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Yadav A, Teware R, Bhatt A, Bhavsar Y, Maurya A, Thorat V, Vemuluri VR, Kirdat K. Ureibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. Nov. Arch Microbiol 2024; 206:242. [PMID: 38698177 DOI: 10.1007/s00203-024-03970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/19/2024] [Indexed: 05/05/2024]
Abstract
A Gram-stain-positive aerobic, rod-shaped, spore-producing bacterium forming colonies with convex elevation and a smooth, intact margin was isolated from a freshwater sample collected from a well situated in an agricultural field. The 16S rRNA gene sequence of the isolated strain BA0131T showed the highest sequence similarity to Lysinibacillus yapensis ylb-03T (99.25%) followed by Ureibacillus chungkukjangi 2RL3-2T (98.91%) and U. sinduriensis BLB-1T (98.65%). The strain BA0131T was oxidase and catalase positive and urease negative. It also tested positive for esculin hydrolysis and reduction of potassium nitrate, unlike its phylogenetically closest relatives. The predominant fatty acids in strain BA0131T included were anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 and the major polar lipids comprised were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The respiratory quinones identified in strain BA0131T were MK8 (H2) (major) and MK8 (minor). The strain BA0131T shared the lowest dDDH values with L. yapensis ylb-03T (21%) followed by U. chungkukjangi 2RL3-2T (24.2%) and U. sinduriensis BLB-1T (26.4%) suggesting a closer genetic relationship U. sinduriensis BLB-1T. The ANI percentage supported the close relatedness with U. sinduriensis BLB-1T (83.61%) followed by U. chungkukjangi 2RL3-2T (82.03%) and U. yapensis ylb-03T (79.57%). The core genome-based phylogeny constructed using over 13,704 amino acid positions and 92 core genes revealed the distinct phylogenetic position of strain BA0131T among the genus Ureibacillus. The distinct physiological, biochemical characteristics and genotypic relatedness data indicate the strain BA0131T represents a novel species of the genus Ureibacillus for which the name Ureibacillus aquaedulcis sp. nov. (Type strain, BA0131T = MCC 5284 = JCM 36475) is proposed. Additionally, based on extensive genomic and phylogenetic analyses, we propose reclassification of two species, L. yapensis and L. antri, as U. yapensis comb. nov. (Type strain, ylb-03T = JCM 32871T = MCCC 1A12698T) and U. antri (Type strain, SYSU K30002T = CGMCC 1.13504T = KCTC 33955T).
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Affiliation(s)
- Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India.
| | - Ruchi Teware
- Department of Microbiology, Fergusson College, Shivajinagar, Pune, 411 004, India
| | - Agrima Bhatt
- Department of Biosciences and Technology, School of Science and Environmental Studies, Dr. Vishwanath Karad MIT World Peace University, Pune, 411 038, India
| | - Yash Bhavsar
- Department of Microbiology, Fergusson College, Shivajinagar, Pune, 411 004, India
| | - Akanksha Maurya
- Khwaja Moinuddin Chishti Language University, Sitapur Hardoi Road, Lucknow, 226 013, India
| | - Vipool Thorat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India
| | - Venkata Ramana Vemuluri
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, 160 003, India
| | - Kiran Kirdat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India.
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Liu XD, Zhao JY, Li LL, Li JY, Yang PW, Liang SG, Feng LY, Shi ZF, Ding ZG, Li MG, Tang SK. Solibacillus ferritrahens sp. nov., a novel siderophore-producing bacterium isolated from Wumeng Mountain National Nature Reserve in Yunnan Province. Antonie Van Leeuwenhoek 2024; 117:48. [PMID: 38429402 DOI: 10.1007/s10482-024-01942-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
A gram-stain-positive, aerobic, rod-shaped bacterial strain capable of producing siderophores, named YIM B08730T, was isolated from a soil sample collected from Wumeng Mountain National Nature Reserve, Zhaotong City, Yunnan Province. Growth occurred at 10-45 °C (optimum, 35-40 ℃), pH 7.0-9.0 (optimum, 7.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 0-1 %, w/v). A comparative analysis of the 16S rRNA gene sequence (1558 bp) of strain YIM B08730T showed the highest similarity to Solibacillus isronensis JCM 13838T (96.2 %), followed by Solibacillus silvestris DSM 12223T (96.0 %) and Solibacillus kalamii ISSFR-015T (95.4 %). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and one unidentified lipid. The main respiratory quinone of strain YIM B08730T was menaquinone 7 (MK-7). The major fatty acids were iso-C15:0 and C16:1ω7c alcohol. The digital DNA-DNA hybridization and average nucleotide identity values between strain YIM B08730T and the reference strain S. isronensis JCM 13838T were 24.8 % and 81.2 %, respectively. The G + C content of the genomic DNA was 37.1 mol%. The genome of the novel strain contained genes associated with the production of siderophores, and it also revealed other functional gene clusters involved in plant growth promotion and soil bioremediation. Based on these phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM B08730T is considered to be a novel species of the genus Solibacillus, for which the name Solibacillus ferritrahens sp. nov. is proposed. The type strain is YIM B08730T (= NBRC 116268T = CGMCC 1.60169T).
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Affiliation(s)
- Xiao-Di Liu
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jiang-Yuan Zhao
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Le-Le Li
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China.
- Department of Medicine, Qujing Vocational and Technical College, Qujing, 655000, People's Republic of China.
| | - Jian-Yu Li
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Pei-Wen Yang
- Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People's Republic of China
| | - Song-Guo Liang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Lu-Yao Feng
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
- Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People's Republic of China
| | - Zhu-Feng Shi
- Institute of Agricultural Environmental Resources, Yunnan Academy of Agricultural Sciences, Kunming, 650205, People's Republic of China
| | - Zhang-Gui Ding
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ming-Gang Li
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China.
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Jo JH, Lee SY, Rhee MS, Lee KH, Chun SY, Im WT. Solibacillus palustris sp. nov., isolated from wetland soil of ecology park. Int J Syst Evol Microbiol 2024; 74. [PMID: 38323635 DOI: 10.1099/ijsem.0.006065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
A Gram-staining-positive, motile, aerobic and rod-shaped bacterium, designated strain MA9T was isolated from wetland soil of ecology park, in Seoul, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using the polyphasic approach. Strain MA9T grew at 10-37 °C and at pH 6.0-9.5 on TSB. Menaquinone MK-7 was the predominant respiratory quinone and iso-C15 : 0, iso-C16 : 0 and C16 : 1 ω7c alcohol were the major fatty acids. The main polar lipids were phosphatidylethanolamine (PE), phosphatidylserine (PS), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The peptidoglycan type of the cell wall was A4α l-Lys-d-Glu. Based on 16S rRNA gene sequencing, strain MA9T clustered with species of the genus Solibacillus and appeared closely related to S. silvestris DSM 12223T (97.8 % sequence similarity), S. cecembensis DSM 21993T (97.6 %), S. isronensis DSM 21046T (97.6 %) and S. kalamii DSM 101595T (96.6 %). The G+C content of the genomic DNA was 37.0 mol%. Digital DNA-DNA hybridization between strain MA9T and type strains of S. silvestris, S. isronensis, S. cecembensis and S. kalamii resulted in values below 70 %. Strain MA9T could be differentiated genotypically and phenotypically from the recognized species of the genus Solibacillus. The isolate therefore represents a novel species, for which the name Solibacillus palustris sp. nov. is proposed, with the type strain MA9T (=KACC 22212T = LMG 32188T).
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Affiliation(s)
- Jung-Hun Jo
- Major in Applied Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do 17579, Republic of Korea
- AceEMzyme Co. Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Gyeonggi-do 17579, Republic of Korea
| | - Soon-Youl Lee
- Major in Applied Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do 17579, Republic of Korea
| | - Moon-Soo Rhee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Kang-Hyun Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Se-Yoon Chun
- Major in Applied Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do 17579, Republic of Korea
- AceEMzyme Co. Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Gyeonggi-do 17579, Republic of Korea
| | - Wan-Taek Im
- Major in Applied Biotechnology, Hankyong National University, Anseong-si, Gyeonggi-do 17579, Republic of Korea
- AceEMzyme Co. Ltd., Academic Industry Cooperation, 327 Chungang-no Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, 327 Chungang-no Anseong-si, Gyeonggi-do 17579, Republic of Korea
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Liang Y, Shi W, Wu LH, Zhang XJ, Chai LJ, Liu GQ, Zheng L, Wang ST, Zhang SY, Chen FW, Shen CH, Xu ZH, Lu ZM. Solibacillus daqui sp. nov., isolated from high-temperature Daqu. Int J Syst Evol Microbiol 2023; 73. [PMID: 37916708 DOI: 10.1099/ijsem.0.006109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterial strain, designated ZS111008T, was isolated from high-temperature Daqu, a starter for production of Chinese Jiang-flavour Baijiu, and was characterized by polyphasic taxonomy. This novel isolate grew in the presence of 0-5 % (w/v) NaCl, at pH 6.0-9.0 and 25-45 °C; optimum growth was observed with 1 % (w/v) NaCl, at pH 8.0 and 30 °C. A comparative analysis of the 16S rRNA gene sequence (1461 bp) of strain ZS111008T showed highest similarity to Solibacillus silvestris DSM12223T (96.7%), followed by Solibacillus cecembensis PN5T (96.6%) and Solibacillus isronensis AMCK01000046 (96.5%). The DNA G+C content of strain ZS111008T was 37.21 mol%. The respiratory quinone was identified as menaquinone-7 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and one unknown phospholipid. Lys was detected as the diagnostic diamino acid in the cell wall. Based on morphological characteristics, chemotaxonomic characteristics and physiological properties, strain ZS111008T represents a novel species of the genus Solibacillus, for which the name Solibacillus daqui sp. nov. is proposed. The type strain for this proposed species is ZS111008T (=CGMCC 1.19455T=JCM 35214T).
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Affiliation(s)
- Yuan Liang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
| | - Wei Shi
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
| | - Lin-Huan Wu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiao-Juan Zhang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
| | - Li-Juan Chai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
| | - Guang-Qian Liu
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Lei Zheng
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Song-Tao Wang
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Su-Yi Zhang
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Fu-Wei Chen
- Guizhou Zhongjian Wine Industry Group Co. LTD, Zunyi 564500, PR China
| | - Cai-Hong Shen
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Zheng-Hong Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Zhen-Ming Lu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, PR China
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
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Li N, Han Z, Guo N, Zhou Z, Liu Y, Tang Q. Microplastics spatiotemporal distribution and plastic-degrading bacteria identification in the sanitary and non-sanitary municipal solid waste landfills. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129452. [PMID: 35777149 DOI: 10.1016/j.jhazmat.2022.129452] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
The municipal solid waste landfill (MSWL) is an important source of microplastics (MPs) and a huge bioreactor for plastic-degrading microorganisms (PDM). However, the spatiotemporal distribution and degradation mechanisms of MPs in MSWLs are unclear. Therefore, they were studied using the samples drilled in a sanitary landfill (SL) and an non-sanitary landfill (NSL). The results showed that there were a lot of polyethylene (PE), polypropylene (PP), polystyrene (PS), polyurethane (PU), Polyamide (PA), Polyethylene terephthalate (PET) and Polyvinyl chloride (PVC) in the landfill, and their abundance ranged from 0 to 80 items/g. The MPs surface gradually faded, became rough and even yielded cracks and holes with the landfill depth and age increase. The tiny-size MPs (< 100 µm) were the most abundant and their amount significantly increased from 28.14% to 49.13% in SL and from 24.54% to 59.51% in NSL, respectively, while large-size MPs were significantly reduced from the top to the bottom. Lysinibacillus (0.21%~67.87%) and Bacillus (0.10%~67.00%) were the dominate PDMs in SL and Candidatus_Caldatribacterium (5.06%~73.48%) was the dominate in NSL. The PE degradation was closely related to Candidatus_Cloacimonas (r = 0.688*) and Candidatus_Caldatribacterium (r = 0.680*); PS and PA were closely related to Candidatus_Contubernalis (r = 0.595*~0.705*) and PVC was closely related to Candidatus_Caldatribacterium (r = 0.547*). In addition to physical and chemical effects, biological effects can also promote the MPs formation in MSWLs.
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Affiliation(s)
- Naying Li
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection (Chengdu University of Technology), Chengdu 610059, China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution (Chengdu University of Technology), Chengdu 610059, China; College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Zhiyong Han
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection (Chengdu University of Technology), Chengdu 610059, China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution (Chengdu University of Technology), Chengdu 610059, China; College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China.
| | - Nanfei Guo
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection (Chengdu University of Technology), Chengdu 610059, China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution (Chengdu University of Technology), Chengdu 610059, China; College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Zhiqiang Zhou
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection (Chengdu University of Technology), Chengdu 610059, China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution (Chengdu University of Technology), Chengdu 610059, China; College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Ying Liu
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection (Chengdu University of Technology), Chengdu 610059, China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution (Chengdu University of Technology), Chengdu 610059, China; College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Qianggang Tang
- Chengdu XingRong Environmental Technology Co., Ltd, Chengdu 610108, China
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Chavez IN, Brown TM, Assié A, Bryant AS, Samuel BS, Hallem EA. Skin-penetrating nematodes exhibit life-stage-specific interactions with host-associated and environmental bacteria. BMC Biol 2021; 19:221. [PMID: 34620172 PMCID: PMC8499433 DOI: 10.1186/s12915-021-01153-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Skin-penetrating nematodes of the genus Strongyloides infect over 600 million people, posing a major global health burden. Their life cycle includes both a parasitic and free-living generation. During the parasitic generation, infective third-stage larvae (iL3s) actively engage in host seeking. During the free-living generation, the nematodes develop and reproduce on host feces. At different points during their life cycle, Strongyloides species encounter a wide variety of host-associated and environmental bacteria. However, the microbiome associated with Strongyloides species, and the behavioral and physiological interactions between Strongyloides species and bacteria, remain unclear. Results We first investigated the microbiome of the human parasite Strongyloides stercoralis using 16S-based amplicon sequencing. We found that S. stercoralis free-living adults have an associated microbiome consisting of specific fecal bacteria. We then investigated the behavioral responses of S. stercoralis and the closely related rat parasite Strongyloides ratti to an ecologically diverse panel of bacteria. We found that S. stercoralis and S. ratti showed similar responses to bacteria. The responses of both nematodes to bacteria varied dramatically across life stages: free-living adults were strongly attracted to most of the bacteria tested, while iL3s were attracted specifically to a narrow range of environmental bacteria. The behavioral responses to bacteria were dynamic, consisting of distinct short- and long-term behaviors. Finally, a comparison of the growth and reproduction of S. stercoralis free-living adults on different bacteria revealed that the bacterium Proteus mirabilis inhibits S. stercoralis egg hatching, and thereby greatly decreases parasite viability. Conclusions Skin-penetrating nematodes encounter bacteria from various ecological niches throughout their life cycle. Our results demonstrate that bacteria function as key chemosensory cues for directing parasite movement in a life-stage-specific manner. Some bacterial genera may form essential associations with the nematodes, while others are detrimental and serve as a potential source of novel nematicides. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01153-7.
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Affiliation(s)
- Ivan N Chavez
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Taylor M Brown
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Astra S Bryant
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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Salam LB, Obayori OS. Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment. J Genet Eng Biotechnol 2020; 18:70. [PMID: 33175233 PMCID: PMC7658278 DOI: 10.1186/s43141-020-00089-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/02/2020] [Indexed: 12/02/2022]
Abstract
Background Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD). Results Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected. Conclusion This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-020-00089-9.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology unit, Summit University, Offa, Kwara, Nigeria.
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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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Gupta RS, Patel S. Robust Demarcation of the Family Caryophanaceae ( Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures. Front Microbiol 2020; 10:2821. [PMID: 32010063 PMCID: PMC6971209 DOI: 10.3389/fmicb.2019.02821] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
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Draft Genome Sequence of Solibacillus kalamii, Isolated from an Air Filter Aboard the International Space Station. GENOME ANNOUNCEMENTS 2017; 5:5/35/e00696-17. [PMID: 28860236 PMCID: PMC5578834 DOI: 10.1128/genomea.00696-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report here the draft genome of Solibacillus kalamii ISSFR-015, isolated from a high-energy particulate arrestance filter aboard the International Space Station. The draft genome sequence of this strain contains 3,809,180 bp with an estimated G+C content of 38.61%.
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Igalavithana AD, Park J, Ryu C, Lee YH, Hashimoto Y, Huang L, Kwon EE, Ok YS, Lee SS. Slow pyrolyzed biochars from crop residues for soil metal(loid) immobilization and microbial community abundance in contaminated agricultural soils. CHEMOSPHERE 2017; 177:157-166. [PMID: 28288424 DOI: 10.1016/j.chemosphere.2017.02.112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 06/06/2023]
Abstract
This study evaluated the feasibility of using biochars produced from three types of crop residues for immobilizing Pb and As and their effects on the abundance of microbial community in contaminated lowland paddy (P-soil) and upland (U-soil) agricultural soils. Biochars were produced from umbrella tree [Maesopsis eminii] wood bark [WB], cocopeat [CP], and palm kernel shell [PKS] at 500 °C by slow pyrolysis at a heating rate of 10 °C min-1. Soils were incubated with 5% (w w-1) biochars at 25 °C and 70% water holding capacity for 45 d. The biochar effects on metal immobilization were evaluated by sequential extraction of the treated soil, and the microbial community was determined by microbial fatty acid profiles and dehydrogenase activity. The addition of WB caused the largest decrease in Pb in the exchangeable fraction (P-soil: 77.7%, U-soil: 91.5%), followed by CP (P-soil: 67.1%, U-soil: 81.1%) and PKS (P-soil: 9.1%, U-soil: 20.0%) compared to that by the control. In contrast, the additions of WB and CP increased the exchangeable As in U-soil by 84.6% and 14.8%, respectively. Alkalinity and high phosphorous content of biochars might be attributed to the Pb immobilization and As mobilization, respectively. The silicon content in biochars is also an influencing factor in increasing the As mobility. However, no considerable effects of biochars on the microbial community abundance and dehydrogenase activity were found in both soils.
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Affiliation(s)
- Avanthi Deshani Igalavithana
- Korea Biochar Research Center & School of Natural Resources and Environmental Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jinje Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Changkook Ryu
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Young Han Lee
- Division of Plant Environmental Research, Gyeongsangnam-do Agricultural Research & Extension Services, Jinju 52773, Republic of Korea
| | - Yohey Hashimoto
- Department of Bioapplication and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eilhann E Kwon
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea
| | - Yong Sik Ok
- Korea Biochar Research Center & School of Natural Resources and Environmental Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
| | - Sang Soo Lee
- Korea Biochar Research Center & School of Natural Resources and Environmental Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
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Checinska Sielaff A, Kumar RM, Pal D, Mayilraj S, Venkateswaran K. Solibacillus kalamii sp. nov., isolated from a high-efficiency particulate arrestance filter system used in the International Space Station. Int J Syst Evol Microbiol 2017; 67:896-901. [DOI: 10.1099/ijsem.0.001706] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Rajendran Mathan Kumar
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Deepika Pal
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
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