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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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Colautti A, Comi G, Peterlunger E, Iacumin L. Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans? Microbiol Spectr 2023; 11:e0068623. [PMID: 37975675 PMCID: PMC10714998 DOI: 10.1128/spectrum.00686-23] [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] [Received: 02/14/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Since 1988, through the United States government's founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific advancement. The universality and total freedom of use if on the one hand allow the use of this database on a global level by all researchers for their valuable work, on the other hand, it has the disadvantage of making it difficult to check the correctness of all the materials present. It is, therefore, of fundamental importance for the correctness and ethics of research to improve the databases at our disposal, identifying and amending the critical issues. This work aims to provide the scientific community with a new sequence for the type strain Paenisporosarcina quisquiliarum SK 55 and broaden the knowledge of the Psychrobacillus psychrodurans species, in particular, considering the ancient strain Aquil_B6 found in an ancient Roman amphora.
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Affiliation(s)
- Andrea Colautti
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Giuseppe Comi
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Enrico Peterlunger
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Lucilla Iacumin
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
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da Silva MBF, da Mota FF, Cypriano J, Abreu F, Seldin L. Psychrobacillus antarcticus sp. nov., a psychrotolerant bioemulsifier producer isolated from King George Island, Antarctica. Int J Syst Evol Microbiol 2023; 73. [PMID: 38009904 DOI: 10.1099/ijsem.0.006181] [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: 11/29/2023] Open
Abstract
A Gram-stain-positive rod, psychrotolerant, aerobic and bioemulsifier-producing strain, denoted as Val9T, was isolated from soil sampled at Vale Ulman, King George Island, Antarctica. The strain grew at up to 30 °C (optimum, 15 °C), at pH 6-9 (optimum, pH 8) and with up to 5 % w/v NaCl (optimum, 3 %). The strain was motile and positive for catalase, oxidase and H2S. It did not hydrolyse starch, casein or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Val9T belonged to the genus Psychrobacillus and was closely related to Psychrobacillus psychrotolerans DSM 11706T (99.9 % similarity), Psychrobacillus psychrodurans DSM 11713T (99.8 %) and Psychrobacillus glaciei PB01T (99.2 %). Digital DNA-DNA hybridization and average nucleotide identity values were lower than 37.3 and 85.5 %, respectively, with the closest phylogenetic neighbours. The DNA G+C content of strain Val9T calculated from the complete genome sequence was 36.6 mol%. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 1ω11c. Menaquinone-8 was the major respiratory quinone. The peptidoglycan type was A4β l-Orn-d-glu. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids. Based on 16S rRNA phylogenetic and multilocus sequence analyses (recA, rpoB and gyrB), as well as phylogenomic, chemotaxonomic and phenotypic tests, we demonstrate that strain Val9T represents a novel species of the genus Psychrobacillus, for which the name Psychrobacillus antarcticus sp. nov. is proposed. The type strain is Val9T (=DSM 115096T=CCGB 1952T=NRRL B-65674T).
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Affiliation(s)
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Huang Y, Cai H, Qin S, Yang L, Zhou Y, Wu J, Chen X, Jiang M, Jiang Y, Ihsan YN. Bacillus pinisoli sp. nov., Isolated from Soil of a Decayed Pine Tree. Curr Microbiol 2022; 80:55. [PMID: 36585981 DOI: 10.1007/s00284-022-03130-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/24/2022] [Indexed: 01/01/2023]
Abstract
A Gram-stain-positive, rod-shaped, facultatively anaerobic, motile and spore-forming bacterium with multiple flagella designated GXH0341T was isolated from the soil associated with decayed pine tree samples collected from Weizhou Island, Beihai, Guangxi, China. Growth occurred at 4-37 °C (optimum 30 °C), at pH 5.0-11.0 (optimum 8.0) and in the presence of 0-7% (w/v) NaCl (optimum 2%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GXH0341T was most closely related to Bacillus mesophilus DSM 101000 T (98.9%), followed by Bacillus salitolerans KC1T (96.95%) and Margalitia shackletonii DSM 18435 T (96.67%). Phylogenetic analysis revealed that strain GXH0341T represented a separate lineage within the genus Bacillus. Peroxidase is positive. The predominant quinone was MK-7 and the cell-wall diagnostic diamino acid was meso-diaminopimelic acid. The predominant polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and two unidentified phospholipids. The major fatty acids are iso-C14:0, iso-C15:0, anteiso-C15:0 and iso-C16:0. The genome of GXH0341T comprises the biosynthetic gene cluster for T3PKS, terpene, lassopeptide and RRE-containing element as secondary metabolites. The average nucleotide identity values and the digital DNA-DNA hybridization values between GXH0341T and B. mesophilus DSM 101000 T were 78.22% and 21.00%, respectively, which were in the range of the recommended level for interspecies identity. The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated strain GXH0341T represents a novel species of the genus Bacillus, for which the name Bacillus pinisoli sp. nov. is proposed. The type strain is GXH0341T (= MCCC 1K07157T = JCM 35212 T).
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Affiliation(s)
- Ying Huang
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Hanqin Cai
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Siqi Qin
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Lifang Yang
- School of Chemistry and Chemical Engineering, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Yan Zhou
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Jiafa Wu
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Xuemei Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Mingguo Jiang
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China.
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Yudi N Ihsan
- Department of Marine Science, Universitas Padjadjaran, Jatinangor, 45363, Bandung, Indonesia
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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:microorganisms10122355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
| | - Mohammad J. Taherzadeh
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
- Correspondence:
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Genomic analyses of a novel bioemulsifier-producing Psychrobacillus strain isolated from soil of King George Island, Antarctica. Polar Biol 2022. [DOI: 10.1007/s00300-022-03028-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zeng T, Li X, Guan H, Yang W, Liu W, Liu J, Du Z, Li X, Xiao Q, Wang X, Zhang X, Huang L, Xiang Q, Peng Q, Yan Y. Dynamic microbial diversity and fermentation quality of the mixed silage of corn and soybean grown in strip intercropping system. BIORESOURCE TECHNOLOGY 2020; 313:123655. [PMID: 32559709 DOI: 10.1016/j.biortech.2020.123655] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
This study assessed the fermentation quality and microbial community of corn (Zea mays L.) and soybean (Glycine max Merr.) (CS) mixed silage in strip intercropping system. CS mixed silage increased lactic acid content and decreased ammonia-N content compared to 100% soybean (S) silage, while it decreased ammonia-N content compared to 100% corn (C) silage. The largest number of epiphytic lactic acid bacteria was detected in CS fresh materials. During ensiling, Weissella and Lactobacillus dominated silage, the relative abundance of Lactobacillus in mixed silage was higher than that in S silage with the same S variety. After aerobic exposure (AE), synergistic effect existed in low relative abundance bacteria correlating with ammonia-N content and pH at ensiling 60 days and AE 7 days. In conclusion, CS mixed silage modified microbial community and improved fermentation quality.
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Affiliation(s)
- Tairu Zeng
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu 610000, China
| | - Xiaoling Li
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu 610000, China
| | - Hao Guan
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu 610000, China
| | - Wenyu Yang
- College of Agronmy, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Weiguo Liu
- College of Agronmy, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Jiang Liu
- College of Agronmy, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Zhaochang Du
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu 610000, China
| | - Xiaomei Li
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu 610000, China; College of Grassland Science and Technology China Agricultural University, Peking 100000, China
| | - Qiyin Xiao
- Institute of Agricultural Science, Garze Prefecture, Kangding 626000, China
| | - Xiaochun Wang
- College of Agronmy, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Xinquan Zhang
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu 610000, China
| | - Linkai Huang
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu 610000, China
| | - Quanju Xiang
- College of Resource, Sichuan Agricultural University, Chengdu 610000, China
| | - Quanhui Peng
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanhong Yan
- Animal Science and Technology College, Sichuan Agricultural University, Chengdu 610000, China.
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Schröer L, De Kock T, Cnudde V, Boon N. Differential colonization of microbial communities inhabiting Lede stone in the urban and rural environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139339. [PMID: 32446079 DOI: 10.1016/j.scitotenv.2020.139339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Air pollution is one of the main actors of stone deterioration. It influences not only the material itself but also prokaryotes colonizing rocks. Prokaryotes can affect rock substrates and biological colonization will most likely become relatively more important during the course of the 21st century. Therefore, it is necessary to understand the effects of air pollution on biological colonization and on the impact of this colonization on rock weathering. For this reason, we studied the prokaryotic community of Lede stone from two deteriorated monuments in Belgium: one in the urban and one in the rural environment. This research conducts 16S rRNA gene Next Generation Sequencing combined with an isolation campaign. It revealed diverse and complex prokaryotic communities with more specialized bacteria present in the urban environment, while archaea were barely detected. Some genera could cause biodeterioration but the isolates did not produce a significant amount of acid. Soluble salts analysis revealed an important effect of salts on the prokaryotic community. Colour measurements at least indicate that a main effect of prokaryotes might be on the aesthetics: In the countryside prokaryotic communities seemed to discolour Lede stone, while pollution most likely blackened building stones in the urban environment.
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Affiliation(s)
- Laurenz Schröer
- PProGRess, Department of Geology, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium; Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Tim De Kock
- PProGRess, Department of Geology, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium; Antwerp Cultural Heritage Sciences (ARCHES), University of Antwerp, Mutsaardstraat 31, 2000 Antwerp, Belgium.
| | - Veerle Cnudde
- PProGRess, Department of Geology, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium; Environmental Hydrogeology, Department of Earth Sciences, Utrecht University, Princetonlaan 8a, 3584 Utrecht, the Netherlands.
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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Choi JY, Kim SC, Lee PC. Comparative Genome Analysis of Psychrobacillus Strain PB01, Isolated from an Iceberg. J Microbiol Biotechnol 2020; 30:237-243. [PMID: 31838800 PMCID: PMC9728334 DOI: 10.4014/jmb.1909.09008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel psychrotolerant Psychrobacillus strain PB01, isolated from an Antarctic iceberg, was comparatively analyzed with five related strains. The complete genome of strain PB01 consists of a single circular chromosome (4.3 Mb) and a plasmid (19 Kb). As potential low-temperature adaptation strategies, strain PB01 has four genes encoding cold-shock proteins, two genes encoding DEAD-box RNA helicases, and eight genes encoding transporters for glycine betaine, which can serve as a cryoprotectant, on the genome. The pan-genome structure of the six Psychrobacillus strains suggests that strain PB01 might have evolved to adapt to extreme environments by changing its genome content to gain higher capacity for DNA repair, translation, and membrane transport. Notably, strain PB01 possesses a complete TCA cycle consisting of eight enzymes as well as three additional Helicobacter pylori-type enzymes: ferredoxin-dependent 2-oxoglutarate synthase, succinyl-CoA/acetoacetyl-CoA transferase, and malate/quinone oxidoreductase. The co-existence of the genes for TCA cycle enzymes has also been identified in the other five Psychrobacillus strains.
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Affiliation(s)
- Jun Young Choi
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 6499, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 6499, Republic of Korea,Corresponding author Phone: +82-31-219-2461 Fax: +82-31-219-1610 E-mail:
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Choi JY, Lee PC. Psychrobacillus glaciei sp. nov., a psychrotolerant species isolated from an Antarctic iceberg. Int J Syst Evol Microbiol 2020; 70:1947-1952. [PMID: 31985396 DOI: 10.1099/ijsem.0.003998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We performed taxonomic studies on a psychrotolerant strain, designated PB01T, isolated from an Antarctic iceberg. The cells of strain PB01T were Gram-stain-positive, strictly aerobic, white-yellow and rod-shaped. The results of 16S rRNA gene sequence analysis revealed that strain PB01T was closely related to Psychrobacillus psychrodurans DSM 11713T (99.19 % similarity), Psychrobacillus psychrotolerans DSM 11706T (98.91 %) and Psychrobacillus insolitus DSM 5T (98.85 %). Despite high 16S rRNA gene sequence similarity, the degrees of DNA-DNA relatedness between strain PB01T and its three closest phylogenetic neighbours were 62.4±7.3 % for P. psychrodurans DSM 11713T, 61.1±5.4 % for P. psychrotolerans DSM 11706T and 56.1±6.9 % for P. insolitus DSM 5T. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 1ω7с-OH. Menaquinone-8 was the major respiratory quinone, and phosphatidylethanolamine was the major polar lipid. The DNA G+C content of strain PB01T calculated from the complete genome sequence was 36.0 mol%. Based on the phenotypic, chemotaxonomic, genomic and phylogenetic data obtained in the present study, we conclude that strain PB01T represents a novel species of the genus Psychrobacillus, for which we propose the name Psychrobacillus glaciei sp. nov. The type strain is PB01T (=CECT 9792T=KCTC 43041T).
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Affiliation(s)
- Jun Young Choi
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 16499, Republic of Korea
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Rodríguez M, Reina JC, Béjar V, Llamas I. Psychrobacillus vulpis sp. nov., a new species isolated from faeces of a red fox in Spain. Int J Syst Evol Microbiol 2019; 70:882-888. [PMID: 31833832 DOI: 10.1099/ijsem.0.003840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive rod, designated as strain Z8T, was isolated from red fox (Vulpes vulpes) faeces sampled at Tablas de Daimiel National Park, Ciudad Real, Spain. Strain Z8T grew at 0-37 °C (optimum, 28 °C), in the presence of 0-5.5 % (w/v) NaCl (2.5 %, w/v) and at pH 6-10 (pH 7). The strain was motile and positive for catalase, oxidase, H2S and siderophore production, acid and alkaline phosphatases, and N-acetylglucosamine, adipic acid and malate assimilation. It hydrolysed starch, DNA, l-tyrosine, Tween 20, Tween 80 and lecithovitellin. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Z8T is a member of the genus Psychrobacillus, showing high sequence similarity to Psychrobacillus lasiicapitis NEAU-3TGS17T (99.2 %) and Psychrobacillus soli NHI-2TT (99.1 %), and around 98 % to other known species of the genus Psychrobacillus. Digital DNA-DNA hybridization and average nucleotide identity values were lower than 24 and 79 %, respectively, with the most related species. In silico G+C content was 35.9 mol%. The major cellular fatty acids of strain Z8T were iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids, and the main respiratory isoprenoid quinone was MK-8. Based on the 16S rRNA phylogenetic analysis, together with MLSA (recA, rpoB and gyrB), phylogenomic, chemotaxonomic and phenotypic results, we demonstrate that strain Z8T represents a novel species of the genus Psychrobacillus, for which the name Psychrobacillus vulpis sp. nov., is proposed. The type strain is Z8T (=CECT 9721T=LMG 31001T).
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Affiliation(s)
- Miguel Rodríguez
- Biomedical Research Center (CIBM), Biotechnology Institute, Parque Tecnológico Ciencias de la Salud (PTS), Avenida del Conocimiento s/n, 18100, Armilla, Granada, Spain.,Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus Universitario Cartuja s/n, 18071 Granada, Spain
| | - José Carlos Reina
- Biomedical Research Center (CIBM), Biotechnology Institute, Parque Tecnológico Ciencias de la Salud (PTS), Avenida del Conocimiento s/n, 18100, Armilla, Granada, Spain.,Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus Universitario Cartuja s/n, 18071 Granada, Spain
| | - Victoria Béjar
- Biomedical Research Center (CIBM), Biotechnology Institute, Parque Tecnológico Ciencias de la Salud (PTS), Avenida del Conocimiento s/n, 18100, Armilla, Granada, Spain.,Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus Universitario Cartuja s/n, 18071 Granada, Spain
| | - Inmaculada Llamas
- Biomedical Research Center (CIBM), Biotechnology Institute, Parque Tecnológico Ciencias de la Salud (PTS), Avenida del Conocimiento s/n, 18100, Armilla, Granada, Spain.,Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus Universitario Cartuja s/n, 18071 Granada, Spain
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12
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Verma A, Pal Y, Ojha AK, Kumari M, Khatri I, Rameshkumar N, Schumann P, Dastager SG, Mayilraj S, Subramanian S, Krishnamurthi S. Taxonomic insights into the phylogeny of Bacillus badius and proposal for its reclassification to the genus Pseudobacillus as Pseudobacillus badius comb. nov. and reclassification of Bacillus wudalianchiensis Liu et al., 2017 as Pseudobacillus wudalianchiensis comb. nov. Syst Appl Microbiol 2019; 42:360-372. [DOI: 10.1016/j.syapm.2019.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 11/26/2022]
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13
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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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14
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Gomri MA, El Moulouk Khaldi T, Kharroub K. Analysis of the diversity of aerobic, thermophilic endospore-forming bacteria in two Algerian hot springs using cultural and non-cultural methods. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1401-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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15
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MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci U S A 2018; 115:E5213-E5222. [PMID: 29686086 PMCID: PMC5984513 DOI: 10.1073/pnas.1722335115] [Citation(s) in RCA: 410] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Plant roots nurture a large diversity of soil microbes via exudation of chemical compounds into the rhizosphere. In turn, beneficial root microbiota promote plant growth and immunity. The root-specific transcription factor MYB72 has emerged as a central regulator in this process. Here, we show that MYB72 regulates the excretion of the coumarin scopoletin, an iron-mobilizing phenolic compound with selective antimicrobial activity that shapes the root-associated microbial community. Selected soil-borne fungal pathogens appeared to be highly sensitive to the antimicrobial activity of scopoletin, while two MYB72-inducing beneficial rhizobacteria were tolerant. Our results suggest that probiotic root-associated microbes that activate the iron-deficiency response during colonization stimulate MYB72-dependent excretion of scopoletin, thereby potentially improving their niche establishment and enhancing plant growth and protection. Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana–Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses. MYB72 regulates the biosynthesis of iron-mobilizing fluorescent phenolic compounds, after which BGLU42 activity is required for their excretion into the rhizosphere. Metabolite fingerprinting revealed the antimicrobial coumarin scopoletin as a dominant metabolite that is produced in the roots and excreted into the rhizosphere in a MYB72- and BGLU42-dependent manner. Shotgun-metagenome sequencing of root-associated microbiota of Col-0, myb72, and the scopoletin biosynthesis mutant f6′h1 showed that scopoletin selectively impacts the assembly of the microbial community in the rhizosphere. We show that scopoletin selectively inhibits the soil-borne fungal pathogens Fusarium oxysporum and Verticillium dahliae, while the growth-promoting and ISR-inducing rhizobacteria P. simiae WCS417 and Pseudomonas capeferrum WCS358 are highly tolerant of the antimicrobial effect of scopoletin. Collectively, our results demonstrate a role for coumarins in microbiome assembly and point to a scenario in which plants and probiotic rhizobacteria join forces to trigger MYB72/BGLU42-dependent scopolin production and scopoletin excretion, resulting in improved niche establishment for the microbial partner and growth and immunity benefits for the host plant.
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16
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Montaño-Salazar SM, Lizarazo-Marriaga J, Brandão PFB. Isolation and Potential Biocementation of Calcite Precipitation Inducing Bacteria from Colombian Buildings. Curr Microbiol 2017; 75:256-265. [PMID: 29043388 DOI: 10.1007/s00284-017-1373-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
Abstract
Microbiological induced calcium carbonate or calcite precipitation (MICP) has become a highly researched issue due to its multiple applications in the construction industry, being a promising alternative with a great biotechnological importance. In this work, potential calcite precipitation inducing bacteria were isolated from mortar and concrete samples of different buildings at the National University of Colombia. Eighteen crystal-precipitating strains were recovered in Urea-CaCl2 solid medium. The 16S rRNA gene sequencing identified isolates as Arthrobacter, Psychrobacillus and Rhodococcus genera. It is reported, for the first time, the calcite precipitation by P. psycrodurans and R. qingshengii. Optical microscopy and Scanning Electron Microscopy showed crystals with irregular and spherical shapes, and beige and white colours. Furthermore, crystals formation appeared to be strain-specific. X-Ray diffraction analysis confirmed crystals composition as CaCO3. Biocementation tests showed that MICP treatments of mortar cubes using P. psycrodurans caused an increase in their compressive strength compared to control samples. The positive action of a native MICP strain in mortar blocks biomineralization is shown, which is of great interest and potential for the construction industry.
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Affiliation(s)
- Sandra M Montaño-Salazar
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Lizarazo-Marriaga
- Grupo de Investigación en Análisis, Diseño y Materiales - GIES, Facultad de Ingeniería, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Pedro F B Brandão
- Grupo de Estudios para la Remediación y Mitigación de Impactos Negativos al Ambiente (G.E.R.M.I.N.A.), Laboratorio de Microbiología Ambiental y Aplicada, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.
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17
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Shen Y, Fu Y, Yu Y, Zhao J, Li J, Li Y, Wang X, Zhang J, Xiang W. Psychrobacillus lasiicapitis sp. nov., isolated from the head of an ant (Lasius fuliginosus). Int J Syst Evol Microbiol 2017; 67:4462-4467. [PMID: 28933325 DOI: 10.1099/ijsem.0.002315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A novel Gram-stain-positive, motile, endospore-forming, rod-shaped bacterium, designated strain NEAU-3TGS17T, was isolated from the head of an ant (Lasius fuliginosus). The isolate grew at 0-35 °C (optimum 28-30 °C), at pH 6.0-11.0 (optimum pH 7.0-8.0) and with 0-6 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-3TGS17T belonged to the genus Psychrobacillus. Sequence similarities between strain NEAU-3TGS17T and members of the genus Psychrobacillus with validly published names (Psychrobacillus psychrotolerans DSM 11706T, Psychrobacillus insolitus DSM 5T, Psychrobacillus psychrodurans DSM 11713T and Psychrobacillus soli NBRC 110600T) were 98.4-99.1 %. DNA-DNA relatedness values between strain NEAU-3TGS17T and its closest relatives were below 70 %. The major cellular fatty acids (>5 %) were iso-C14 : 0, anteiso-C15 : 0, C16 : 0 and iso-C15 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The cell-wall peptidoglycan type was A4β with ornithine as the diamino acid and the predominant menaquinones were MK-8 and some MK-7. The DNA G+C content was 35.8 mol%. On the basis of phenotypic data and phylogenetic inference, strain NEAU-3TGS17T was classified as representing a novel species in the genus Psychrobacillus, for which the name Psychrobacillus lasiicapitis sp. nov. is proposed. The type strain is NEAU-3TGS17T (=DSM 100484T=CGMCC 1.15308T).
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Affiliation(s)
- Yibo Shen
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yansong Fu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yang Yu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Jiansong Li
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yao Li
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Ji Zhang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.,Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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18
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Verma A, Pal Y, Khatri I, Ojha AK, Gruber-Vodicka H, Schumann P, Dastager S, Subramanian S, Mayilraj S, Krishnamurthi S. Examination into the taxonomic position of Bacillus thermotolerans Yang et al., 2013, proposal for its reclassification into a new genus and species Quasibacillus thermotolerans gen. nov., comb. nov. and reclassification of B. encimensis Dastager et al., 2015 as a later heterotypic synonym of B. badius. Syst Appl Microbiol 2017; 40:411-422. [PMID: 28947104 DOI: 10.1016/j.syapm.2017.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 07/26/2017] [Indexed: 11/28/2022]
Abstract
Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8T confirmed their separation into a novel genus with B. badius and genus Domibacillus as the closest phylogenetic relatives. The major fatty acids of the strains are iso-C15:0 and iso-C16:0 and MK-7 is the only quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The digital DNA-DNA hybridization (DDH) and ortho average nucleotide identity (ANI) values calculated through whole genome sequences indicated that the three strains showed low relatedness with their phylogenetic neighbours. Based on evidences from phylogenomic analyses and polyphasic taxonomic characterization we propose reclassification of the species B. thermotolerans into a novel genus named Quasibacillus thermotolerans gen. nov., comb. nov with the type strain SgZ-8T (=CCTCC AB2012108T=KACC 16706T). Further our analyses also revealed that B. encimensis SGD-V-25T is a later heterotypic synonym of Bacillus badius DSM 23T.
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Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Yash Pal
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Indu Khatri
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Anup Kumar Ojha
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Harald Gruber-Vodicka
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Peter Schumann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, GmBH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
| | - Syed Dastager
- NCIM Resource Center, CSIR-National Chemical Laboratory, Pune 411 008, Maharashtra, India
| | | | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India.
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19
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Pal D, Mathan Kumar R, Kaur N, Kumar N, Kaur G, Singh NK, Krishnamurthi S, Mayilraj S. Bacillus maritimus sp. nov., a novel member of the genus Bacillus isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67:60-66. [DOI: 10.1099/ijsem.0.001569] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Deepika Pal
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Rajendran Mathan Kumar
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Navjot Kaur
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Narender Kumar
- Division of Protein Science and Engineering, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Gurwinder Kaur
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Nitin Kumar Singh
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Srinivasan Krishnamurthi
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shanmugam Mayilraj
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
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20
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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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21
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Abstract
Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.
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22
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Abbas S, Ahmed I, Kudo T, Iqbal M, Lee YJ, Fujiwara T, Ohkuma M. A heavy metal tolerant novel bacterium, Bacillus malikii sp. nov., isolated from tannery effluent wastewater. Antonie van Leeuwenhoek 2015; 108:1319-1330. [PMID: 26362330 DOI: 10.1007/s10482-015-0584-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
Abstract
The taxonomic position of a Gram-stain positive and heavy metal tolerant bacterium, designated strain NCCP-662(T), was investigated by polyphasic characterisation. Cells of strain NCCP-662(T) were observed to be rod to filamentous shaped, motile and strictly aerobic, and to grow at 10-50 °C (optimum 30-37 °C) and at pH range of 6-10 (optimum pH 7-8). The strain was found to be able to tolerate 0-12 % NaCl (w/v) and heavy metals (Cr 1200 ppm, Pb 1800 ppm and Cu 1200 ppm) in tryptic soya agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence of strain NCCP-662(T) showed that it belongs to the genus Bacillus and showed high sequence similarity (98.2 and 98.0 %, respectively) with the type strains of Bacillus niabensis 4T19(T) and Bacillus halosaccharovorans E33(T). The chemotaxonomic data showed that the major quinone is MK-7; the predominant cellular fatty acids are anteiso-C15 :0, iso-C14:0, iso-C16:0 and C16:0 and iso-C15:0; the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol along with several unidentified glycolipids, phospholipids and polar lipids. The DNA G+C content was determined to be 36.9 mol%. These data also support the affiliation of strain NCCP-662(T) with the genus Bacillus. The level of DNA-DNA relatedness between strain NCCP-662(T) and B. niabensis JCM 16399(T) was 20.5 ± 0.5 %. On the basis of physiological and biochemical characteristics, phylogenetic analyses and DNA-DNA hybridization data, strain NCCP-662(T) can be clearly differentiated from the validly named Bacillus species and thus represents a new species, for which the name Bacillus malikii sp. nov. is proposed with the type strain NCCP-662(T) (= LMG 28369(T) = DSM 29005(T) = JCM 30192(T)).
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Affiliation(s)
- Saira Abbas
- National Culture Collection of Pakistan (NCCP), National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan.,Department of Plant Genomics and Biotechnology (PGB), PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan.,Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.,Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan. .,Department of Plant Genomics and Biotechnology (PGB), PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan. .,Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan. .,Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Muhammad Iqbal
- Department of Plant Genomics and Biotechnology (PGB), PARC Institute of Advanced Studies in Agriculture (PIASA), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Yong-Jae Lee
- Korean Collection for Type Cultures, Biological Resources Centre, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea
| | - Toru Fujiwara
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
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23
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Abstract
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
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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: 41] [Impact Index Per Article: 4.6] [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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25
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Pham VHT, Jeong SW, Kim J. Psychrobacillus soli sp. nov., capable of degrading oil, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2015; 65:3046-3052. [PMID: 26065735 DOI: 10.1099/ijs.0.000375] [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, aerobic, psychrotolerant, Gram-stain-positive, endospore-forming strain, NHI-2(T), was isolated from oil-contaminated soil near a gas station in Mongolia. This strain was characterized by motile rods and grew over a wide range of temperatures ( -2 to 40 °C) with optimal growth at 28-30 °C. It tolerated salt concentrations of up to 7% over a five-day incubation period. Analysis of 16S rRNA gene sequence indicated that strain NHI-2(T) belongs to the genus Psychrobacillus. Sequence similarity between NHI-2(T) and members of the genus Psychrobacillus with validly published names ranged from 97.83 to 98.18%. DNA-DNA hybridization indicated less than 70% relatedness to reference strains within the genus. The G+C content of the genomic DNA was 36 mol%. This strain contained MK-8 as a predominant isoprenoid menaquinone. NHI-2(T) had ornithine in the cell wall similar to reference strains of the genus Psychrobacillus. The major fatty acids present in NHI-2(T )were anteiso-C15 : 0 (51.0%), iso-C15 : 0 (9.1%) and anteiso-C17 : 0 (8.0%). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. These data highlight that the phenotype of strain NHI-2(T) differs from that of related species in terms of chemotaxonomic properties and genotype characteristics. Therefore, this strain is proposed as a representative of a novel species, named Psychrobacillus soli. The type strain is NHI-2(T) ( = KEMB 9005-135(T) = KACC 18243(T) = NBRC 110600(T)).
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Affiliation(s)
- Van Hong Thi Pham
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon 443-760, Republic of Korea
| | - Seung-Woo Jeong
- Department of Environmental Engineering, Kunsan National University, Kunsan 573-701, Republic of Korea
| | - Jaisoo Kim
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon 443-760, Republic of Korea
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26
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Savagea faecisuis gen. nov., sp. nov., a tylosin- and tetracycline-resistant bacterium isolated from a swine-manure storage pit. Antonie van Leeuwenhoek 2015; 108:151-61. [DOI: 10.1007/s10482-015-0473-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
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27
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Seiler H, Wenning M, Scherer S. Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room. Int J Syst Evol Microbiol 2013; 63:2054-2061. [DOI: 10.1099/ijs.0.044396-0] [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 novel red-pigmented bacterial strain, designated WS 4628T, was isolated from a pharmaceutical clean room of a vaccine-producing company and was investigated in a taxonomic study using a polyphasic approach. The strain was Gram-stain-positive, strictly aerobic, motile, catalase-positive and produced spherical to slightly ellipsoidal endospores in rods. The genomic DNA G+C content was 44.1 mol%. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 and the predominant quinone was MK-6. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and an unidentified phospholipid. meso-diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan and the major whole-cell sugars were glucose and ribose. The closest phylogenetic neighbours were identified as
Bacillus badius
ATCC 14574T (95.8 % 16S rRNA gene sequence similarity),
Bacillus indicus
Sd/3T (94.8 %),
Jeotgalibacillus alimentarius
YKJ-13T (94.8 %) and
Bacillus cibi
JG-30T (94.8 %). Phylogenetic, physiological, biochemical and morphological differences between strain WS 4628T and its closest relatives in the families
Bacillaceae
and
Planococcaceae
suggest that this strain represents a novel species in a new genus in the family
Bacillaceae
for which the name Domibacillus robiginosus gen. nov., sp. nov. is proposed; the type strain of the type species is WS 4628T ( = DSM 25058T = LMG 26645T).
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Affiliation(s)
- Herbert Seiler
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| | - Mareike Wenning
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
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28
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Krishnamurthi S, Chakrabarti T. Diversity of bacteria and archaea from a landfill in Chandigarh, India as revealed by culture-dependent and culture-independent molecular approaches. Syst Appl Microbiol 2012; 36:56-68. [PMID: 23274043 DOI: 10.1016/j.syapm.2012.08.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 08/15/2012] [Accepted: 08/17/2012] [Indexed: 11/29/2022]
Abstract
The bacterial community structure of a municipal landfill in Chandigarh, India was analysed by culture-dependent as well as culture-independent molecular approaches, and archaeal structure by the latter method. Samples were collected in two phases from the surface and a depth of 0.91 m in June, 2004 and from 0.91 m, 1.52 m and 1.68 m in May, 2005. After serial dilutions, samples were plated onto tryptic soy agar (TSA), plate count agar (PCA), tryptic soy broth agar (TSBA) and TSBA100 (TSBA diluted 100 times and solidified with agarose), and incubated aerobically at 30°C. The number of bacteria (CFU) on different media ranged between 9.4×10⁵g⁻¹ (on PCA) and 1.9×10⁷g⁻¹ (on TSA) (wet weight). The numbers of bacteria enumerated from plates incubated anaerobically (anaerobic agar and reinforced clostridial agar) were 2.1×10⁷and 1.7×10⁶g⁻¹, respectively. Of the 468 isolated and purified bacteria (183 in the first phase and 285 in the second phase), 135 were characterised using phenotypic characteristics as well as 16S rRNA gene sequence analysis. It was found that members of the phylum Firmicutes were overwhelmingly predominant (86.6%) in the landfill, followed by Actinobacteria (9.6%) and Proteobacteria (3.7%). Among the Firmicutes, at least 17 species from the single genus Bacillus were the most abundant inhabitants of the landfill. Detailed polyphasic characterisation of many of these isolates led to the discovery of a novel genus Paenisporosarcina (and the species P. quisquiliarum), a novel species of Microbacterium, M. immunditiarum, and reclassification of Sporosarcina macmurdoensis, Pelagibacillus goriensis, Bacillus silvestris, Bacillus insolitus, Bacillus psychrotolerans and Bacillus psychrodurans. Culture-independent analysis of two 16S rRNA gene libraries also revealed that the phylum Firmicutes was the predominant group in this community. The diversity of Archaea was found to be limited mainly to members of two orders: Methanosarcinales and Methanomicrobiales of the phylum Euryarchaeota. When these results were compared to those reported earlier on similar studies, it was found that irrespective of differences in composition of municipal solid waste (especially compostable organic matter and paper) and climate, the members of bacterial and archaeal communities in landfills of many countries remained broadly similar.
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Affiliation(s)
- S Krishnamurthi
- Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India.
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29
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Verma P, Pandey PK, Gupta AK, Seong CN, Park SC, Choe HN, Baik KS, Patole MS, Shouche YS. Reclassification of
Bacillus beijingensis
Qiu et al. 2009 and
Bacillus ginsengi
Qiu et al. 2009 as Bhargavaea beijingensis comb. nov. and Bhargavaea ginsengi comb. nov. and emended description of the genus
Bhargavaea. Int J Syst Evol Microbiol 2012; 62:2495-2504. [DOI: 10.1099/ijs.0.034850-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have carried out a polyphasic taxonomic characterization of
Bacillus beijingensis
DSM 19037T and
Bacillus ginsengi
DSM 19038T, which are closely related phylogenetically to
Bhargavaea cecembensis
LMG 24411T. All three strains are Gram-stain-positive, non-motile, moderately halotolerant and non-spore-forming. 16S rRNA gene sequence analyses showed that the strains constituted a coherent cluster, with sequence similarities between 99.7 and 98.7 %. The percentage similarity on the basis of amino acid sequences deduced from partial gyrB gene nucleotide sequences of these three type strains was 96.1–92.7 %. Phylogenetic trees based on the 16S rRNA gene and GyrB amino acid sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a deeply rooted cluster separated from the clades represented by the genera
Bacillus
,
Planococcus
,
Planomicrobium
,
Sporosarcina
,
Lysinibacillus
,
Viridibacillus
,
Kurthia
and
Geobacillus
, supporting their placement in the genus
Bhargavaea
. All three type strains have menaquinone MK-8 as the major respiratory quinone and showed similar fatty acid profiles. The main polar lipids present in the three type strains were diphosphatidylglycerol and phosphatidylglycerol, and the three strains showed peptidoglycan type A4α with l-lysine as the diagnostic diamino acid. The DNA G+C contents of
Bacillus beijingensis
DSM 19037T,
Bacillus ginsengi
DSM 19038T and
Bhargavaea cecembensis
LMG 24411T were 53.1, 50.2 and 53.7 mol%, respectively. The level of DNA–DNA hybridization among the three strains was 57–39 %, indicating that they are members of different species of the genus
Bhargavaea
. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data, we have emended the description of the genus
Bhargavaea
and propose the reclassification of
Bacillus beijingensis
and
Bacillus ginsengi
to the genus
Bhargavaea
, as Bhargavaea beijingensis comb. nov. (type strain ge10T = DSM 19037T = CGMCC 1.6762T) and Bhargavaea ginsengi comb. nov. (type strain ge14T = DSM 19038T = CGMCC 1.6763T).
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Affiliation(s)
- Pankaj Verma
- Molecular Biology Unit, National Centre for Cell Science, University of Pune, Pune 411 007, Maharashtra, India
| | - Prashant Kumar Pandey
- Molecular Biology Unit, National Centre for Cell Science, University of Pune, Pune 411 007, Maharashtra, India
| | - Arvind Kumar Gupta
- Molecular Biology Unit, National Centre for Cell Science, University of Pune, Pune 411 007, Maharashtra, India
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Seong Chan Park
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Han Na Choe
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Keun Sik Baik
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Milind Shivaji Patole
- Molecular Biology Unit, National Centre for Cell Science, University of Pune, Pune 411 007, Maharashtra, India
| | - Yogesh Shreepad Shouche
- Microbial Culture Collection, Hindustan Antibiotics Ltd. Complex, Pimpri, Pune 411 018, Maharashtra, India
- Molecular Biology Unit, National Centre for Cell Science, University of Pune, Pune 411 007, Maharashtra, India
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30
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Jung MY, Kim JS, Paek WK, Styrak I, Park IS, Sin Y, Paek J, Park KA, Kim H, Kim HL, Chang YH. Description of
Lysinibacillus sinduriensis
sp. nov., and transfer of
Bacillus massiliensis
and
Bacillus odysseyi
to the genus
Lysinibacillus
as
Lysinibacillus massiliensis
comb. nov. and
Lysinibacillus odysseyi
comb. nov. with emended description of the genus
Lysinibacillus. Int J Syst Evol Microbiol 2012; 62:2347-2355. [DOI: 10.1099/ijs.0.033837-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, rod-shaped, endospore-forming bacterium, designated strain BLB-1T, was isolated from samples of tidal flat sediment from the Yellow Sea. 16S rRNA gene sequence analysis demonstrated that the isolate belonged to the
Bacillus
rRNA group 2 and was closely related to
Bacillus massiliensis
CIP 108446T (97.4 %),
Bacillus odysseyi
ATCC PTA-4993T (96.7 %),
Lysinibacillus fusiformis
DSM 2898T (96.2 %) and
Lysinibacillus boronitolerans
DSM 17140T (95.9 %). Sequence similarities with related species in other genera, including
Caryophanon
,
Sporosarcina
and
Solibacillus
, were <96.1 %. Chemotaxonomic data supported the affiliation of strain BLB-1T with the genus
Lysinibacillus
. The major menaquinone was MK-7, the cell-wall sugars were glucose and xylose, the cell-wall peptidoglycan type was A4α (l-Lys–d-Asp), the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown phospholipids, and the major fatty acids were anteiso-C15 : 0 (35.6 %), iso-C15 : 0 (25.6 %) and anteiso-C17 : 0 (16.5 %). The most closely related species,
Bacillus massiliensis
and
Bacillus odysseyi
, were also assigned to this genus based on phylogenetic analysis and phenotypic data. The results of DNA–DNA hybridizations and phenotypic tests supported the differentiation of all three taxa from species of the genus
Lysinibacillus
with validly published names. Thus, strain BLB-1T ( = KCTC 13296T = JCM 15800T) represents a novel species, for which the name
Lysinibacillus sinduriensis
sp. nov. is proposed. It is also proposed that
Bacillus massiliensis
CIP 108446T ( = 4400831T = CCUG49529T = KCTC 13178T) and
Bacillus odysseyi
NBRC 100172T ( = 34hs-1T = ATCC PTA-4993T = NRRL B-30641T = DSM 18869T = CIP 108263T = KCTC 3961T) be transferred to the genus
Lysinibacillus
as
Lysinibacillus massiliensis
comb. nov. and
Lysinibacillus odysseyi
comb. nov., respectively.
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Affiliation(s)
- Min Young Jung
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Joong-Su Kim
- Jeonbuk Branch Institute, Molecular Bioprocess Research Center, KRIBB, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 580-185, Republic of Korea
| | - Woon Kee Paek
- National Science Museum, 32-2 Guseong-dong, Yuseong-gu, Daejeon 305-705, Republic of Korea
| | - Igor Styrak
- Department of Biotechnology, Institute of Geotechnics, Watsonova 45, 043 53 Kosice, Slovakia
- Department of Microbiology, Institute of Animal Physiology, Soltesovej 4-6, 04001 Kosice, Slovakia
| | - In-Soon Park
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Yeseul Sin
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jayoung Paek
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Keun Ae Park
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Hongik Kim
- R&D Division, Vitabio Inc., Yongjeon-dong 21-3, Daejeon 300-824, Republic of Korea
| | - Hong Lim Kim
- Namhae Sub-Station, National Horticultural Research Institute, RDA, Namhae, 668-812, Republic of Korea
| | - Young-Hyo Chang
- Korean Collection for Type Cultures, Biological Resource Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Identification and characterization of psychrotolerant sporeformers associated with fluid milk production and processing. Appl Environ Microbiol 2012; 78:1853-64. [PMID: 22247129 DOI: 10.1128/aem.06536-11] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Psychrotolerant spore-forming bacteria represent a major challenge to the goal of extending the shelf life of pasteurized dairy products. The objective of this study was to identify prominent phylogenetic groups of dairy-associated aerobic sporeformers and to characterize representative isolates for phenotypes relevant to growth in milk. Analysis of sequence data for a 632-nucleotide fragment of rpoB showed that 1,288 dairy-associated isolates (obtained from raw and pasteurized milk and from dairy farm environments) clustered into two major divisions representing (i) the genus Paenibacillus (737 isolates, including the species Paenibacillus odorifer, Paenibacillus graminis, and Paenibacillus amylolyticus sensu lato) and (ii) Bacillus (n = 467) (e.g., Bacillus licheniformis sensu lato, Bacillus pumilus, Bacillus weihenstephanensis) and genera formerly classified as Bacillus (n = 84) (e.g., Viridibacillus spp.). When isolates representing the most common rpoB allelic types (ATs) were tested for growth in skim milk broth at 6°C, 6/9 Paenibacillus isolates, but only 2/8 isolates representing Bacillus subtypes, grew >5 log CFU/ml over 21 days. In addition, 38/40 Paenibacillus isolates but only 3/47 Bacillus isolates tested were positive for β-galactosidase activity (including some isolates representing Bacillus licheniformis sensu lato, a common dairy-associated clade). Our study confirms that Paenibacillus spp. are the predominant psychrotolerant sporeformers in fluid milk and provides 16S rRNA gene and rpoB subtype data and phenotypic characteristics facilitating the identification of aerobic spore-forming spoilage organisms of concern. These data will be critical for the development of detection methods and control strategies that will reduce the introduction of psychrotolerant sporeformers and extend the shelf life of dairy products.
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Coorevits A, Dinsdale AE, Heyrman J, Schumann P, Van Landschoot A, Logan NA, De Vos P. Lysinibacillus macroides sp. nov., nom. rev. Int J Syst Evol Microbiol 2011; 62:1121-1127. [PMID: 21724959 DOI: 10.1099/ijs.0.027995-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
'Bacillus macroides' ATCC 12905(T) ( = DSM 54(T) = LMG 18474(T)), isolated in 1947 from cow dung, was not included in the Approved Lists of Bacterial Names and so it lost standing in bacteriological nomenclature. Reinvestigation of the strain, including DNA-DNA relatedness experiments, revealed that 'Bacillus macroides' is genomically distinct from its closest relatives Lysinibacillus xylanilyticus, Lysinibacillus boronitolerans and Lysinibacillus fusiformis (as determined by 16S rRNA gene sequence analysis, with pairwise similarity values of 99.2, 98.8 and 98.5 %, respectively, with the type strains of these species). Further analysis showed that 'Bacillus macroides' shares the A4α L-Lys-D-Asp peptidoglycan type with other members of the genus Lysinibacillus and can thus be attributed to this genus. These results, combined with additional phenotypic data, justify the description of strain LMG 18474(T) ( = DSM 54(T) = ATCC 12905(T)) as Lysinibacillus macroides sp. nov., nom. rev.
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Affiliation(s)
- An Coorevits
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Laboratory of Biochemistry and Brewing, Faculty of Applied Engineering Sciences, University College Ghent, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Anna E Dinsdale
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA, UK
| | - Jeroen Heyrman
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Peter Schumann
- DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Anita Van Landschoot
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Laboratory of Biochemistry and Brewing, Faculty of Applied Engineering Sciences, University College Ghent, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Niall A Logan
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA, UK
| | - Paul De Vos
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Parker CT, Taylor D, Garrity GM. Nomenclature Abstract for Psychrobacillus psychrodurans (Abd El-Rahman et al. 2002) Krishnamurthi et al. 2011. THE NAMESFORLIFE ABSTRACTS 2011. [DOI: 10.1601/nm.21361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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34
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Parker CT, Taylor D, Garrity GM. Nomenclature Abstract for Psychrobacillus psychrotolerans (Abd El-Rahman et al. 2002) Krishnamurthi et al. 2011. THE NAMESFORLIFE ABSTRACTS 2011. [DOI: 10.1601/nm.21362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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35
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2011. [DOI: 10.1099/ijs.0.033498-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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36
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Wolfgang WJ, Coorevits A, Cole JA, De Vos P, Dickinson MC, Hannett GE, Jose R, Nazarian EJ, Schumann P, Van Landschoot A, Wirth SE, Musser KA. Sporosarcina newyorkensis sp. nov. from clinical specimens and raw cow's milk. Int J Syst Evol Microbiol 2011; 62:322-329. [PMID: 21421928 DOI: 10.1099/ijs.0.030080-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twelve independent isolates of a gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, USA, and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.13 % similarity). DNA-DNA hybridization studies demonstrate that the new isolates belong to a species distinct from their nearest phylogenetic neighbours. The partial sequences of the 23S rRNA gene for the novel strains and their nearest neighbours also provide support for the novel species designation. Maximum-likelihood phylogenetic analysis of the 16S rRNA gene sequences confirmed that the new isolates are in the genus Sporosarcina. The predominant menaquinone is MK-7, the peptidoglycan has the type A4α L-Lys-Gly-D-Glu, and the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids are iso-C(14 : 0), iso-C(15 : 0) and anteiso-C(15 : 0). In addition, biochemical and morphological analyses support designation of the twelve isolates as representatives of a single new species within the genus Sporosarcina, for which the name Sporosarcina newyorkensis sp. nov. (type strain 6062(T) = DSM 23544(T) = CCUG 59649(T) = LMG 26022(T)) is proposed.
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Affiliation(s)
- William J Wolfgang
- Department of Biomedical Sciences, State University of New York, Albany, NY 12201, USA.,Wadsworth Center, Bacteriology Laboratory, New York State Department of Health, PO Box 22002, Albany, NY 12201, USA
| | - An Coorevits
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Department of Applied Engineering Sciences, Laboratory of Biochemistry and Brewing, University College Ghent, Schoonmeersstraat 52, 9000 Ghent, Belgium
| | - Jocelyn A Cole
- Wadsworth Center, Bacteriology Laboratory, New York State Department of Health, PO Box 22002, Albany, NY 12201, USA
| | - Paul De Vos
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Michelle C Dickinson
- Wadsworth Center, Bacteriology Laboratory, New York State Department of Health, PO Box 22002, Albany, NY 12201, USA
| | - George E Hannett
- Wadsworth Center, Bacteriology Laboratory, New York State Department of Health, PO Box 22002, Albany, NY 12201, USA
| | - Reashma Jose
- Department of Biomedical Technology, Albany College of Pharmacy, 106 New Scotland Ave, Albany, NY 12208, USA
| | - Elizabeth J Nazarian
- Wadsworth Center, Bacteriology Laboratory, New York State Department of Health, PO Box 22002, Albany, NY 12201, USA
| | - Peter Schumann
- DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Anita Van Landschoot
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Department of Applied Engineering Sciences, Laboratory of Biochemistry and Brewing, University College Ghent, Schoonmeersstraat 52, 9000 Ghent, Belgium
| | - Samantha E Wirth
- Wadsworth Center, Bacteriology Laboratory, New York State Department of Health, PO Box 22002, Albany, NY 12201, USA
| | - Kimberlee A Musser
- Department of Biomedical Sciences, State University of New York, Albany, NY 12201, USA.,Wadsworth Center, Bacteriology Laboratory, New York State Department of Health, PO Box 22002, Albany, NY 12201, USA
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Arora PK, Chauhan A, Pant B, Korpole S, Mayilraj S, Jain RK. Chryseomicrobium imtechense gen. nov., sp. nov., a new member of the family Planococcaceae. Int J Syst Evol Microbiol 2010; 61:1859-1864. [PMID: 20833890 DOI: 10.1099/ijs.0.023184-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, yellow, non-motile, non-spore-forming, strictly aerobic bacterial strain, designated MW 10(T), was isolated from seawater of the Bay of Bengal, India, and was subjected to a polyphasic taxonomic study. Analysis of the 16S rRNA gene sequence revealed that strain MW 10(T) showed highest similarity to the type strains of Psychrobacillus psychrodurans (96.15 %) and Psychrobacillus psychrotolerans (96.01 %) and showed less than 96 % similarity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MW 10(T) formed a clade separate from members of closely related genera. The morphological, physiological and chemotaxonomic characteristics of strain MW 10(T) differed from those of members of closely related genera. The major fatty acid in strain MW 10(T) was iso-C(15 : 0) and the menaquinones were MK-7 (48.4 %), MK-8 (32.3 %), MK-7(H(2)) (13.7 %) and MK-6 (5.6 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown phospholipid, an unknown lipid and an unknown glycolipid. The cell-wall peptidoglycan type was l-Lys-d-Asp. The genomic DNA G+C content (53.4 mol%) of strain MW 10(T) was significantly different from those of members of closely related genera. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as our phylogenetic analysis, we conclude that strain MW 10(T) is a member of a novel genus and species, for which the name Chryseomicrobium imtechense gen. nov., sp. nov., is proposed. The type strain of Chryseomicrobium imtechense is MW 10(T) ( = MTCC 10098(T) = JCM 16573(T)).
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Affiliation(s)
- Pankaj Kumar Arora
- Environmental Biotechnology, Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology (CSIR), Sector-39A, Chandigarh - 160036, India
| | - Archana Chauhan
- Environmental Biotechnology, Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology (CSIR), Sector-39A, Chandigarh - 160036, India
| | - Bhawana Pant
- Environmental Biotechnology, Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology (CSIR), Sector-39A, Chandigarh - 160036, India
| | - Suresh Korpole
- Environmental Biotechnology, Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology (CSIR), Sector-39A, Chandigarh - 160036, India
| | - Shanmugam Mayilraj
- Environmental Biotechnology, Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology (CSIR), Sector-39A, Chandigarh - 160036, India
| | - Rakesh Kumar Jain
- Environmental Biotechnology, Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology (CSIR), Sector-39A, Chandigarh - 160036, India
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Parker CT, Taylor D, Garrity GM. Exemplar Abstract for Psychrobacillus psychrotolerans (Abd El-Rahman et al. 2002) Krishnamurthi et al. 2011 and Bacillus psychrotolerans Abd El-Rahman et al. 2002. THE NAMESFORLIFE ABSTRACTS 2010. [DOI: 10.1601/ex.4970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Parker CT, Taylor D, Garrity GM. Exemplar Abstract for Bacillus psychrodurans Abd El-Rahman et al. 2002 and Psychrobacillus psychrodurans (Abd El-Rahman et al. 2002) Krishnamurthi et al. 2011. THE NAMESFORLIFE ABSTRACTS 2009. [DOI: 10.1601/ex.4967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Parker CT, Osier ND, Garrity GM. Nomenclature Abstract for Bacillus psychrotolerans Abd El-Rahman et al. 2002. THE NAMESFORLIFE ABSTRACTS 2009. [DOI: 10.1601/nm.4970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Parker CT, Osier ND, Garrity GM. Nomenclature Abstract for Bacillus psychrodurans Abd El-Rahman et al. 2002. THE NAMESFORLIFE ABSTRACTS 2009. [DOI: 10.1601/nm.4967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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