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Manetsberger J, Caballero Gómez N, Soria-Rodríguez C, Benomar N, Abriouel H. Simply Versatile: The Use of Peribacillus simplex in Sustainable Agriculture. Microorganisms 2023; 11:2540. [PMID: 37894197 PMCID: PMC10608964 DOI: 10.3390/microorganisms11102540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Peribacillus simplex is a Gram-positive, spore-forming bacterium derived from a vast range of different origins. Notably, it is part of the plant-growth-promoting rhizobacterial community of many crops. Although members of the Bacillaceae family have been widely used in agriculture, P. simplex has, so far, remained in the shadow of its more famous relatives, e.g., Bacillus subtilis or Bacillus thuringiensis. Recent studies have, however, started to uncover the bacterium's highly promising and versatile properties, in particular in agricultural and environmental applications. Hence, here, we review the plant-growth-promoting features of P. simplex, as well as its biocontrol activity against a variety of detrimental plant pests in different crops. We further highlight the bacterium's potential as a bioremediation agent for environmental contaminants, such as metals, pesticide residues, or (crude) oil. Finally, we examine the recent developments in the European regulatory landscape to facilitate the use of microorganisms in plant protection products. Undoubtedly, further studies on P. simplex will reveal additional benefits for agricultural and environmentally friendly applications.
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Affiliation(s)
- Julia Manetsberger
- Area of Microbiology, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
| | - Natacha Caballero Gómez
- Area of Microbiology, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
| | - Carlos Soria-Rodríguez
- Area of Public International Law and International Relations, Department of Public and European Common Law, University of Jaén, 23071 Jaén, Spain
| | - Nabil Benomar
- Area of Microbiology, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
| | - Hikmate Abriouel
- Area of Microbiology, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
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Bacillus litorisediminis sp. nov., a Thermophilic Bacterium Isolated from Mangrove Sediment. Curr Microbiol 2023; 80:79. [PMID: 36656344 DOI: 10.1007/s00284-023-03180-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023]
Abstract
Two aerobic, Gram-staining-positive, rod-shaped, endospore-forming, thermophilic bacterial strains, designated FJAT-47801T and FJAT-47835, were isolated from the sediment collected from Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. Growth was observed at 25-55 °C (optimum, 50 °C) and pH 7.0-9.0 (optimum, pH 7.0), with up to 4.0% (w/v) NaCl (optimum, without NaCl). Strains FJAT-47801T and FJAT-47835 showed the highest 16S rRNA gene sequence similarity to Bacillus oleivorans (98.5%). The 16S rRNA gene sequence similarity between FJAT-47801T and FJAT-47835 was 99.9% indicating they were the same species. Phylogenetic (based on 16S rRNA gene sequences) and phylogenomic (based on 120 conserved bacterial single-copy genes) trees showed that strains FJAT-47801T and FJAT-47835 should be affiliated to the genus Bacillus. The of menaquinone of strain FJAT-47801T was MK-7. The major fatty acids of strain FJAT-47801T were iso-C15:0, anteiso-C15:0, iso-C17:0, and C16:0. The major polar lipids strain FJAT-47801T were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). The genomic DNA G+C content of strain FJAT-47801T was 39.3%. The average nucleotide identity (84.3%) and the digital DNA-DNA hybridization value (28.1%) between strain FJAT-47801T and B. oleivorans CCTCC AB 2013353T were below the cut-off level for species delineation. Based on the above results, strain FJAT-47801T represents a novel species of the genus Bacillus, for which the name Bacillus litorisediminis sp. nov., is proposed. The type strain is FJAT-47801T (=GDMCC 1.2712T = JCM 34875T).
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Rodríguez M, Reina JC, Sampedro I, Llamas I, Martínez-Checa F. Peribacillus castrilensis sp. nov.: A Plant-Growth-Promoting and Biocontrol Species Isolated From a River Otter in Castril, Granada, Southern Spain. FRONTIERS IN PLANT SCIENCE 2022; 13:896728. [PMID: 35812926 PMCID: PMC9262404 DOI: 10.3389/fpls.2022.896728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
A strictly aerobic, chemoheterotrophic, endospore-forming, Gram-positive, rod-shaped bacterial strain N3T was isolated from the feces of a river otter in Castril (Granada, southern Spain). It is halotolerant, motile, and catalase-, oxidase-, ACC deaminase-, and C4- and C8-lipase-positive. It promotes tomato plant growth and can reduce virulence in Erwinia amylovora CECT 222T and Dickeya solani LMG 25993T through interference in their quorum-sensing systems, although other antagonistic mechanisms could also occur. A phylogenetic analysis of the 16S rRNA gene sequence as well as the phenotypic and phylogenomic analyses indicated that the strain N3T is a novel species of the genus Peribacillus, with the highest 16S rRNA sequence similar to that of Bacillus frigoritolerans DSM 8801T (99.93%) and Peribacillus simplex DSM 1321T (99.80%). Genomic digital DNA-DNA hybridization (dDDH) between the strain N3T and Bacillus frigoritolerans DSM 8801T and Peribacillus simplex was 12.8 and 69.1%, respectively, and the average nucleotide identity (ANIb) of strain N3T and Bacillus frigoritolerans DSM 8801T and Peribacillus simplex was 67.84 and 93.21%, respectively. The genomic G + C content was 40.3 mol%. Its main cellular fatty acids were anteiso-C15:0 and iso-C15:0. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with the chemotaxonomic and phenotypic data, we demonstrated that the type strain N3T (=CECT 30509T = LMG 32505T) is a novel species of the genus Peribacillus and the name Peribacillus castrilensis sp. nov. is proposed.
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Affiliation(s)
- Miguel Rodríguez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - José Carlos Reina
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Inmaculada Sampedro
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Inmaculada Llamas
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Biomedical Research Centre (CIBM), Institute of Biotechnology, University of Granada, Granada, Spain
| | - Fernando Martínez-Checa
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Biomedical Research Centre (CIBM), Institute of Biotechnology, University of Granada, Granada, Spain
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Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics. 3 Biotech 2021; 11:252. [PMID: 33968595 DOI: 10.1007/s13205-021-02809-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/23/2021] [Indexed: 10/21/2022] Open
Abstract
Coastal sand dunes (CSDs), unique, stressed and hostile habitats act as a barrier between marine and terrestrial ecosystems. CSDs are stressed in terms of nutrition and fluctuating physio-chemical conditions. CSD is classified into several types, each of which presents different challenges for life forms. This study focuses on exploring bacterial and archaeal diversity and community structure in four CSD namely, Embryo, Fore, Gray, and Mature dunes of Keri beach, Goa along the west coast of India. The study was carried out using Next Generation Sequencing of hypervariable V3-V4 regions of the 16S rRNA gene using Illumina HiSeq platform. The present study hypothesizes that the prokaryotic communities at each dune may be different and could have different role in the ecosystem. The NGS for Embryo, Fore, Gray, and Mature dunes gave 1,045,447, 1,451,753, 1,321,867, and 1,537,758 paired-end reads, respectively, out of which 54,500, 50,032, 37,819, and 111,186 were retained through various quality filtrations. A total of 74, 63, 65, and 65% of OTUs, respectively, remained unknown at the species level. The highest bacterial and archaeal abundance was reported from Mature and Embryo dunes, respectively. Phylum Actinobacteria dominated the Embryo, Fore, and Mature dunes, whereas phylum Proteobacteria was the dominant in the Gray dune. Streptomyces was predominant in overall CSD followed by Bacillus, Acidobacterium, and Kouleothrix. The commonly and exclusively found members in each dune are cataloged. The highest species dominance, diversity, species richness, and abundance were observed in Embryo, Fore, Gray, and Mature dunes, respectively. The present study clearly elucidates that each dune has a distinct microbial community structure. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02809-5.
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Jiang L, Jung WY, Li Z, Lee MK, Park SH, Kang SW, Lee JS, Jung H, Hur TY, Kim HB, Kim JK, Lee JH, Lee JH, Lee J. Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow. Int J Syst Evol Microbiol 2021; 71. [PMID: 33650947 DOI: 10.1099/ijsem.0.004721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic, endospore-forming, rod-shaped strain, AGMB 02131T, which grew at 20-40 °C (optimum 30 °C), pH 3.0-11.0 (optimum pH 4.0) and in the presence of 0-18 % (w/v) NaCl (optimum 10 %), was isolated from a cow faecal sample and identified as a novel strain using a polyphasic taxonomic approach. The phylogenetic analysis based on 16S rRNA gene sequences along with the whole genome (92 core gene sets) revealed that AGMB 02131T formed a group within the genus Peribacillus, and showed the highest sequence similarity with Peribacillus endoradicis DSM 28131T (96.9 %), following by Peribacillus butanolivorans DSM 18926T (96.6 %). The genome of AGMB 02131T comprised 70 contigs, the chromosome length was 4 038 965 bp and it had a 38.5 % DNA G+C content. Digital DNA-DNA hybridization revealed that AGMB 02131T displayed 21.4 % genomic DNA relatedness with the most closely related strain, P. butanolivorans DSM 18926T. AGMB 02131T contains all of the conserved signature indels that are specific for members of the genus Peribacillus. The major cellular fatty acids (>10 %) of AGMB 02131T were C18 : 1ω9c, C18:0 and C16 : 0. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic features, AGMB 02131T represents a novel species of the genus Peribacillus, for which the name Peribacillus faecalis sp. nov. is proposed. The type strain is AGMB 02131T (=KCTC 43221T=CCTCC AB 2020077T).
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Affiliation(s)
- Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Won Yong Jung
- Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Zhun Li
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Mi-Kyung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Hyunjung Jung
- Swine Science Division, National Institute of Animal Science, Cheonan 31000, Republic of Korea
| | - Tai-Young Hur
- Division of Animal Disease and Health, National Institute of Animal Science, Wanju-Gun 55365, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan 3116, Republic of Korea
| | - Jae-Kyung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
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Liu GH, Narsing Rao MP, Wang XY, Chu TW, Liu B, Li WJ. Bacillus alkalicellulosilyticus sp. nov., isolated from extremely alkaline bauxite residue (red mud) site. Arch Microbiol 2020; 203:719-723. [PMID: 33047173 DOI: 10.1007/s00203-020-02063-y] [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] [Received: 06/09/2020] [Revised: 08/28/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022]
Abstract
A Gram-stain-negative, rod-shaped, facultatively anaerobic, motile and spore-forming strain designated FJAT-44921T was isolated from red mud collected from Chiping County, Shandong Province, China. The 16S rRNA gene sequence result showed that strain FJAT-44921T shared a low sequence identity (96.6%) with the members of the genus Bacillus. Growth was observed at pH 8.0-10.0 (optimum pH 9.0), 10-40 °C (optimum 20-25 °C) with 0-8% (v/w %) NaCl (optimum 4-6 v/w %). FJAT-44921T consists of MK-7 as the isoprenoid quinone and meso-2,6-diaminopimelic acid as the cell-wall diamino acid. The predominant fatty acids were anteiso-C15:0, iso-C15:0, C16:0, and anteiso-C17:0. The polar lipids were diphosphatidylglycerol, phosphatidyl glycerol, phosphatidylmethylethanolamine, unidentified phospholipid, and unidentified aminophospholipid. The genomic DNA G + C content was 37.3 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between FJAT-44921T and other closely related Bacillus members were lower than the recognized threshold values of ANI (95-96%) and dDDH (70%) recommended as the criterion for interspecies identity. The type strain is FJAT-44921T (=CCTCC AB 2016196T =DSM 104630T).
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Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, PR China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Xiao-Ying Wang
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, PR China
| | - Tong-Wei Chu
- Chiping Agricultural Bureau, Chiping, 252100, PR China
| | - Bo Liu
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China.
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Zheng X, Liu G, Wang Z, Wang J, Zhang H, Liu B. Bacillus dafuensis sp. Nov., Isolated from a Forest Soil in China. Curr Microbiol 2020; 77:2049-2055. [PMID: 32382951 DOI: 10.1007/s00284-020-02014-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/24/2020] [Indexed: 11/29/2022]
Abstract
A Gram-staining-positive, motile, rod-shaped, aerobic bacterial strain FJAT-25496 T was isolated from a forest soil sample collected from Dafu County, Chengdu City, Sichuan Province, China. Strain FJAT-25496 T grew at 15-50 °C (optimum 35 °C), pH 6.0-10.0 (optimum 8.0), and NaCl tolerance of 0-4.0% (w/v) (optimum 0%). The strain contained iso-C15:0 and anteiso-C15:0 as the predominant cellular fatty acids as well as MK-7 as the only menaquinone. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidyl glycerol (PG). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FJAT-25496 T was a member of the genus Bacillus, and most closely related to Bacillus solani FJAT-18043 T (97.8%), Bacillus praedii FJAT-25547 T (97.8%), Bacillus depressus BZ1T (97.7%), Bacillus oceanisediminis H2T (97.7%), and Bacillus ciccensis 5L6T (97.6%). Based on complete genome comparisons between strain FJAT-25496 T and the type strains of its closely related species, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 73.4-76.3% and 21.7-23.2%, respectively. The genomic DNA G + C content of strain FJAT-25496 T was 36.9%. On the basis of phenotypic, phylogenetic, chemotaxonomic, and genomic features, strain FJAT-25496 T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus dafuensis sp. nov. is proposed. The type strain is FJAT-25496 T (= CCTCC AB 2019182 T = KCTC 43120 T).
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Affiliation(s)
- Xuefang Zheng
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | | | - Ziran Wang
- Dean of Department of Biochemistry and Biotechnology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jieping Wang
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | - Haifeng Zhang
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | - Bo Liu
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China.
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Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406-438. [PMID: 31617837 DOI: 10.1099/ijsem.0.003775] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.
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Affiliation(s)
- Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
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Rao MPN, Dong ZY, Zhang H, Niu XK, Zhang K, Fang BZ, Xiao M, Kang YQ, Li WJ. Bacillus antri sp. nov., isolated from cave soil. Int J Syst Evol Microbiol 2019; 69:2335-2339. [DOI: 10.1099/ijsem.0.003473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Manik Prabhu Narsing Rao
- 1State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhou-Yan Dong
- 1State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Hui Zhang
- 2Kunming Medical University Haiyuan College, Kunming, 650106, PR China
| | - Xue-Ke Niu
- 3Key Laboratory of Medical Microbiology and Parasitology & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Talent Base of Microbiology and Human health of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, PR China
| | - Kun Zhang
- 4School of Eco-environment Technology, Guangdong Industry Polytechnic, Guangzhou 510300, PR China
| | - Bao-Zhu Fang
- 1State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Min Xiao
- 1State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ying-Qian Kang
- 3Key Laboratory of Medical Microbiology and Parasitology & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Talent Base of Microbiology and Human health of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, PR China
| | - Wen-Jun Li
- 1State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- 5Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
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Liu B, Liu GH, Wang XY, Wang JP, Chen Z, Chen MC, Zhang HF, Singonca C. Bacillus urbisdiaboli sp. nov., isolated from soil sampled in Xinjiang. Int J Syst Evol Microbiol 2019; 69:1591-1596. [DOI: 10.1099/ijsem.0.003363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo Liu
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Xiao-Ying Wang
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jie-Ping Wang
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Zheng Chen
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Mei-Chun Chen
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Hai-Feng Zhang
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Singonca
- 2Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A D-53115 Bonn, Germany
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Shafi S, Kamili AN, Shah MA, Bandh SA, Dar R. Dynamics of bacterial class Bacilli in the deepest valley lake of Kashmir-the Manasbal Lake. Microb Pathog 2017; 104:78-83. [DOI: 10.1016/j.micpath.2017.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/07/2017] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
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13
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Bacillus nitroreducens sp. nov., a humus-reducing bacterium isolated from a compost. Arch Microbiol 2016; 198:347-52. [DOI: 10.1007/s00203-016-1193-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/28/2015] [Accepted: 01/14/2016] [Indexed: 10/22/2022]
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Liu B, Liu GH, Cetin S, Schumann P, Pan ZZ, Chen QQ. Bacillus gobiensis sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2015; 66:379-384. [PMID: 26530456 DOI: 10.1099/ijsem.0.000729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium designated FJAT-4402T, was isolated from the weed rhizosphere soil of the Gobi desert in the Xinjiang Autonomous Region in the north-west of China. Isolate FJAT-4402T grew at 15-40 °C (optimum 30 °C), pH 5-10 (optimum pH 7) and in 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses, based on 16S rRNA gene sequences, showed that isolate FJAT-4402T was a member of the genus Bacillus and was most closely related to Bacillus licheniformis DSM 13T (96.2 %). The isolate showed 33.3 % DNA-DNA relatedness to the closest reference isolate, B. licheniformis DSM 13T. The diagnostic diamino acid of the peptidoglycan of isolate FJAT-4402T was meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (28.5 %), iso-C15 : 0 (20.1 %), anteiso-C17 : 0 (14.3 %), iso-C16 : 0 (9.6 %), C16 : 0 (8.4 %), iso-C17 : 0 (6.2 %) and iso-C14 : 0 (4.7 %) and the DNA G+C content was 42.0 mol%. The phenotypic, chemotaxonomic and genotypic properties indicated that strain FJAT-4402T represents a novel species within the genus Bacillus, for which the name Bacillus gobiensis sp. nov. is proposed. The type strain is FJAT-4402T ( = DSM 29500T = CGMCC 1.12902T).
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Affiliation(s)
- Bo Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Sengonca Cetin
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A, D-53115 Bonn, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Zhi-Zhen Pan
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Qian-Qian Chen
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
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Liu B, Liu GH, Sengonca C, Schumann P, Ge CB, Wang JP, Cui WD, Lin NQ. Bacillus solani sp. nov., isolated from rhizosphere soil of a potato field. Int J Syst Evol Microbiol 2015; 65:4066-4071. [DOI: 10.1099/ijsem.0.000539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, endospore-forming bacterium, designated strain FJAT-18043T, was isolated from a soil sample of a potato field in Xinjiang Autonomous Region, China. Cells were rods that were catalase-positive and motile by peritrichous flagella. The strain grew at 20–45 °C (optimum 35 °C), at pH 6.0–10.0 (optimum pH 9) and with 0–10 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FJAT-18043T belonged to the genus Bacillus and exhibited similarities of 97.7, 97.6, 97.2 and 97.2 % with Bacillus eiseniae A1-2T, Bacillus horneckiae DSM 23495T, Bacillus gottheilii WCC 4585T and Bacillus purgationiresistens DS22T, respectively. DNA–DNA relatedness between strain FJAT-18043T and B. eiseniae A1-2 T was lower than 70 % (36.1 %). The menaquinone was identified as MK-7 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids detected were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0, C16 : 0 and iso-C14 : 0. The DNA G+C content was 48.8 mol%. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate FJAT-18043T represents a novel species within the genus Bacillus, for which the name Bacillus solani sp. nov. is proposed. The type strain is FJAT-18043T ( = DSM 29501T = CCTCC AB 2014277T).
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Affiliation(s)
- Bo Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Sengonca
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A, D-53115 Bonn, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Ci-Bin Ge
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jie-Ping Wang
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Wei-Dong Cui
- Institute of Applied for Microorganism of Xinjiang Academy of Agricultural Sciences, PR China
| | - Nai-Quan Lin
- Institute of Plant Protection, Fujian Agriculture and Forestry University, PR China
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Vishnuvardhan Reddy S, Thirumala M, Farooq M. Bacillus caseinilyticus sp. nov., an alkali- and thermotolerant bacterium isolated from a soda lake. Int J Syst Evol Microbiol 2015; 65:2441-2446. [DOI: 10.1099/ijs.0.000275] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, rod-shaped, motile, endospore-forming and proteolytic bacterial strain, SPT, was isolated from Lonar soda lake, in India. On the basis of 16S rRNA gene sequence analysis it was identified as belonging to the class Firmibacteria and was most closely related to Bacillus cellulosilyticus DSM 2522T (96.7 %) and other members of the genus Bacillus ( < 95.9 %). Strain SPT was catalase- and oxidase-positive. The cell-wall peptidoglycan of strain SPT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three phospholipids, two aminolipids and two unknown lipids. The predominant isoprenoid quinone was MK-7. Anteiso-C15 : 0 (26.8 %) was the predominant fatty acid and significant proportions (>5 %) of iso-C15 : 0 (20.9 %), C16 : 1ω7c alcohol (6.3 %), iso-C16 : 0 (6.3 %) and anteiso-C17 : 0 (5.3 %) were also detected in strain SPT. The DNA G+C content of strain SPT was 38.9 mol%. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain SPT from all other members of the genus Bacillus. Strain SPT represents a novel member of the genus Bacillus, for which the name Bacillus
caseinilyticus sp. nov. is proposed. The type strain is SPT ( = MCC 2612T = JCM 30246T).
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Affiliation(s)
- Sultanpuram Vishnuvardhan Reddy
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda- 508254, Telangana, India
| | - Mothe Thirumala
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda- 508254, Telangana, India
| | - Mohammed Farooq
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda- 508254, Telangana, India
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Zhang WY, Hu J, Zhang XQ, Zhu XF, Wu M. Bacillus salitolerans sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China. Antonie van Leeuwenhoek 2015; 108:443-51. [DOI: 10.1007/s10482-015-0497-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
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Bacillus dabaoshanensis sp. nov., a Cr(VI)-tolerant bacterium isolated from heavy-metal-contaminated soil. Arch Microbiol 2015; 197:513-20. [PMID: 25603996 DOI: 10.1007/s00203-015-1082-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 01/03/2015] [Accepted: 01/10/2015] [Indexed: 10/24/2022]
Abstract
A Cr(VI)-tolerant, Gram-staining-positive, rod-shaped, endospore-forming and facultative anaerobic bacterium, designated as GSS04(T), was isolated from a heavy-metal-contaminated soil. Strain GSS04(T) was Cr(VI)-tolerant with a minimum inhibitory concentration of 600 mg l(-1) and was capable of reducing Cr(VI) under both aerobic and anaerobic conditions. Growth occurred with presence of 0-3 % (w/v) NaCl (optimum 1 %), at pH 5.5-10.0 (optimum pH 7.0) and 15-50 °C (optimum 30-37 °C). The main respiratory quinone was MK-7 and the major fatty acids were anteiso-C15:0 and iso-C15:0. The DNA G+C content was 41.1 mol%. The predominant polar lipid was diphosphatidylglycerol. Based on 16S rRNA gene sequence similarity, the closest phylogenetic relative was Bacillus shackletonii DSM 18868(T) (97.6 %). The DNA-DNA hybridization between GSS04(T) and its closest relatives revealed low relatedness (<70 %). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain GSS04(T) represents a novel species of the genus Bacillus, for which the name Bacillus dabaoshanensis sp. nov. is proposed. The type strain is GSS04(T) (=CCTCC AB 2013260(T) = KCTC 33191(T)).
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Bacillus daqingensis sp. nov., a halophilic, alkaliphilic bacterium isolated from saline-sodic soil in Daqing, China. J Microbiol 2014; 52:548-53. [PMID: 24879344 DOI: 10.1007/s12275-014-3376-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
Abstract
An alkaliphilic, moderately halophilic, bacterium, designated strain X10-1(T), was isolated from saline-alkaline soil in Daqing, Heilongjiang Province, China. Strain X10-1(T) was determined to be a Gram-positive aerobe with rod-shaped cells. The isolate was catalase-positive, oxidase-negative, non-motile, and capable of growth at salinities of 0-16% (w/v) NaCl (optimum, 3%). The pH range for growth was 7.5-11.0 (optimum, pH 10.0). The genomic DNA G+C content was 47.7 mol%. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C15:0, anteiso-C17:0, iso-C15:0, C16:0, and iso-C16:0. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that X10-1(T) is a member of the genus Bacillus, being most closely related to B. saliphilus DSM15402(T) (97.8% similarity) and B. agaradhaerens DSM 8721(T) (96.2%). DNA-DNA relatedness to the type strains of these species was less than 40%. On the basis of the phylogenetic, physiological, and biochemical data, strain X10-1(T) represents a novel species of the genus Bacillus, for which the name Bacillus daqingensis sp. nov. is proposed. The type strain is X10-1(T) (=NBRC 109404(T) = CGMCC 1.12295(T)).
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Zhu D, Tanabe SH, Xie C, Honda D, Sun J, Ai L. Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea. Int J Syst Evol Microbiol 2014; 64:1712-1717. [PMID: 24554634 DOI: 10.1099/ijs.0.058610-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An alkaliphilic and halotolerant Gram-stain-positive bacterium, which was isolated from sediment samples from the South China Sea, was subjected to a taxonomic study. The isolate, strain L1T, grew well at a wide range of temperatures and pH values, 10.0-45.0 °C and pH 6-11, with optima at 30 °C and pH 9.0, respectively. The growth of strain L1T occurred at total salt concentrations of 0-10% (w/v) with an optimum at 2% (w/v). Phylogenetic analysis based on 16S rRNA sequence comparison indicated that the isolate represented a member of the genus Bacillus. The strains most closely related to strain L1T were Bacillus nanhaiisediminis JCM 16507T, Bacillus halodurans DSM 497T and Bacillus pseudofirmus DSM 8715T, with 16S rRNA similarities of 96.5%, 95.9% and 95.7%, respectively. DNA-DNA hybridization of strain L1T with the type strains of the most closely related species, B. nanhaiisediminis JCM 16507T, B. halodurans DSM 497T and B. pseudofirmus DSM 8715T, showed reassociation values of about 21.7%, 14.3% and 13.9%, respectively. The DNA G+C content of strain L1T was 40.76 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids of strain L1T were iso-C14 : 0 and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the phenotypic and phylogenetic characteristics, it is proposed that strain L1T (=JCM 18543T=DSM 26145T) should be classified as the type strain of Bacillus ligniniphilus sp. nov.
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Affiliation(s)
- Daochen Zhu
- School of Environmental Engineering, Jiangsu University, 301 Xuefu Road Zhenjiang 212013, PR China.,State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co. Ltd, Shanghai 200436, PR China
| | - Shoko-Hosoi Tanabe
- Department of Ecosystem Studies, School of Environmental Science, University of Shiga Prefecture, Hikone, Shiga, Japan
| | - Changxiao Xie
- School of Environmental Engineering, Jiangsu University, 301 Xuefu Road Zhenjiang 212013, PR China
| | - Daiske Honda
- Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1, Okamoto, Higashinada, Kobe, 658-8501, Japan
| | - Jianzhong Sun
- School of Environmental Engineering, Jiangsu University, 301 Xuefu Road Zhenjiang 212013, PR China
| | - Lianzhong Ai
- State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co. Ltd, Shanghai 200436, PR China
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Liu B, Liu GH, Hu GP, Cetin S, Lin NQ, Tang JY, Tang WQ, Lin YZ. Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin’s Terra-cotta warriors in China. Antonie van Leeuwenhoek 2013; 105:501-10. [DOI: 10.1007/s10482-013-0102-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 12/15/2013] [Indexed: 10/25/2022]
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An S, Couteau C, Luo F, Neveu J, DuBow MS. Bacterial diversity of surface sand samples from the Gobi and Taklamaken deserts. MICROBIAL ECOLOGY 2013; 66:850-60. [PMID: 23963222 DOI: 10.1007/s00248-013-0276-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 08/01/2013] [Indexed: 05/10/2023]
Abstract
Arid regions represent nearly 30 % of the Earth's terrestrial surface, but their microbial biodiversity is not yet well characterized. The surface sands of deserts, a subset of arid regions, are generally subjected to large temperature fluctuations plus high UV light exposure and are low in organic matter. We examined surface sand samples from the Taklamaken (China, three samples) and Gobi (Mongolia, two samples) deserts, using pyrosequencing of PCR-amplified 16S V1/V2 rDNA sequences from total extracted DNA in order to gain an assessment of the bacterial population diversity. In total, 4,088 OTUs (using ≥97 % sequence similarity levels), with Chao1 estimates varying from 1,172 to 2,425 OTUs per sample, were discernable. These could be grouped into 102 families belonging to 15 phyla, with OTUs belonging to the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria phyla being the most abundant. The bacterial population composition was statistically different among the samples, though members from 30 genera were found to be common among the five samples. An increase in phylotype numbers with increasing C/N ratio was noted, suggesting a possible role in the bacterial richness of these desert sand environments. Our results imply an unexpectedly large bacterial diversity residing in the harsh environment of these two Asian deserts, worthy of further investigation.
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Affiliation(s)
- Shu An
- Univ. Paris-Sud, Laboratoire de Génomique et Biodiversité Microbienne des Biofilms (LGBMB), Institut de Génétique et Microbiologie, CNRS UMR 8621, Bâtiment 409, 91405, Orsay, France
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Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013; 10:996-998. [PMID: 23955772 DOI: 10.1007/978-3-319-44409-3_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 07/15/2013] [Indexed: 05/20/2023]
Abstract
Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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Wang YQ, Yuan Y, Yu Z, Yang GQ, Zhou SG. Bacillus borbori sp. Nov., isolated from an electrochemically active biofilm. Curr Microbiol 2013; 67:718-24. [PMID: 23896693 DOI: 10.1007/s00284-013-0426-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/12/2013] [Indexed: 10/26/2022]
Abstract
A Gram-positive, facultative anaerobic, motile, endospore-forming rod strain, designated DX-4(T), was isolated from an electrochemically active biofilm. Growth occurred at 30-65 °C (optimum 55 °C), at pH 6.0-8.5 (optimum pH 7.0-7.5) and with <6 % (w/v) NaCl. Cells were catalase- and oxidase-positive. The main respiratory quinone was MK-7, the predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannoside, and unidentified aminophospholipid, the DNA G+C content was 38.6 mol% and the major fatty acids (>5 %) were iso-C15:0 (38.9 %), iso-C17:0 (30.5 %), iso-C16:0 (5.6 %), and anteiso-C17:0 (5.2 %). The phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain DX-4(T) is a member of the genus Bacillus. The results of phenotypic, chemotaxonomic, and genotypic analyses clearly indicated that strain DX-4(T) represents a novel species, for which the name Bacillus borbori sp. nov. is proposed. The type strain is DX-4(T) (= CCTCC AB2012196(T) = KCTC 33103(T)).
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Affiliation(s)
- Yue-Qiang Wang
- Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, 510650, People's Republic of China
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Han L, Yang G, Zhou X, Yang D, Hu P, Lu Q, Zhou S. Bacillus thermocopriae sp. nov., isolated from a compost. Int J Syst Evol Microbiol 2013; 63:3024-3029. [PMID: 23396718 DOI: 10.1099/ijs.0.046953-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-positive, facultatively anaerobic, motile, endospore-forming, rod-shaped strain, designated SgZ-7(T), was isolated from a windrow compost pile and was characterized by means of a polyphasic approach. Growth occurred with 0-3 % (w/v) NaCl (optimum 1 %), at pH 6.0-10.0 (optimum pH 7.2) and at 40-60 °C (optimum 50 °C). The main respiratory quinone was MK-7. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 46.6 mol%. The phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain SgZ-7(T) should be assigned to the genus Bacillus and was related most closely to Bacillus drentensis LMG 21831(T) (sequence similarity 97.2 %). The result of the DNA-DNA hybridization experiment revealed a low relatedness (27.2 %) between the isolate and B. drentensis LMG 21831(T). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain SgZ-7(T) represents a novel species, for which the name Bacillus thermocopriae sp. nov. is proposed. The type strain is SgZ-7(T) (= CCTCC AB 2012030(T) = KACC 16700(T)).
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Affiliation(s)
- Luchao Han
- Chemistry and Materials Institute, Sichuan Normal University, Chengdu 610068, PR China.,Guangdong Institute of Eco-Environmental and Soil Science, Guangzhou 510650, PR China
| | - Guiqin Yang
- Guangdong Institute of Eco-Environmental and Soil Science, Guangzhou 510650, PR China
| | - Xuemei Zhou
- 101 Research Institute of the Ministry of Civil Affairs, Beijing 100070, PR China
| | - Dehui Yang
- 101 Research Institute of the Ministry of Civil Affairs, Beijing 100070, PR China
| | - Pei Hu
- Chemistry and Materials Institute, Sichuan Normal University, Chengdu 610068, PR China
| | - Qin Lu
- Guangdong Institute of Eco-Environmental and Soil Science, Guangzhou 510650, PR China
| | - Shungui Zhou
- Guangdong Institute of Eco-Environmental and Soil Science, Guangzhou 510650, PR China
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Abstract
Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin's Terracotta Warriors in Xi'an City, People's Republic of China. The isolate showed a close relationship to the Bacillus cereus group. The draft genome sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of 5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and a G+C value of 36.36%.
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2012. [DOI: 10.1099/ijs.0.048033-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [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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