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Kennedy SJ, Atkinson CGF, Tubbs TJ, Baker BJ, Shaw LN. Culture-dependent identification of rare marine sediment bacteria from the Gulf of Mexico and Antarctica. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598530. [PMID: 38915660 PMCID: PMC11195218 DOI: 10.1101/2024.06.11.598530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Laboratory-viable cultivars of previously uncultured bacteria further taxonomic understanding. Despite many years of modern microbiological investigations, the vast majority of bacterial taxonomy remains uncharacterized. While many attempts have been made to decrease this knowledge gap, culture-based approaches parse away at the unknown and are critical for improvement of both culturing techniques and computational prediction efficacy. To this end of providing culture-based approaches, we present a multi-faceted approach to recovering marine environmental bacteria. We employ combinations of nutritional availability, inoculation techniques, and incubation parameters in our recovery of marine sediment-associated bacteria from the Gulf of Mexico and Antarctica. The recovered biodiversity spans several taxa, with 16S-ITS-23S rRNA gene-based identification of multiple isolates belonging to rarer genera increasingly undergoing phylogenetic rearrangements. Our modifications to traditional culturing techniques have not only recovered rarer taxa, but also resulted in the recovery of biotechnologically promising bacteria. Together, we propose our stepwise combinations of recovery parameters as a viable approach to decreasing the bacterial knowledge gap.
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Affiliation(s)
- Sarah J. Kennedy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, ISA2015, Tampa, Florida 33620, United States
| | - Celine Grace F. Atkinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, ISA2015, Tampa, Florida 33620, United States
| | - Tristan J. Tubbs
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, ISA2015, Tampa, Florida 33620, United States
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620, United States
| | - Bill J. Baker
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620, United States
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, ISA2015, Tampa, Florida 33620, United States
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2
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Narsing Rao MP, Banerjee A, Liu GH, Thamchaipenet A. Genome-based reclassification of Bacillus acidicola, Bacillus pervagus and the genera Heyndrickxia, Margalitia and Weizmannia. Int J Syst Evol Microbiol 2023; 73. [PMID: 37462355 DOI: 10.1099/ijsem.0.005961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
In the present study, the taxonomic positions of Bacillus acidicola, Bacillus pervagus and members of the genera Heyndrickxia, Margalitia and Weizmannia were evaluated. The 16S rRNA gene sequence similarity between Bacillus acidicola DSM 14745T, Bacillus pervagus DSM 23947T and members of the genera Heyndrickxia and Margalitia were above the cut-off level (>95 %) for genus delineation. Amino acid identity (AAI) values and the results of phylogenomic analysis suggested that B. acidicola and the members of the genera Heyndrickxia, Margalitia and Weizmannia belong to the same genus. Furthermore, the AAI and phylogenomic results also differentiate B. pervagus from B. acidicola and the members of the genera Heyndrickxia, Margalitia and Weizmannia. Based on the results, we propose to transfer Bacillus acidicola, Margalitia and Weizmannia to the genus Heyndrickxia. We also propose the reclassification of B. pervagus into a new genus Oikeobacillus gen. nov., with the type species Oikeobacillus pervagus comb. nov.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Aparna Banerjee
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca 3460000, Chile
| | - Guo-Hong Liu
- Agricultural Bio‑ Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, Fujian, PR China
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University, Bangkok 10900, Thailand
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Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753-5798. [PMID: 33112222 DOI: 10.1099/ijsem.0.004475] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.
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Key Words
- classification of Bacillus species
- conserved signature indels
- emendation of genus Bacillus
- genus Bacillus and the family Bacillaceae
- novel Bacillaceae genera Alteribacter, Ectobacillus, Evansella, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Niallia, Priestia, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sutcliffiella and Weizmannia
- phylogenomic and comparative genomic analyses
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
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Wang Y, Gong J, Li J, Xin Y, Hao Z, Chen C, Li H, Wang B, Ding M, Li W, Zhang Z, Xu P, Xu T, Ding GC, Li J. Insights into bacterial diversity in compost: Core microbiome and prevalence of potential pathogenic bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137304. [PMID: 32087588 DOI: 10.1016/j.scitotenv.2020.137304] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Fertilizer-replacement programs by the ministry of agriculture and rural affairs are extraordinary actions for environment protection and sustainable agriculture in China. A national-level survey was performed to acquire consensuses of bio-physiochemical properties for composts. A total of 116 compost samples collected from 16 provinces in China were analyzed by high throughput sequencing of bacterial 16S rRNA gene amplicons. The germination index and bacterial alpha-diversity were lower in composts from poultry manure than others. This large-scale survey revealed that bacterial communities were distinct among different composts and slightly explained by pH, moisture and total nitrogen, but not by raw material or composting process. Nevertheless, 26 OTUs affiliated with Firmicutes (Cerasibacillus, Atopostipes and Bacillus) and Actinobacteria (Thermobifida, Actinomadura and Nocardiopsis) were present in most (>90%) composts and majority of these bacterial species were possibly associated with the biodegradation of organic materials. Surprisingly, 629 potential human or animal bacterial pathogens accounting an average of 1.21% of total 16S rRNA gene were detected and these bacteria were mainly affiliated with Helicobacter, Staphylococcus, Acinotobacter, Streptococcus, Mycobacterium and Enterococcus. In summary, this study provides baseline data for the diversity and abundance of core microbiome and potential pathogens in composts.
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Affiliation(s)
- Yue Wang
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Jingyang Gong
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Jiaxin Li
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Yuanyuan Xin
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Ziyi Hao
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Chen Chen
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Huixiu Li
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Bo Wang
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Min Ding
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Wanwan Li
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Zeyu Zhang
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Pengxiang Xu
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Ting Xu
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University and Suzhou ViHong Biotechnology, Wuzhong District, 215128, Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University and Suzhou ViHong Biotechnology, Wuzhong District, 215128, Jiangsu Province, China.
| | - Ji Li
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University and Suzhou ViHong Biotechnology, Wuzhong District, 215128, Jiangsu Province, China.
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5
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Ding GC, Bai M, Han H, Li H, Ding X, Yang H, Xu T, Li J. Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming. FEMS Microbiol Ecol 2020; 95:5423879. [PMID: 30927421 DOI: 10.1093/femsec/fiz042] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/29/2019] [Indexed: 11/14/2022] Open
Abstract
Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.
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Affiliation(s)
- Guo-Chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
| | - Mohan Bai
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Hui Han
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Huixiu Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Xiaoyan Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Hefa Yang
- Quzhou Experimental Station of China Agricultural University, 057250, Quzhou County, Hebei Province, China
| | - Ting Xu
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
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6
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Kang H, Kang J, Cha I, Kim H, Joung Y, Jang TY, Joh K. Bacillus salinus sp. nov., isolated from commercial solar salt. Int J Syst Evol Microbiol 2020; 70:2696-2702. [PMID: 32213250 DOI: 10.1099/ijsem.0.004096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-stain-positive, strictly aerobic, motile, spore-forming, rod-shaped, moderately halotolerant bacteria, designated as HMF5848T and HME7618, were isolated from salt/brine and subjected to a polyphasic taxonomic investigation. Growth of both yellow-coloured strains occurred in the presence of 1-9 % NaCl (w/v; optimum, 2-3 %), at 15-45 °C (optimum, 37 °C) and pH 6-9 (optimum, pH 7). The major fatty acids were iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The cell-wall peptidoglycan was meso-diaminopimelic acid. The only respiratory quinone was menaquinone-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, four unidentified glycolipids, three unidentified phospholipids and two unidentified polar lipids. DNA G+C content was 37.4 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strains HMF5848T and HME7618 clustered with Bacillus luteolus YIM 93174T. Strains HMF5848T showed the highest 16S rRNA gene sequence similarities to Bacillus humi LMG 22167T (96.1 %), Bacillus isabeliae CVS-8T (96.0 %) and Bacillus luteolus YIM 93174T (96.0 %). The values of in silico DNA-DNA hybridization and average nucleotide identity between strains HMF5848T and B. humi DSM 16318T were 25.8 and 69.7 %, respectively. On the basis of phylogenetic, physiological and chemotaxonomic properties, strain HMF5848T represents a novel species, Bacillus salinus sp. nov. The type strain is HMF5848T (=KCTC 43010T=CECT 9695T).
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Affiliation(s)
- Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Jinkyeong Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Inseong Cha
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Yochan Joung
- Department of Life Science, College of Natural Science, Kyonggi University, Gyeonggi 16227, Republic of Korea
| | - Tae Yong Jang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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7
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Son JS, Hwang YJ, Lee SY, Ghim SY. Bacillus salidurans sp. nov., isolated from salt-accumulated pepper rhizospheric soil. Int J Syst Evol Microbiol 2019; 69:116-122. [DOI: 10.1099/ijsem.0.003110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jin-Soo Son
- 1School of Life Sciences, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
- 2School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| | - Ye-Ji Hwang
- 1School of Life Sciences, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| | - Soo-Yeong Lee
- 1School of Life Sciences, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
- 2School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| | - Sa-Youl Ghim
- 2School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
- 1School of Life Sciences, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
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8
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Bacillus spongiae sp. nov., isolated from sponge of Jeju Island. J Microbiol 2018; 56:217-222. [PMID: 29492866 DOI: 10.1007/s12275-018-7511-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/17/2018] [Accepted: 01/17/2018] [Indexed: 10/17/2022]
Abstract
A Gram-reaction-positive, strictly aerobic, motile, endospore- forming, and rod-shaped bacterial strain designated 135PIL107-10T was isolated from a sponge on Jeju Island, and its taxonomic position was investigated using a polyphasic approach. Strain 135PIL107-10T grew at 20-37°C (optimum temperature, 25°C) and pH 6.0-10.0 (optimum pH, 6.0) on marine and R2A agars. Based on 16S rRNA gene phylogeny analysis, the novel strain formed a new branch within the genus Bacillus of the family Bacillaceae, and formed clusters with Bacillus thaohiensis NHI-38T (96.8%), Bacillus fengqiuensis NPK15T (96.7%), and Bacillus songklensis CAU 1033T (96.7%). Lower sequence similarities (97.0%) were found with the type strains of all other recognized members of the genus Bacillus (95.6-96.8% similarity). The G + C content of the genomic DNA was 43.6 mol%. The predominant respiratory quinone was menaquinone-7 and the major fatty acids were iso-C15:0 and iso-C17:1ω10c. The overall polar lipid patterns were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The isolate therefore represents a novel species, for which the name Bacillus spongiae sp. nov. is proposed, with the type strain 135PIL107-10T (= KACC 19275T = LMG 30080T).
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Wang YQ, Liu XM, Tang J, Yang GQ, Yu Z. Salibacterium lacus sp. nov., a halophilic, non-spore-forming bacterium isolated from sediment of a saline lake. Int J Syst Evol Microbiol 2018; 68:113-117. [DOI: 10.1099/ijsem.0.002467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yue-qiang Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou 510650, PR China
| | - Xiao-ming Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou 510650, PR China
| | - Jia Tang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou 510650, PR China
| | - Gui-qin Yang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou 510650, PR China
| | - Zhen Yu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou 510650, PR China
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10
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Li J, Liu J, Shen Y, Ni J. Swionibacillus sediminis gen. nov., sp. nov., a member of the family Bacillaceae isolated from ocean sediment. Int J Syst Evol Microbiol 2017; 67:3440-3445. [DOI: 10.1099/ijsem.0.002133] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jingjing Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Junfeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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11
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Zhao B, Lu W, Zhang S, Liu K, Yan Y, Li J. Reclassification of Bacillus saliphilus as Alkalicoccus saliphilus gen. nov., comb. nov., and description of Alkalicoccus halolimnae sp. nov., a moderately halophilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2017; 67:1557-1563. [DOI: 10.1099/ijsem.0.001759] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Baisuo Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
- Graduate School, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Weidong Lu
- School of Life Sciences, Qingdao Agricultural University, 266109 Qingdao, PR China
| | - Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Kang Liu
- Graduate School, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
- School of Life Sciences, Qingdao Agricultural University, 266109 Qingdao, PR China
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
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12
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Zhang S, Li Z, Yan Y, Zhang C, Li J, Zhao B. Bacillus urumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:2305-2312. [DOI: 10.1099/ijsem.0.001028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaojun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanlun Zhang
- The School of Ocean and Earth Sciences, Tongji University, Shanghai 200092, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Zhou YX, Liu GH, Liu B, Chen GJ, Du ZJ. Bacillus mesophilus sp. nov., an alginate-degrading bacterium isolated from a soil sample collected from an abandoned marine solar saltern. Antonie van Leeuwenhoek 2016; 109:937-43. [PMID: 27084709 DOI: 10.1007/s10482-016-0692-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/28/2016] [Indexed: 11/28/2022]
Abstract
A novel Gram-stain positive, endospore-forming bacterium, designated SA4(T), was isolated from a soil sample collected from an abandoned marine solar saltern at Wendeng, Shandong Province, PR China. Cells were observed to be rod shaped, alginase positive, catalase positive and motile. The strain was found to grow at temperatures ranging from 15 to 40 °C (optimum 35 °C), and pH 5.0-11.0 (optimum pH 8.0) with 0-7.0 % (w/v) NaCl concentration (optimum NaCl 3.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SA4(T) belongs to the genus Bacillus and exhibits 16S rRNA gene sequence similarities of 96.6, 96.5, 96.3 and 96.2 % with Bacillus horikoshii DSM 8719(T), Bacillus acidicola 105-2(T), Bacillus shackletonii LMG 18435(T) and Bacillus pocheonensis Gsoil 420(T), respectively. The menaquinone was identified as MK-7 and the major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids detected were anteiso-C15:0 (22.3 %), iso-C15:0 (22.6 %), iso-C16:0 (14.8 %) and iso-C14:0 (14.7 %). The DNA G+C content was determined to be 42.4 mol %. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate SA4(T) represents a novel species within the genus Bacillus, for which the name Bacillus mesophius sp. nov. is proposed. The type strain is SA4(T) (=DSM 101000(T)=CCTCC AB 2015209(T)).
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Affiliation(s)
- Yan-Xia Zhou
- College of Marine Science, Shandong University at Weihai, Weihai, 264209, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, People's Republic of China
| | - Bo Liu
- Agricultural Bio-Resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, People's Republic of China.
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai, 264209, People's Republic of China
| | - Zong-Jun Du
- College of Marine Science, Shandong University at Weihai, Weihai, 264209, People's Republic of China.
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Bacillus nitroreducens sp. nov., a humus-reducing bacterium isolated from a compost. Arch Microbiol 2016; 198:347-52. [DOI: 10.1007/s00203-016-1193-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/28/2015] [Accepted: 01/14/2016] [Indexed: 10/22/2022]
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Wei X, Xin D, Xin Y, Zhang H, Wang T, Zhang J. Bacillus depressus sp. nov., isolated from soil of a sunflower field. Antonie van Leeuwenhoek 2015; 109:13-20. [DOI: 10.1007/s10482-015-0605-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/05/2015] [Indexed: 11/29/2022]
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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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Abstract
Two bacterial strains (JC247T and JC248) were isolated from soil samples collected from Rann of Kutch, Gujarat, India. Colonies of both strains were creamy white. Cells were Gram-stain-positive, rods-to-curved rods (crescent-shaped), and produced centrally located oval-shaped endospores. Major (>5 %) fatty acids of both strains were iso-C16
:
0, iso-C14
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0, iso-C15
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0, C16
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1ω11c and C16
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0, with minor ( < 5 but >1 %) amounts of anteiso-C15
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0, anteiso-C17
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0, iso-C16
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1 H, iso-C17
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0, iso-C18
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0, C14
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0, C17
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0, C18
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0, C18
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1ω9c, iso-C17
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1ω10c and anteiso-C17
:
0B/isoI. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell-wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. The genomic DNA G+C content of strains JC247T and JC248 was 48.2 and 48.1 mol%, respectively. Both strains were closely related with mean DNA–DNA hybridization >90 %. 16S rRNA gene sequence analysis of both strains indicated that they are members of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a 16S rRNA gene sequence similarity of 96.93 % with Bacillus firmus NCIMB 9366T and < 96.92 % with other members of the genus Bacillus. Sequence similarity between strain JC247T and JC248 was 100 %. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strains JC247T and JC248 as representatives of a novel species of the genus Bacillus, for which the name Bacillus
crescens sp. nov. is proposed. The type strain is JC247T ( = KCTC 33627T = LMG 28608T).
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Chen JH, Tian XR, Ruan Y, Yang LL, He ZQ, Tang SK, Li WJ, Shi H, Chen YG. Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis). Int J Syst Evol Microbiol 2015; 65:1561-1566. [PMID: 25713049 DOI: 10.1099/ijs.0.000139] [Citation(s) in RCA: 17] [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-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118(T), was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118(T) was able to grow with 0-13% (w/v) NaCl (optimum 2-5%), at pH 5.5-10.0 (optimum pH 7.5) and at 5-50 °C (optimum 30-35 °C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 100118(T) belonged to the genus Bacillus , and was most closely related to Bacillus litoralis SW-211(T) (98.9% 16S rRNA gene sequence similarity), Bacillus halosaccharovorans E33(T) (98.3%), Bacillus niabensis 4T19(T) (97.8%) and Bacillus herbersteinensis D-1,5a(T) (97.1%). The combination of results from the phylogenetic analysis, DNA-DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118(T) represents a novel species of the genus Bacillus , for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118(T) ( = CTCC AB 2010452(T) =DSM 24486(T) =JCM 17523(T)).
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Affiliation(s)
- Jin-Hua Chen
- College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, PR China.,Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural University, 410128 Changsha, PR China
| | - Xiang-Rong Tian
- College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, PR China
| | - Ying Ruan
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural University, 410128 Changsha, PR China
| | - Ling-Ling Yang
- The Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, 650091 Kunming, PR China
| | - Ze-Qiang He
- College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, PR China
| | - Shu-Kun Tang
- The Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, 650091 Kunming, PR China
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, 650091 Kunming, PR China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Yi-Guang Chen
- College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, PR China
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Subhash Y, Sasikala C, Ramana CV. Bacillus luteus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:1580-1586. [PMID: 24478212 DOI: 10.1099/ijs.0.053504-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5%) were anteiso-C15:0, iso-C16:0, iso-C15:0, anteiso-C17:0, iso-C14:0 and C16:0 with minor (<5 but >1%) amounts of iso-C17:0, anteiso-C17:0 B/iso-C17:0 I and C16:1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were L-alanine, D-alanine, D-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA-DNA hybridization>90%). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a sequence similarity of 97.6% with Bacillus saliphilus 6AGT and <96.8% with other members of the genus Bacillus. Sequence similarity between strain JC167T and 168 was 100%. Strain JC167T showed 25.8±1% reassociation (based on DNA-DNA hybridization) with B. saliphilus DSM 15402T (=6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus, for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T (=KCTC 33100T=LMG 27257T).
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Affiliation(s)
- Y Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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