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Li JY, Liu YF, Zhou L, Gang HZ, Liu JF, Sun GZ, Wang WD, Yang SZ, Mu BZ. A new biosurfactant-producing strain, Fictibacillus nanhaiensis ME46, isolated from an oil field in China. ENVIRONMENTAL TECHNOLOGY 2024; 45:4089-4095. [PMID: 37647352 DOI: 10.1080/09593330.2023.2240947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/16/2023] [Indexed: 09/01/2023]
Abstract
The genus Fictibacillus contains twelve species significant in the synthesis of cellulose-degrading enzymes and phenylalanine dehydrogenase, isolated mainly from marine sedimentary environments. Here, we report a new biosurfactant-producing strain, Fictibacillus nanhaiensis ME46, isolated from Daqing oil field in China. The biosurfactant extracted from Strain ME46 was determined as surfactin, one of the representative families of lipopeptide biosurfactants. The yield of the surfactin produced by strain ME46 was 0.62 g·L-1 as determined by high-performance liquid chromatography, and the critical micelle concentration (CMC) of the surfactin was estimated to be about 68 mg·L-1 and the surface tension at CMC was 35.1 mN·m-1. This study extended our knowledge about the role of the species Fictibacillus nanhaiensis in the ecosystem of natural environments such as the oil field.
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Affiliation(s)
- Jia-Yi Li
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Hong-Ze Gang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- Daqing Huali Biotechnology Co., Ltd, Daqing, People's Republic of China
| | - Gang-Zheng Sun
- Research Institute of Petroleum Engineering and Technology, Shengli Oilfield Company, Sinopec, Dongying, People's Republic of China
| | - Wei-Dong Wang
- Research Institute of Petroleum Engineering and Technology, Shengli Oilfield Company, Sinopec, Dongying, People's Republic of China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- Engineering Research Center of Microbial Enhanced Oil Recovery (MEOR), East China University of Science and Technology, Shanghai, People's Republic of China
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Pellegrinetti TA, de Cássia Mesquita da Cunha I, Chaves MGD, Freitas ASD, Passos GS, Silva AVRD, Cotta SR, Tsai SM, Mendes LW. Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths. Braz J Microbiol 2024; 55:1817-1828. [PMID: 38358421 PMCID: PMC11153436 DOI: 10.1007/s42770-024-01268-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.
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Affiliation(s)
- Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
- Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Piracicaba, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Anderson Santos de Freitas
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Gabriel Schimmelpfeng Passos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Simone Raposo Cotta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil.
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Zhao Y, Sun T, Li Y, Yang Z, Chen J, Wang J, Yu X, Tang X, Xiao H. The host sex contributes to the endophytic bacterial community in Sargassum thunbergii and their receptacles. Front Microbiol 2024; 15:1334918. [PMID: 38559345 PMCID: PMC10978810 DOI: 10.3389/fmicb.2024.1334918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/14/2024] [Indexed: 04/04/2024] Open
Abstract
Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.
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Affiliation(s)
- Yayun Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Tao Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Qingdao Branch CCCC Water Transportation Consultants Co.,LTD, Qingdao, China
| | - Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Shandong Marine Forecast and Hazard Mitigation Service, Qingdao, China
| | - Zhibo Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinlong Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
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Zhao Z, Oury BM, Xia L, Qin Z, Pan X, Qian J, Luo F, Wu Y, Liu L, Wang W. The ecological response and distribution characteristics of microorganisms and polycyclic aromatic hydrocarbons in a retired coal gas plant post-thermal remediation site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159314. [PMID: 36220477 DOI: 10.1016/j.scitotenv.2022.159314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/16/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Thermal remediation is one of the most common approaches of removing organic pollutants in the retired contamination sites. However, little is known about the performance of bacterial community characteristics after in situ thermal remediation. In this study, the ecological response and spatial distributional characteristics of microorganisms and polycyclic aromatic hydrocarbons (PAHs) were investigated using a high throughput sequencing method in a retired coal gas plant site after in situ thermal remediation in Nanjing, China. Combination of Venn, clustering-correlation heatmap and two - factor correlation network analysis revealed that, microbial communities were obviously affected and classified by soil depths, temperature, and contamination level, respectively. The common and endemic microorganisms of each group were identified. The relative abundances of Thermaerobacter, Calditerricola, Brevibacillus, Ralstonia and Rhodococcus (aerobic bacteria) gradually declined with the increase of soil depth, while those of Bacillus, Fictibacillus, Paenibacillus, Rheinheimera presented opposite tendency. Some thermophilic degradation bacteria of PAHs, including Thermaerobacter, Calditerricola, Bacillus, Rhodococcus, unclassified_p__Firmicutes, Arthrobacter and Deinococcus, were identified and increased in the abundance at heavily polluted sites. Additionally, Proteobacteria, Bacteroidota, Deinococcota, Chloroflexi, Acidobacteriota, and Actinobacteriota showed negative response to the increase of soil depth, temperature and pollution level, while Firmicutes presented a positive response. This implied that Firmicutes has better stress resistance and adaptability to thermal remediation condition. The key environmental factors affecting microorganism composition and distribution were Temperature, Total nitrogen, Oxidation-Reduction Potential, Organic matters, and PAHs concentrations, which explains the dominant driving mechanism of soil depth, temperature, and contamination level on microbial characteristics in thermal remediation site. Our study could contribute to a better understanding of the resilience and adaptation mechanisms of microbial community at the contaminated site after the in situ thermal remediation.
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Affiliation(s)
- Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.
| | - Barry Mody Oury
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing 210016, China.
| | - Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xiangyu Pan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jichan Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Fangzhou Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yong Wu
- Nanjing Qingzhan Environmental Engineering CO. Ltd, China
| | - Luqi Liu
- SUMEC Complete Equipment & Engineering CO. LTD, Nanjing 210018, China
| | - Wei Wang
- SUMEC Complete Equipment & Engineering CO. LTD, Nanjing 210018, China
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Sood U, Gupta V, Kumar R, Lal S, Fawcett D, Rattan S, Poinern GEJ, Lal R. Chicken Gut Microbiome and Human Health: Past Scenarios, Current Perspectives, and Futuristic Applications. Indian J Microbiol 2020; 60:2-11. [PMID: 32089569 PMCID: PMC7000578 DOI: 10.1007/s12088-019-00785-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022] Open
Abstract
Sustainable poultry practices are needed to maintain an adequate supply of poultry products to the increasing human population without compromising human wellbeing. In order to achieve the understanding of the core microbiome that assumes an imperative role in digestion, absorption, and assimilation of feed as well as restrict the growth of pathogenic strains, a proper meta-data survey is required. The dysbiosis of the core microbiome or any external infection in chickens leads to huge losses in the poultry production worldwide. Along with this, the consumption of infected meat also impacts on human health as chicken meat is a regular staple in many diets as a vital source of protein. To tackle these losses, sub-therapeutic doses of antibiotics are being used as a feed additive along with other conventional approaches including selective breeding and modulation in feed composition. Altogether, these conventional approaches have improved the yield and quality of poultry products, however, the use of antibiotics encompasses the risk of developing multi-drug resistant pathogenic strains that can be harmful to human beings. Thus, there is an urgent need to understand the chicken microbiome in order to modulate chicken gut microbiome and provide alternatives to the conventional methods. Although there is now emerging literature available on some of these important microbiome aspects, in this article, we have analysed the relevant recent developments in understanding the chicken gut microbiome including the establishment of integrated gene catalogue for chicken microbiome. We have also focussed on novel strategies for the development of a chicken microbial library that can be used to develop novel microbial consortia as novel probiotics to improve the poultry meat production without compromising human health. Thus, it can be an alternative and advanced step compared to other conventional approaches to improve the gut milieu and pathogen-mediated loss in the poultry industry.
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Affiliation(s)
- Utkarsh Sood
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Roshan Kumar
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA
- South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| | - Sukanya Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi, 110007 India
| | - Derek Fawcett
- Physics and Nanotechnology, Murdoch University, Perth, WA Australia
| | - Supriya Rattan
- Physics and Nanotechnology, Murdoch University, Perth, WA Australia
| | | | - Rup Lal
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
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Phylogenetic Analysis and Screening of Antimicrobial and Antiproliferative Activities of Culturable Bacteria Associated with the Ascidian Styela clava from the Yellow Sea, China. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7851251. [PMID: 31559313 PMCID: PMC6735190 DOI: 10.1155/2019/7851251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/04/2019] [Accepted: 07/28/2019] [Indexed: 01/01/2023]
Abstract
Over 1,000 compounds, including ecteinascidin-743 and didemnin B, have been isolated from ascidians, with most having bioactive properties such as antimicrobial, antitumor, and enzyme-inhibiting activities. In recent years, direct and indirect evidence has shown that some bioactive compounds isolated from ascidians are not produced by ascidians themselves but by their symbiotic microorganisms. Isolated culturable bacteria associated with ascidians and investigating their potential bioactivity are an important approach for discovering novel compounds. In this study, a total of 269 bacteria were isolated from the ascidian Styela clava collected from the coast of Weihai in the north of the Yellow Sea, China. Phylogenetic relationships among 183 isolates were determined using their 16S rRNA gene sequences. Isolates were tested for antimicrobial activity against seven indicator strains, and an antiproliferative activity assay was performed to test for inhibition of human hepatocellular carcinoma Bel 7402 and human cervical carcinoma HeLa cell proliferation. Our results showed that the isolates belonged to 26 genera from 18 families in four phyla (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes). Bacillus and Streptomyces were the most dominant genera; 146 strains had potent antimicrobial activities and inhibited at least one of the indicator strains. Crude extracts from 29 strains showed antiproliferative activity against Bel 7402 cells with IC50 values below 500 μg·mL-1, and 53 strains showed antiproliferative activity against HeLa cells, with IC50 values less than 500 μg·mL-1. Our results suggest that culturable bacteria associated with the ascidian Styela clava may be a promising source of novel bioactive compounds.
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Draft Genome Sequence of Deinococcus sp. Strain S9, Isolated from Microbial Mat Deposits of Hot Springs Located atop the Himalayan Ranges at Manikaran, India. Microbiol Resour Announc 2019; 8:8/28/e00316-19. [PMID: 31296675 PMCID: PMC6624758 DOI: 10.1128/mra.00316-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the draft genome sequence of Deinococcus sp. strain S9, a red-pigmented and moderately thermophilic bacterium isolated from microbial mat deposits around the hot springs at Manikaran, Himachal Pradesh, India. The draft genome (3.34 Mb) contains 101 contigs with an average GC content of 66.4%. Here, we present the draft genome sequence of Deinococcus sp. strain S9, a red-pigmented and moderately thermophilic bacterium isolated from microbial mat deposits around the hot springs at Manikaran, Himachal Pradesh, India. The draft genome (3.34 Mb) contains 101 contigs with an average GC content of 66.4%.
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8
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Singh DN, Sood U, Singh AK, Gupta V, Shakarad M, Rawat CD, Lal R. Genome Sequencing Revealed the Biotechnological Potential of an Obligate Thermophile Geobacillus thermoleovorans Strain RL Isolated from Hot Water Spring. Indian J Microbiol 2019; 59:351-355. [PMID: 31388213 DOI: 10.1007/s12088-019-00809-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 01/11/2023] Open
Abstract
In the present study, we report the draft genome sequence of an obligate thermophile Geobacillus thermoleovorans strain RL isolated from Manikaran hot water spring located atop the Himalayan ranges, India. Strain RL grew optimally at 70 °C but not below 45 °C. The draft genome (3.39 Mb) obtained by Illumina sequencing contains 138 contigs with an average G + C content of 52.30%. RAST annotation showed that amino acid metabolism pathways were most dominant followed by carbohydrate metabolism. Genome-wide analysis using NCBI's Prokaryotic Genome Annotation Pipeline revealed that strain RL encodes for a cocktail of industrially important hydrolytic enzymes glycoside hydrolase, α-and β-glucosidase, xylanase, amylase, neopullulanase, pullulanase and lipases required for white biotechnology. In addition, the presence of genes encoding green biocatalyst multicopper polyphenol oxidase (laccase) and an anticancer enzyme l-glutaminase reflects the significance of strain RL in gray and red biotechnology, respectively. Strain RL is a thermophilic multi-enzyme encoding bacterium which could be the source for the recombinant production of biotechnologically significant enzymes. In, addition whole cells of strain RL may be used in bioremediation studies.
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Affiliation(s)
| | - Utkarsh Sood
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
| | - Amit Kumar Singh
- 3Department of Biotechnology, Jamia Millia Islamia, New Delhi, Delhi 110025 India
| | - Vipin Gupta
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
| | | | - Charu Dogra Rawat
- 4Department of Zoology, Ramjas College, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
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Mahato NK, Sharma A, Singh Y, Lal R. Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics. Arch Microbiol 2019; 201:377-388. [PMID: 30683956 DOI: 10.1007/s00203-018-01616-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 12/29/2018] [Indexed: 11/26/2022]
Abstract
Metagenomic surveys across microbial mat (~ 55 °C) samples of high-altitude (1760 m above sea level) Himalayan geothermal springs have revealed specialized community enriched with niche-specific functions. In this study, we have performed metagenomic sequence-based analyses to get insights into taxonomic composition and functional potential of hyperthermophiles in water (~ 95 °C) and sediment samples (78-98 °C). Community analyses revealed predominance of thermophilic bacterial and archeal genera dwelling in water in contrast to microbial mats (55 °C), namely Methylophilus, Methyloversatilis, Emticicia, Caulobacter, Thermus, Enhydrobacter and Pyrobaculum. Sediment samples having surface temperature (~ 78 °C) were colonized by Pyrobaculum and Chloroflexus while genus Massilia was found to be inhabited in high-temperature sediments (~ 98 °C). Functional analyses of metagenomic sequences revealed genetic enrichment of genes such as type IV secretion system, flagellar assembly and two-component system in contrast to mats. Furthermore, inter-sample comparison of enriched microbial diversity among water, sediment and microbial mats revealed habitat-specific clustering of the samples within same environment highlighting the role of temperature dynamics in modulating community structure across different habitats in same niche. However, function-based analysis demonstrated site-specific clustering among sediment, microbial mat and water samples. Furthermore, a novel thermophilic genotype of the genus Emticicia (designated as strain MM) was reconstructed from metagenome data. This is a correlative study between three major habitats present in geothermal spring environment, i.e., water, sediment and microbial mats revealing greater phylogenetic and functional dispersion emphasizing changing habitat-specific dynamics with temperature.
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Affiliation(s)
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India.
- PhiXgen Pvt. Ltd, Gurugram, India.
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10
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Sharma A, Schmidt M, Kiesel B, Mahato NK, Cralle L, Singh Y, Richnow HH, Gilbert JA, Arnold W, Lal R. Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes. Front Microbiol 2018; 9:3095. [PMID: 30619174 PMCID: PMC6302217 DOI: 10.3389/fmicb.2018.03095] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/29/2018] [Indexed: 11/30/2022] Open
Abstract
Hot spring-associated viruses, particularly the archaeal viruses, remain under-examined compared to bacteriophages. Previous metagenomic studies of the Manikaran hot springs in India suggested an abundance of viral DNA, which prompted us to examine the virus–host (bacterial and archaeal) interactions in sediment and microbial mat samples collected from the thermal discharges. Here, we characterize the viruses (both bacterial and archaeal) from this Himalayan hot spring using both metagenomics assembly and electron microscopy. We utilized four shotgun samples from sediment (78–98°C) and two from microbial mats (50°C) to reconstruct 65 bacteriophage genomes (24–200 kb). We also identified 59 archaeal viruses that were notably abundant across the sediment samples. Whole-genome analyses of the reconstructed bacteriophage genomes revealed greater genomic conservation in sediments (65%) compared to microbial mats (49%). However, a minimal phage genome was still maintained across both sediment and microbial mats suggesting a common origin. To complement the metagenomic data, scanning-electron and helium-ion microscopy were used to reveal diverse morphotypes of Caudovirales and archaeal viruses. The genome level annotations provide further evidence for gene-level exchange between virus and host in these hot springs, and augments our knowledgebase for bacteriophages, archaeal viruses and Clustered Regularly Interspaced Short Palindromic Repeat cassettes, which provide a critical resource for studying viromes in extreme natural environments.
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Affiliation(s)
- Anukriti Sharma
- Department of Zoology, University of Delhi, New Delhi, India.,Biosciences Division, Argonne National Laboratory, Lemont, IL, United States.,Department of Surgery, University of Chicago, Chicago, IL, United States
| | - Matthias Schmidt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Bärbel Kiesel
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Nitish K Mahato
- Department of Zoology, University of Delhi, New Delhi, India
| | - Lauren Cralle
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States.,Department of Surgery, University of Chicago, Chicago, IL, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, New Delhi, India
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States.,Department of Surgery, University of Chicago, Chicago, IL, United States
| | - Wyatt Arnold
- Department of Surgery, University of Chicago, Chicago, IL, United States
| | - Rup Lal
- Department of Zoology, University of Delhi, New Delhi, India
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11
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Fictibacillus iocasae sp. nov., isolated from the deep-sea sediment in Pacmanus, Manus Basin. Arch Microbiol 2018; 200:1123-1128. [DOI: 10.1007/s00203-018-1527-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/18/2017] [Accepted: 05/18/2018] [Indexed: 11/25/2022]
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Takahashi M, Aoyagi H. Effect of intermittent opening of breathable culture plugs and aeration of headspace on the structure of microbial communities in shake-flask culture. J Biosci Bioeng 2018; 126:96-101. [PMID: 29501524 DOI: 10.1016/j.jbiosc.2018.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/29/2017] [Accepted: 01/11/2018] [Indexed: 11/27/2022]
Abstract
In this study, we found that opening breathable culture plugs for 30 s during periodic and aseptic sampling affects the community structure of cultured soil microbes. Similar effects were observed using an automatic aeration flask system that mimics aseptic opening of the breathable culture plug during sampling, but without interruption in shaking. Thus, the observed changes in the microbial consortia appear to be due exclusively to the intermittent ventilation of the flask headspace. To elucidate the mechanism driving this phenomenon, we monitored CO2 and O2 concentrations in both headspace and culture broth using the new system termed as circulation direct monitoring and sampling system. The data show that the CO2 concentration in the culture broth temporarily decreased with the CO2 concentration in the headspace, strongly suggesting that the effect of intermittent ventilation of the headspace on the microbial consortia depends on CO2. Importantly, the data also imply that environmental variables during shake flask culture, especially CO2 concentration, is important for screening aerobic microorganisms.
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Affiliation(s)
- Masato Takahashi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hideki Aoyagi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
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Pal D, Bhardwaj A, Kaur N, Sudan SK, Bisht B, Kumari M, Vyas B, Krishnamurthi S, Mayilraj S. Fictibacillus aquaticus sp. nov., isolated from downstream river water. Int J Syst Evol Microbiol 2017; 68:160-164. [PMID: 29116040 DOI: 10.1099/ijsem.0.002474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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 bacterial strain, GDSW-R2A3T, was isolated from a downstream water sample collected from the river Ganges, India. Analysis of the 16S rRNA gene sequence of strain GDSW-R2A3T revealed its affiliation to the family Bacillaceae. Further analysis using a polyphasic approach revealed that strain GDSW-R2A3T was most closely related to the genus Fictibacillus. Analysis of the almost-complete (1488 bp) 16S rRNA gene sequence of strain GDSW-R2A3T revealed the highest level of sequence similarity with Fictibacillus phosphorivorans CCM 8426T (98.3 %) and Fictibacillus nanhaiensis KCTC 13712T (98.3 %) followed by Fictibacillus barbaricus DSM 14730T (98.0 %). The digital DNA-DNA hybridization and average nucleotide identity (ANI) values between strain GDSW-R2A3T and the most closely related taxon, F. phosphorivorans CCM 8426T, were 20.3 and 78.2 %, respectively. The DNA G+C content of the strain was 44.2 mol%. The cell-wall amino acid was meso-diaminopimelic acid. Polar lipids present were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three aminophospholipids, two phospholipids and one unidentified lipid; the major menaquinone was MK-7; iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0 were the major fatty acids. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it can be concluded that strain GDSW-R2A3T represents a novel species of the genus Fictibacillus, for which the name Fictibacillus aquaticus sp. nov. is proposed. The type strain is GDSW-R2A3T (=VTCC-B-910015T=CCM 8782T).
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Affiliation(s)
- Deepika Pal
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Ayanka Bhardwaj
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Navjot Kaur
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Sarabjeet Kour Sudan
- Division of Protein Science and Engineering, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Bhawana Bisht
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Munesh Kumari
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Bhawna Vyas
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Srinivasan Krishnamurthi
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shanmugam Mayilraj
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
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Poddar A, Das SK. Microbiological studies of hot springs in India: a review. Arch Microbiol 2017; 200:1-18. [PMID: 28887679 DOI: 10.1007/s00203-017-1429-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/22/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37-99 °C and 6.8-10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.
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Affiliation(s)
- Abhijit Poddar
- Biosafety Support Unit, Regional Centre for Biotechnology, NPC Building, 5-6 Institutional Area, Lodhi Road, New Delhi, 110003, India.
| | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences, Bhubaneswar, 751023, India.
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Mahato NK, Gupta V, Singh P, Kumari R, Verma H, Tripathi C, Rani P, Sharma A, Singhvi N, Sood U, Hira P, Kohli P, Nayyar N, Puri A, Bajaj A, Kumar R, Negi V, Talwar C, Khurana H, Nagar S, Sharma M, Mishra H, Singh AK, Dhingra G, Negi RK, Shakarad M, Singh Y, Lal R. Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques. Antonie van Leeuwenhoek 2017; 110:1357-1371. [PMID: 28831610 DOI: 10.1007/s10482-017-0928-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 08/10/2017] [Indexed: 02/06/2023]
Abstract
The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.
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Affiliation(s)
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Rashmi Kumari
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Charu Tripathi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Pooja Rani
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Anukriti Sharma
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Utkarsh Sood
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Princy Hira
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Puneet Kohli
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Namita Nayyar
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Akshita Puri
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Vivek Negi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Himani Khurana
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Monika Sharma
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Harshita Mishra
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Amit Kumar Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Gauri Dhingra
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007, India.
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