and 69.0 to 73.0 %, respectively. In addition, clades 1 and 2 possessed 18 unique signature nucleotides, at positions 132, 184 : 193, 185 : 192, 230, 616 : 624, 631, 632, 633, 738, 829, 1257, 1265, 1281, 1356 and 1366, in the 16S rRNA gene sequence and can be differentiated by the occurrence of a 15 nt signature motif 5'-CAAATCAGAATGTTG at positions 1354-1368 in members of clade 2. Robust clustering of the genus Glaciecola into two clades based on analysis of 16S rRNA gene and GyrB protein sequences, 16S rRNA gene sequence similarity of ≤95.0 % and the occurrence of signature nucleotides and signature motifs in the 16S rRNA gene suggested that the genus should be split into two genera. The genus Paraglaciecola gen. nov. is therefore created to accommodate the seven species of clade 1, while the name Glaciecola sensu stricto is retained to represent species of clade 2. The species of clade 1 are transferred to the genus Paraglaciecola as Paraglaciecola mesophila comb. nov. (type strain DSM 15026(T) = KMM 241(T)), P. agarilytica comb. nov. (type strain NO2(T) = KCTC 12755(T) = LMG 23762(T)), P. aquimarina comb. nov. (type strain GGW-M5(T) = KCTC 32108(T) = CCUG 62918(T)), P. arctica comb. nov. (type strain BSs20135(T) = CCTCC AB 209161(T) = KACC 14537(T)), P. chathamensis comb. nov. (type strain E3(T) = CGMCC 1.7001(T) = JCM 15139(T)), P. polaris comb. nov. (type strain ARK 150(T) = CIP 108324(T) = LMG 21857(T)) and P. psychrophila comb. nov. (type strain 170(T) = CGMCC1.6130(T) = JCM 13954(T)). The type species of the genus Paraglaciecola is Paraglaciecola mesophila. An emended description of the genus Glaciecola is provided. In addition, a novel strain, 162Z-12(T), was isolated from seawater collected as part of an iron fertilization experiment (LOHAFEX) conducted in the Southern Ocean in 2009 and was subjected to polyphasic taxonomic characterization. Cells of 162Z-12(T) were Gram-negative, aerobic, motile, ovoid to short rod-shaped, obligatorily halophilic and possessed all the characteristics of the genus Paraglaciecola. Strain 162Z-12(T) shared the highest 16S rRNA gene sequence similarity with the type strains of P. agarilytica (99.7 %), P. chathamensis (99.7 %), P. mesophila (98.5 %) and P. polaris (98.3 %). However, it exhibited DNA-DNA relatedness of less than 70.0 % with its nearest phylogenetic relatives, well below the threshold value for species delineation. Further, strain 162Z-12(T) differed from the nearest species in several phenotypic characteristics, in addition to the occurrence of unique nucleotides G, T, T and T at positions 1194, 1269, 1270 and 1271 of the 16S rRNA gene. Based on the cumulative differences it exhibited from its nearest phylogenetic neighbours, strain 162Z-12(T) was identified as a novel member of the genus Paraglaciecola and assigned to the novel species Paraglaciecola oceanifecundans sp. nov. The type strain of Paraglaciecola oceanifecundans is 162Z-12(T) ( = KCTC 32337(T) = LMG 27453(T)).
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Affiliation(s)
- Sisinthy Shivaji
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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20
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Reddy GSN, Manasa BP, Singh SK, Shivaji S. Paenisporosarcina
indica sp. nov., a psychrophilic bacterium from a glacier, and reclassification of
Sporosarcina antarctica
Yu et al., 2008 as
Paenisporosarcina
antarctica comb. nov. and emended description of the genus
Paenisporosarcina. Int J Syst Evol Microbiol 2013; 63:2927-2933. [DOI: 10.1099/ijs.0.047514-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, spore-forming, rod-shaped bacterium, PN2T, was isolated from a soil sample collected near the Pindari glacier. It contained anteiso-C15 : 0, iso-C15 : 0 and C16 : 1ω7c alcohol as the predominant fatty acids, MK-7 as the major menaquinone and A4α type (l-Lys–d-Glu) peptidoglycan. Based on these characteristics, strain PN2T was assigned to the genus
Paenisporosarcina
. Phylogenetic analysis based on 16S rRNA gene sequence placed strain PN2T within the genus
Paenisporosarcina
and showed a sequence similarity of 98.5–99.0 % with members of this genus.
Paenisporosarcina macmurdoensis
CMS 21wT,
Paenisporosarcina quisquiliarum
SK 55T and
Sporosarcina antarctica
N-05T were identified as the most closely related species with 16S rRNA gene sequence similarities of 98.6 %, 99.0 % and 98.4 %, respectively. The values for DNA–DNA relatedness between strain PN2T and
P. macmurdoensis
,
P. quisquiliarum
and
S. antarctica
were below the 70 % threshold value (32.0 %, 42.0 % and 38.0 % respectively). In addition, strain PN2T exhibited a number of phenotypic differences from
P. macmurdoensis
,
P. quisquiliarum
and
S. antarctica
. Based on the cumulative differences, strain PN2T was identified as representing a novel species and the name
Paenisporosarcina
indica sp. nov. was proposed. The type strain of
Paenisporosarcina
indica sp. nov. is PN2T (LMG 23933T = JCM 15114T). Furthermore, based on the morphological and chemotaxonomic characteristics, the species
Sporosarcina antarctica
was reclassified as a species of the genus
Paenisporosarcina
and renamed
Paenisporosarcina
antarctica comb. nov. In addition, an emended description of the genus
Paenisporosarcina
is presented.
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Affiliation(s)
- G. S. N. Reddy
- Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500 007, India
| | - B. Poorna Manasa
- Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500 007, India
| | - Sanjay K. Singh
- Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500 007, India
| | - S. Shivaji
- Centre for Cellular and Molecular Biology Uppal Road, Hyderabad 500 007, India
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21
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Prakash O, Jangid K, Shouche YS. Carl woese: from biophysics to evolutionary microbiology. Indian J Microbiol 2013; 53:247-52. [PMID: 24426118 DOI: 10.1007/s12088-013-0401-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/26/2013] [Indexed: 10/27/2022] Open
Abstract
This article is a tribute to Carl R. Woese, a biophysicist turned evolutionary microbiologist who passed away on December 30, 2012. We focus on his life, achievements, the discovery of Archaea and contributions to the development of molecular phylogeny. Further, the authors share their views and the lessons learnt from Woese's life with the microbiologists in India. We also emphasize the need for interdisciplinary collaboration and interaction for the progress and betterment of science.
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Affiliation(s)
- Om Prakash
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 Maharashtra India
| | - Kamlesh Jangid
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 Maharashtra India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Ganeshkhind, Pune, 411007 Maharashtra India
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22
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Shivaji S, Reddy PVV, Rao SSSN, Begum Z, Manasa P, Srinivas TNR. Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment. Int J Syst Evol Microbiol 2012; 62:2133-2139. [DOI: 10.1099/ijs.0.038661-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11BT, was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C15 : 0 (14.9 %), anteiso-C15 : 0 (11.4 %), iso-C15 : 1 G (13.1 %), C15 : 1ω6c (5.4 %), C17 : 1ω6c (6.7 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c; 5.9 %). Strain M12-11BT contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of
Cyclobacterium amurskyense
,
Cyclobacterium marinum
and
Cyclobacterium lianum
were most closely related to M12-11BT with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family
Cyclobacteriaceae
had sequence similarities of <92.0 %. However, DNA–DNA hybridization with
Cyclobacterium amurskyense
KCTC 12363T and
Cyclobacterium marinum
DSM 745T showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11BT. Based on the results of DNA–DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11BT represents a novel species of the genus
Cyclobacterium
, for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11BT ( = KCTC 23011T = NBRC 106168T) and it has a DNA G+C content of 40.5 mol%.
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Affiliation(s)
- S. Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - P. Vishnu Vardhan Reddy
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - S. S. S. Nageshwara Rao
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - Zareena Begum
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - Poorna Manasa
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - T. N. R. Srinivas
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
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23
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Kumar PA, Srinivas TNR, Manasa P, Madhu S, Shivaji S. Lutibaculum baratangense gen. nov., sp. nov., a proteobacterium isolated from a mud volcano. Int J Syst Evol Microbiol 2012; 62:2025-2031. [DOI: 10.1099/ijs.0.036350-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, oval to rod-shaped, motile bacterium, strain AMV1T, was isolated from a soil sample collected from a mud volcano of Baratang Island, Andamans, India. The predominant fatty acids were C16 : 0 (5.7 %), C18 : 1ω7c (78.6 %) and C19 : 0 cyclo ω8c (6.3 %). Strain AMV1T contained ubiquinone 10 (Q-10) as the major respiratory quinone and minor quantities of ubiquinone 9 (Q-9). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified lipids, one unidentified phospholipid and one unidentified aminolipid. 16S rRNA gene sequence analysis indicated that strain AMV1T was related most closely to the type strains of
Tepidamorphus gemmatus
,
Bauldia consociata
,
Afifella pfennigii
and
Amorphus coralli
, four members of the order
Rhizobiales
(class
Alphaproteobacteria
), with pairwise sequence similarities of 95.0, 94.5, 94.4 and 94.0 %, respectively; it shared <94 % 16S rRNA gene sequence similarity with all the other members of the order
Rhizobiales
. Phylogenetic analyses indicated that strain AMV1T clustered with
Tepidamorphus gemmatus
and with species of the genera
Amorphus
,
Rhodobium
and
Afifella
. Phenotypic and phylogenetic characteristics thus suggest that strain AMV1T is a representative of a novel species of a new genus, for which the name Lutibaculum baratangense gen. nov., sp. nov. is proposed. The type strain of Lutibaculum baratangense is AMV1T ( = KCTC 22669T = NBRC 105799T = CCUG 58046T).
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Affiliation(s)
- P. Anil Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India
| | - T. N. R. Srinivas
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India
| | - P. Manasa
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India
| | - S. Madhu
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India
| | - S. Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India
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24
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Srinivas TNR, Prasad S, Manasa P, Sailaja B, Begum Z, Shivaji S. Lacinutrix himadriensis sp. nov., a psychrophilic bacterium isolated from a marine sediment, and emended description of the genus Lacinutrix. Int J Syst Evol Microbiol 2012; 63:729-734. [PMID: 22561589 DOI: 10.1099/ijs.0.040907-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel gram-negative, rod-shaped, non-motile, psychrophilic bacterium, designated strain E4-9a(T), was isolated from a marine sediment sample collected at a depth of 276 m from Kongsfjorden, Svalbard, in the Arctic Ocean. The colony colour was golden yellow. Strain E4-9a(T) was positive for amylase activity at 5 °C. The predominant fatty acids were iso-C(15 : 1) G (21.8 %), anteiso-C(15 : 0) (19.1 %), anteiso-C(15 : 1) A (18.6 %), iso-C(15 : 0) (13.8 %) and iso-C(16 : 1) H (6.4 %). Strain E4-9a(T) contained MK-6 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids (AL1, AL4 and AL5), an unidentified phospholipid and four unidentified lipids (L1, L4 to L6). Based on 16S rRNA gene sequence similarity, it was ascertained that the closest related species to E4-9a(T) were Lacinutrix copepodicola, L. algicola and L. mariniflava, with sequence similarity to the respective type strains of 98.5, 96.5 and 95.8 %. Phylogenetic analysis showed that strain E4-9a(T) clustered with the type strain of L. copepodicola and with those of L. algicola and L. mariniflava at distances of 1.5 and 4.8 % (98.5 and 95.2 % similarity), respectively. However, DNA-DNA hybridization with L. copepodicola DJ3(T) showed 59 % relatedness with respect to strain E4-9a(T). The DNA G+C content of strain E4-9a(T) was 29 mol%. Based on the results of DNA-DNA hybridization and phenotypic data, it appears that strain E4-9a(T) represents a novel species of the genus Lacinutrix, for which the name Lacinutrix himadriensis sp. nov. is proposed. The type strain is E4-9a(T) ( = CIP 110310(T) = KCTC 23612(T)).
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Affiliation(s)
- T N R Srinivas
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500 007, India
| | - S Prasad
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500 007, India
| | - P Manasa
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500 007, India
| | - B Sailaja
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500 007, India
| | - Z Begum
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500 007, India
| | - S Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500 007, India
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25
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Misra RV, Ahmod NZ, Parker R, Fang M, Shah H, Gharbia S. Developing an integrated proteo-genomic approach for the characterisation of biomarkers for the identification of Bacillus anthracis. J Microbiol Methods 2011; 88:237-47. [PMID: 22178189 DOI: 10.1016/j.mimet.2011.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 02/02/2023]
Abstract
Bacillus anthracis is the causative agent of anthrax, an acute and often fatal disease in humans. Due to the high genomic relatedness within the Bacillus cereus group of species it is a challenge to identify B. anthracis consistently. Alternative strategies such as proteomics coupled with mass spectrometry (MS) provide a powerful approach for biomarker discovery. However, validating and evaluating these markers, particularly for genetically homogeneous species such as B. anthracis are challenging. The objective of this study is to develop a robust biomarker discovery and validation pipeline, using proteomic methodology combined with in silico and molecular approaches, to determine a biomarker list, using B. anthracis as a model. In this exploratory study we profiled the proteome of B. anthracis and genetically related species using GeLC-Liquid Chromatography MS/MS (GeLC-LC MS/MS), identifying peptides that could be used to detect B. anthracis. Peptides were filtered to remove low quality identifications. Using comparative bioinformatic approaches, matching and searching against genomic sequence data a shortlist of peptide biomarkers was determined and validated using DNA sequencing, against a panel of closely related strains, to determine marker specificity. Further validation was performed using MS quantitation methods to assess sensitivity and specificity. A biomarker discovery pipeline was successfully developed in this study, comprising four distinct stages: proteome profiling, comparative bioinformatic validation, DNA sequencing and MS validation. Using the pipeline, 5379 peptides specific for Bacillus species and 36 peptides specific for B. anthracis were identified and validated. The 36 peptides, representing 30 proteins were derived from over 15 different clusters of orthologous group categories, including proteins involved in transcription, energy production/conservation as well as multifunctional proteins. We demonstrated that the peptide biomarkers identified in this study could be detected in a complex background, in which 0.1 μg of protein extract from B. anthracis was spiked into 9.90 μg of B. cereus protein extracts. The integration of both stable non-redundant peptides with molecular methodology for marker discovery and validation, improves the robustness of identifying and characterising candidate biomarkers for the identification of bacteria such as B. anthracis.
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Affiliation(s)
- Raju V Misra
- Department for Bioanalysis and Horizon Technologies, Health Protection Agency, 61 Colindale Avenue, London NW95EQ, United Kingdom.
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26
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Hanajima D, Fukumoto Y, Yasuda T, Suzuki K, Maeda K, Morioka R. Bacterial community dynamics in aerated cow manure slurry at different aeration intensities. J Appl Microbiol 2011; 111:1416-25. [PMID: 21920002 DOI: 10.1111/j.1365-2672.2011.05151.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS This study aimed to characterize microbial community dynamics in aerated cow manure slurry at different aeration intensities. METHODS AND RESULTS Batch aerobic treatments were set up in 5-l jar fermentor, each containing 3 l of manure slurry; the slurries were subjected to low, medium and high (50, 150 and 250 ml min(-1), respectively) aeration for 9 days. Microbial community composition was determined using terminal restriction fragment length polymorphism and a clone library targeting 16S rRNA genes. High and medium aeration accelerated organic carbon degradation in parallel with the degree of aeration intensity; however, 90% of the initial total organic carbon was retained during low-aeration treatment. During the active stages of organic carbon decomposition, clones belonging to the class Bacilli accumulated. Moreover, Bacilli accumulation occurred earlier under high aeration than under medium aeration. CONCLUSIONS Organic matter degradation was mainly governed by a common microbial assemblage consisting of many lineages belonging to the class Bacilli. The timing of community development differed depending on aeration intensity. SIGNIFICANCE AND IMPACT OF THE STUDY This study reports on changes in several environmentally important parameters and the principal microbial assemblage during the pollution-reducing phase of cattle manure aeration treatment.
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Affiliation(s)
- D Hanajima
- Waste Recycling Research Team, National Agricultural Research Center for Hokkaido Region, Sapporo, Hokkaido, Japan.
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Comparison of bacterial diversity in proglacial soil from Kafni Glacier, Himalayan Mountain ranges, India, with the bacterial diversity of other glaciers in the world. Extremophiles 2011; 15:673-90. [PMID: 21918795 DOI: 10.1007/s00792-011-0398-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
Abstract
Two 16S rRNA gene clone libraries (KF and KS) were constructed using two soil samples (K7s and K8s) collected near Kafni Glacier, Himalayas. The two libraries yielded a total of 648 clones. Phyla Actinobacteria, Bacteroidetes, Chloroflexi Firmicutes, Proteobacteria, Spirochaetae, Tenericutes and Verrucomicrobia were common to the two libraries. Phyla Acidobacteria, Chlamydiae and Nitrospirae were present only in KF library, whereas Lentisphaerae and TM7 were detected only in KS. In the two libraries, clones belonging to phyla Bacteroidetes and Proteobacteria were the most predominant. Principal component analysis (PCA) revealed that KF and KS were different and arsenic content influenced the differences in the percentage of OTUs. PCA indicated that high water content in the K8s sample results in high total bacterial count. PCA also indicated that bacterial diversity of KF and KS was similar to soils from the Pindari Glacier, Himalayas; Samoylov Island, Siberia; Schrimacher Oasis, Antarctica and Siberian tundra. The eleven bacterial strains isolated from the above two soil samples were phylogenetically related to six different genera. All the isolates were psychro-, halo- and alkalitolerant. Amylase, lipase and urease activities were detected in the majority of the strains. Long chain, saturated, unsaturated and branched fatty acids were predominant in the psychrotolerant bacteria.
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Bacterial diversity of soil in the vicinity of Pindari glacier, Himalayan mountain ranges, India, using culturable bacteria and soil 16S rRNA gene clones. Extremophiles 2011; 15:1-22. [PMID: 21061031 DOI: 10.1007/s00792-010-0333-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 10/22/2010] [Indexed: 10/18/2022]
Abstract
Three 16S rRNA gene clone libraries (P1L, P4L and P8L) were constructed using three soil samples (P1S, P4S and P8S) collected near Pindari glacier, Himalayas. The three libraries yielded a total of 703 clones. Actinobacteria, Firmicutes and Proteobacteria were common to the three libraries. In addition to the above P1L and P8L shared the phyla Acidobacteria, Bacteroidetes, Gemmatimonadetes and Planctomycetes. Phyla Chlamydiae, Chlorobi, Chloroflexi, Dictyoglomi, Fibrobacteres, Nitrospirae, Verrucomicrobia, candidate division SPAM and candidate TM7s TM7a phylum were present only in P1L. Rarefaction analysis indicated that the bacterial diversity in P4S and P8S soil samples was representative of the sample. Principal component analysis (PCA) revealed that P1S and P8S were different from P4S soil sample. PCA also indicated that arsenic content, pH, Cr and altitude influence the observed differences in the percentage of specific OTUs in the three 16S rRNA gene clone libraries. The observed bacterial diversity was similar to that observed for other Himalayan and non-polar cold habitats. A total of 40 strains of bacteria were isolated from the above three soil samples and based on the morphology 20 bacterial strains were selected for further characterization. The 20 bacteria belonged to 12 different genera. All the isolates were psychro-, halo- and alkalitolerant. Amylase and urease activities were detected in majority of the strains but lipase and protease activities were not detected. Long chain, saturated, unsaturated and branched fatty acids were predominant in the psychrotolerant bacteria.
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Bacillus beringensis sp. nov., a psychrotolerant bacterium isolated from the Bering Sea. Antonie van Leeuwenhoek 2010; 99:551-7. [PMID: 20963491 DOI: 10.1007/s10482-010-9523-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 10/05/2010] [Indexed: 10/18/2022]
Abstract
Psychrotolerant Bacillus-like strains BR035(T) and BR011 were isolated from seawater of the Bering Sea and were characterized by means of a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that these strains were related to the members of the genus Bacillus and had the highest 16S rRNA gene sequence similarity with Bacillus korlensis ZLC-26(T). DNA-DNA hybridization experiments confirmed that strains BR035(T) and BR011 belonged to the same species and were distinct from their closest relatives. The cells were Gram-positive, rods, motile, spore-forming and psychrotolerant. The temperature range for growth was 4-42°C. The main respiratory quinone was MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown aminolipid and two unknown phospholipids. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C14:0 and C16:1ω7c alcohol. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The genomic DNA G + C content was 37.6-37.8 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, a novel species Bacillus beringensis is proposed and the type strain is BR035(T) (=CGMCC 1.9126(T)=DSM 22571(T)).
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Demergasso C, Dorador C, Meneses D, Blamey J, Cabrol N, Escudero L, Chong G. Prokaryotic diversity pattern in high-altitude ecosystems of the Chilean Altiplano. ACTA ACUST UNITED AC 2010. [DOI: 10.1029/2008jg000836] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cecilia Demergasso
- Centro de Biotecnología; Universidad Católica del Norte; Antofagasta Chile
- Centro de Investigación Científica y Tecnológica para la Minería; Antofagasta Chile
| | - Cristina Dorador
- Centro de Biotecnología; Universidad Católica del Norte; Antofagasta Chile
| | - Daniela Meneses
- Centro de Biotecnología; Universidad Católica del Norte; Antofagasta Chile
| | | | - Nathalie Cabrol
- Space Science Division; NASA Ames Research Center; Moffett Field California USA
- SETI Carl Sagan Center; Mountain View California USA
| | - Lorena Escudero
- Centro de Biotecnología; Universidad Católica del Norte; Antofagasta Chile
- Centro de Investigación Científica y Tecnológica para la Minería; Antofagasta Chile
| | - Guillermo Chong
- Centro de Investigación Científica y Tecnológica para la Minería; Antofagasta Chile
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Pradhan S, Srinivas TNR, Pindi PK, Kishore KH, Begum Z, Singh PK, Singh AK, Pratibha MS, Yasala AK, Reddy GSN, Shivaji S. Bacterial biodiversity from Roopkund Glacier, Himalayan mountain ranges, India. Extremophiles 2010; 14:377-95. [PMID: 20505964 DOI: 10.1007/s00792-010-0318-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
Abstract
The bacterial diversity of two soil samples collected from the periphery of the Roopkund glacial lake and one soil sample from the surface of the Roopkund Glacier in the Himalayan ranges was determined by constructing three 16S rRNA gene clone libraries. The three clone libraries yielded a total of 798 clones belonging to 25 classes. Actinobacteria was the most predominant class (>10% of the clones) in the three libraries. In the library from the glacial soil, class Betaproteobacteria (24.2%) was the most predominant. The rarefaction analysis indicated coverage of 43.4 and 41.2% in the samples collected from the periphery of the lake thus indicating a limited bacterial diversity covered; at the same time, the coverage of 98.4% in the glacier sample indicated most of the diversity was covered. Further, the bacterial diversity in the Roopkund glacier soil was low, but was comparable with the bacterial diversity of a few other glaciers. The results of principal component analysis based on the 16S rRNA gene clone library data, percentages of OTUs and biogeochemical data revealed that the lake soil samples were different from the glacier soil sample and the biogeochemical properties affected the diversity of microbial communities in the soil samples.
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Affiliation(s)
- Suman Pradhan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
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Reddy GSN, Pradhan S, Manorama R, Shivaji S. Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil. Int J Syst Evol Microbiol 2010; 60:866-870. [DOI: 10.1099/ijs.0.011775-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain RuGl7T was isolated from a soil sample collected at the periphery of the glacial Lake Roopkund in the Himalayan mountain range, India. Cells of RuGl7T were Gram-positive, aerobic, rod-shaped, motile and grew optimally between 15 and 18 °C. Cells of RuGl7T contained 2,4-diaminobutyric acid in the cell-wall peptidoglycan and the major menaquinones were MK-10, MK-11 and MK-12. The polar lipids present were diphosphatidylglycerol and phosphatidylglycerol and an unknown lipid and the major fatty acid was anteiso-C15 : 0. Based on the above characteristics, strain RuGl7T was assigned to the genus Cryobacterium. Strain RuGl7T shared a 16S rRNA gene sequence similarity of 97.0 and 99.0 % with Cryobacterium psychrotolerans JCM 13925T and Cryobacterium psychrophilum JCM 1463T, respectively. However, DNA–DNA relatedness values between strain RuGl7T and C. psychrotolerans and C. psychrophilum were 28 and 23 %, respectively. Furthermore, strain RuGl7T exhibited several phenotypic and genotypic differences when compared with C. psychrotolerans, C. psychrophilum and Cryobacterium mesophilum. Based on these differentiating characteristics, strain RuGl7T was identified as a novel species of the genus Cryobacterium for which the name Cryobacterium roopkundense sp. nov. is proposed. The type strain is RuGl7T (=DSM 21065T=JCM 15131T).
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Affiliation(s)
- G. S. N. Reddy
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Suman Pradhan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Ruth Manorama
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - S. Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
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