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Sherpa MT, Das S, Najar IN, Thakur N. Draft genome sequence of Stenotrophomonas maltophilia strain P13 gives insight into its protease production and assessment of sulfur and nitrogen metabolism. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100012. [PMID: 34841305 PMCID: PMC8610322 DOI: 10.1016/j.crmicr.2020.100012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 11/08/2022] Open
Abstract
In this study draft genome sequence of Stenotrophomonas maltophilia strain P13 which was isolated from Kanchengayao glacier, North Sikkim, India. The genome of P13 strain possesses 2689,565 total reads, with an average G + C content of 69.9%. The major enzymes present are beta-galactosidase, thiol peroxidase, thiolredoxin reductase, glutamate synthase, and glutamate-ammonia-ligase adenyltransferase. FAME, morphological and biochemical characterization, and scanning electron microscopy (SEM) of Stenotrophomonas maltophilia strain P13 are provided.
Stenotrophomonas maltophilia strain P13 was isolated from the Kanchengayao glacier's accumulation zone. A comprehensive study was done on this strain as it produced protease enzyme and thus having industrial potential. The whole genome sequence, FAME, morphological and biochemical characteristics of the S. maltophilia strain P13 is being presented. The genome of P13 strain possesses 2,689,565 total reads, with an average G + C content of 69.9%. The whole-genome assembly is having 548 contigs (with PEGs). The genome contains 2,985 coding sequences with 55 rRNA predicted genes. More than 88% of the total pre-processed reads from samples were mapped. The identified coding proteins were classified into 27 functional categories based on COG classification. The genome was found to possess genes for ammonium assimilation, galactosylceramide and sulfatide metabolism. The major enzymes present are beta-galactosidase, thiol peroxidase, thiolredoxin reductase, glutamate synthase, and glutamate-ammonia-ligase adenyltransferase. The genome information of Stenotrophomonas maltophilia P13 provides the basis for understanding the functional properties and abilities to act as a potential cold-active enzyme producer and nitrogen-fixing bacteria.
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Affiliation(s)
- Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur Gangtok, Sikkim 737102, India
| | - Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur Gangtok, Sikkim 737102, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur Gangtok, Sikkim 737102, India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur Gangtok, Sikkim 737102, India
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Zeng B, Zhang S, Xu H, Kong F, Yu X, Wang P, Yang M, Li D, Zhang M, Ni Q, Li Y, Fan X, Yang D, Ning R, Zhao J, Li Y. Gut microbiota of Tibetans and Tibetan pigs varies between high and low altitude environments. Microbiol Res 2020; 235:126447. [PMID: 32114362 DOI: 10.1016/j.micres.2020.126447] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/13/2020] [Accepted: 02/22/2020] [Indexed: 12/17/2022]
Abstract
This study set out to investigate the relationship between gut microbiota composition and host adaptation to high altitude conditions. Fecal samples from both high and low altitude humans and pigs were studied using multi-omics methods. 16S ribosomal meta-analysis results showed significant differences in bacterial diversity and composition between high and low altitude members of the same species, as well as between different species. Acinetobacter, Pseudomonas, and Sphingobacterium were the three most abundant bacterial genera found in high altitude fecal samples of both humans and pigs. The alpha diversities of microbiota from Chinese people were found to be relatively lower than those of people in other countries. We found significant convergent trends in microbial metagenome compositions between Tibetans and Tibetan pigs living at high altitudes, and significant differences between these and their low-altitude counterparts. Metabolic pathways related to energy metabolism, amino-acid metabolism, and carbohydrate metabolism were consistently enriched at high altitudes, in both Tibetans and Tibetan pigs. Propanoic acid and octadecanoic acid were significantly elevated in high-altitude Tibetan pigs, and genes related to these two metabolites were also up-regulated. Thus, this study revealed that unique gut bacteriomes and their functions may be closely related to environmental host adaptation in high altitude conditions, such as those in the Tibetan plateau.
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Affiliation(s)
- Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
| | - Siyuan Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Fanli Kong
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Xianqiong Yu
- Animal Husbandry and Technology Bureau of Daocheng County, Daocheng, Ganzi Tibetan Autonomous Prefecture, China
| | - Ping Wang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Deying Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ruihong Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, USA
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
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Dhakar K, Pandey A. Microbial Ecology from the Himalayan Cryosphere Perspective. Microorganisms 2020; 8:microorganisms8020257. [PMID: 32075196 PMCID: PMC7074745 DOI: 10.3390/microorganisms8020257] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 11/18/2022] Open
Abstract
Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.
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Affiliation(s)
- Kusum Dhakar
- Newe Ya’ar Research Center, Agricultural Research Organization, Ramat Yishay 30095, Israel;
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Bell Road, Clement Town, Dehradun 248002, India
- Correspondence:
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The Diversity of Pseudomonas species from the Accumulation Zone of Kanchengayao Glacier, North Sikkim, India. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.1.37] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Sherpa MT, Najar IN, Das S, Thakur N. Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India. Indian J Microbiol 2018; 58:470-478. [PMID: 30262957 DOI: 10.1007/s12088-018-0747-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/31/2018] [Indexed: 11/25/2022] Open
Abstract
The Himalayas are water tower for billions of people; however in recent years due to climate change several glaciers of Himalaya are receding or getting extinct which can lead to water scarcity and political tensions. Thus, it requires immediate attention and necessary evaluation of all the environmental parameters which can lead to conservation of Himalayan glaciers. This study is the first attempt to investigate the bacterial diversity from debris-free Changme Khang (CKG) and debris-cover Changme Khangpu (CK) glacier, North Sikkim, India. The abundance of culturable bacteria in CKG glaciers was 1.5 × 104 cells/mL and CK glacier 1.5 × 105 cells/mL. A total of 50 isolates were isolated from both the glacier under aerobic growth condition. The majority of the isolates from both the glaciers were psychrotolerant according to their growth temperature. Optimum growth temperatures of the isolates were between 15 and 20 °C, pH 6-8 and NaCl 0-2%. The phylogenetic studies of 16S RNA gene sequence suggest that, these 21 isolates can be assigned within four phyla/class, i.e., Firmicutes, Beta-proteobacteria, Gamma-proteobacteria and Actinobacteria. The dominant phyla were Firmicutes 71.42% followed by Actinobacteria 14.28%, Alpha-proteobacteria 9.52% and Beta-proteobacteria 4.76%. The isolate Bacillus thuringiensis strain CKG2 showed the highest protease activity (2.24 unit/mL/min). Considering the fast rate at which Himalayan glaciers are melting and availability of limited number of research, there is urgent need to study the microbial communities confined in such environments.
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Affiliation(s)
- Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok, Sikkim 737102 India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok, Sikkim 737102 India
| | - Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok, Sikkim 737102 India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok, Sikkim 737102 India
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Yang GL, Hou SG, Le Baoge R, Li ZG, Xu H, Liu YP, Du WT, Liu YQ. Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains. Sci Rep 2016; 6:36548. [PMID: 27811967 PMCID: PMC5109912 DOI: 10.1038/srep36548] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/18/2016] [Indexed: 11/09/2022] Open
Abstract
A detailed understanding of microbial ecology in different supraglacial habitats is important due to the unprecedented speed of glacier retreat. Differences in bacterial diversity and community structure between glacial snow and glacial soil on the Chongce Ice Cap were assessed using 454 pyrosequencing. Based on rarefaction curves, Chao1, ACE, and Shannon indices, we found that bacterial diversity in glacial snow was lower than that in glacial soil. Principal coordinate analysis (PCoA) and heatmap analysis indicated that there were major differences in bacterial communities between glacial snow and glacial soil. Most bacteria were different between the two habitats; however, there were some common bacteria shared between glacial snow and glacial soil. Some rare or functional bacterial resources were also present in the Chongce Ice Cap. These findings provide a preliminary understanding of the shifts in bacterial diversity and communities from glacial snow to glacial soil after the melting and inflow of glacial snow into glacial soil.
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Affiliation(s)
- Guang Li Yang
- Department of Life Science, Shangqiu Normal University, Shangqiu 476000, China
| | - Shu Gui Hou
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210023, China
| | - Ri Le Baoge
- Department of Life Science, Shangqiu Normal University, Shangqiu 476000, China
| | - Zhi Guo Li
- Department of Environment and Planning, Shangqiu Normal University, Shangqiu 476000, China
| | - Hao Xu
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210023, China
| | - Ya Ping Liu
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wen Tao Du
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yong Qin Liu
- Key Laboratory of Tibetan Environmental Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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Chen Y, Li XK, Si J, Wu GJ, Tian LD, Xiang SR. Changes of the Bacterial Abundance and Communities in Shallow Ice Cores from Dunde and Muztagata Glaciers, Western China. Front Microbiol 2016; 7:1716. [PMID: 27847503 PMCID: PMC5088206 DOI: 10.3389/fmicb.2016.01716] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/13/2016] [Indexed: 02/02/2023] Open
Abstract
In this study, six bacterial community structures were analyzed from the Dunde ice core (9.5-m-long) using 16S rRNA gene cloning library technology. Compared to the Muztagata mountain ice core (37-m-long), the Dunde ice core has different dominant community structures, with five genus-related groups Blastococcus sp./Propionibacterium, Cryobacterium-related., Flavobacterium sp., Pedobacter sp., and Polaromas sp. that are frequently found in the six tested ice layers from 1990 to 2000. Live and total microbial density patterns were examined and related to the dynamics of physical-chemical parameters, mineral particle concentrations, and stable isotopic ratios in the precipitations collected from both Muztagata and Dunde ice cores. The Muztagata ice core revealed seasonal response patterns for both live and total cell density, with high cell density occurring in the warming spring and summer months indicated by the proxy value of the stable isotopic ratios. Seasonal analysis of live cell density for the Dunde ice core was not successful due to the limitations of sampling resolution. Both ice cores showed that the cell density peaks were frequently associated with high concentrations of particles. A comparison of microbial communities in the Dunde and Muztagata glaciers showed that similar taxonomic members exist in the related ice cores, but the composition of the prevalent genus-related groups is largely different between the two geographically different glaciers. This indicates that the micro-biogeography associated with geographic differences was mainly influenced by a few dominant taxonomic groups.
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Affiliation(s)
- Yong Chen
- School of Life Science, Lanzhou University, Lanzhou China
| | - Xiang-Kai Li
- School of Life Science, Lanzhou University, Lanzhou China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou China
| | - Guang-Jian Wu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
| | - Li-De Tian
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
| | - Shu-Rong Xiang
- School of Life Science, Lanzhou University, LanzhouChina; Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
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Microbial communities associated with Antarctic snow pack and their biogeochemical implications. Microbiol Res 2016; 192:192-202. [PMID: 27664737 DOI: 10.1016/j.micres.2016.07.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 07/18/2016] [Accepted: 07/18/2016] [Indexed: 11/24/2022]
Abstract
Snow ecosystems represent a large part of the Earth's biosphere and harbour diverse microbial communities. Despite our increased knowledge of snow microbial communities, the question remains as to their functional potential, particularly with respect to their role in adapting to and modifying the specific snow environment. In this work, we investigated the diversity and functional capabilities of microorganisms from 3 regions of East Antarctica, with respect to compounds present in snow and tested whether their functional signature reflected the snow environment. A diverse assemblage of bacteria (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Deinococcus-Thermus, Planctomycetes, Verrucomicrobia), archaea (Euryarchaeota), and eukarya (Basidiomycota, Ascomycota, Cryptomycota and Rhizaria) were detected through culture-dependent and -independent methods. Although microbial communities observed in the three snow samples were distinctly different, all isolates tested produced one or more of the following enzymes: lipase, protease, amylase, β-galactosidase, cellulase, and/or lignin modifying enzyme. This indicates that the snow pack microbes have the capacity to degrade organic compounds found in Antarctic snow (proteins, lipids, carbohydrates, lignin), thus highlighting their potential to be involved in snow chemistry.
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Bacterial diversity of Drass, cold desert in Western Himalaya, and its comparison with Antarctic and Arctic. Arch Microbiol 2015; 197:851-60. [PMID: 26055487 DOI: 10.1007/s00203-015-1121-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/12/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
Abstract
Drass is the coldest inhabited place in India and the second coldest, inhabited place in the world, after Siberia. Using the 16SrDNA amplicon pyrosequencing, bacterial diversity patterns were cataloged across the Drass cold desert. In order to identify the ecotype abundance across cold desert environment, bacterial diversity patterns of Drass were further compared with the bacterial diversity of two other cold deserts, i.e., Antarctic and Arctic. Acidobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Gemmatimonadetes were among the highly abundant taxonomic groups present across all the three cold deserts and were designated as the core phyla. However, Firmicutes, Nitrospirae, Armatimonadetes (former candidate division OP10), Planctomycetes, TM7, Chloroflexi, Deinococcus-Thermus, Tenericutes and candidate phyla WS3 were identified as rare phyla in Drass, Antarctic and Arctic samples. Differential abundance patterns were also computed across all the three samples, i.e., Acidobacteria (32.1 %) were dominant in Drass and Firmicutes (52.9 ± 17.6 %) and Proteobacteria (42 ± 1.3 %) were dominant in Antarctic and Arctic reference samples, respectively. Alpha diversity values Shannon's (H) and Simpson's (1-D) diversity indices were highest for Antarctic samples, whereas richness estimators (ACE and Chao1) were maximum for Drass soil suggesting greater species richness in bacterial communities in Drass than the Antarctic and Arctic samples.
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Venkatachalam S, Gowdaman V, Prabagaran SR. Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal. MICROBIAL ECOLOGY 2015; 69:472-91. [PMID: 25204748 DOI: 10.1007/s00248-014-0476-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 07/28/2014] [Indexed: 05/18/2023]
Abstract
Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills.
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Affiliation(s)
- Siddarthan Venkatachalam
- Molecular Microbiology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
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Comparison of bacterial diversity in proglacial soil from Kafni Glacier, Himalayan Mountain ranges, India, with the bacterial diversity of other glaciers in the world. Extremophiles 2011; 15:673-90. [PMID: 21918795 DOI: 10.1007/s00792-011-0398-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
Abstract
Two 16S rRNA gene clone libraries (KF and KS) were constructed using two soil samples (K7s and K8s) collected near Kafni Glacier, Himalayas. The two libraries yielded a total of 648 clones. Phyla Actinobacteria, Bacteroidetes, Chloroflexi Firmicutes, Proteobacteria, Spirochaetae, Tenericutes and Verrucomicrobia were common to the two libraries. Phyla Acidobacteria, Chlamydiae and Nitrospirae were present only in KF library, whereas Lentisphaerae and TM7 were detected only in KS. In the two libraries, clones belonging to phyla Bacteroidetes and Proteobacteria were the most predominant. Principal component analysis (PCA) revealed that KF and KS were different and arsenic content influenced the differences in the percentage of OTUs. PCA indicated that high water content in the K8s sample results in high total bacterial count. PCA also indicated that bacterial diversity of KF and KS was similar to soils from the Pindari Glacier, Himalayas; Samoylov Island, Siberia; Schrimacher Oasis, Antarctica and Siberian tundra. The eleven bacterial strains isolated from the above two soil samples were phylogenetically related to six different genera. All the isolates were psychro-, halo- and alkalitolerant. Amylase, lipase and urease activities were detected in the majority of the strains. Long chain, saturated, unsaturated and branched fatty acids were predominant in the psychrotolerant bacteria.
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Bacterial diversity of soil in the vicinity of Pindari glacier, Himalayan mountain ranges, India, using culturable bacteria and soil 16S rRNA gene clones. Extremophiles 2011; 15:1-22. [PMID: 21061031 DOI: 10.1007/s00792-010-0333-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 10/22/2010] [Indexed: 10/18/2022]
Abstract
Three 16S rRNA gene clone libraries (P1L, P4L and P8L) were constructed using three soil samples (P1S, P4S and P8S) collected near Pindari glacier, Himalayas. The three libraries yielded a total of 703 clones. Actinobacteria, Firmicutes and Proteobacteria were common to the three libraries. In addition to the above P1L and P8L shared the phyla Acidobacteria, Bacteroidetes, Gemmatimonadetes and Planctomycetes. Phyla Chlamydiae, Chlorobi, Chloroflexi, Dictyoglomi, Fibrobacteres, Nitrospirae, Verrucomicrobia, candidate division SPAM and candidate TM7s TM7a phylum were present only in P1L. Rarefaction analysis indicated that the bacterial diversity in P4S and P8S soil samples was representative of the sample. Principal component analysis (PCA) revealed that P1S and P8S were different from P4S soil sample. PCA also indicated that arsenic content, pH, Cr and altitude influence the observed differences in the percentage of specific OTUs in the three 16S rRNA gene clone libraries. The observed bacterial diversity was similar to that observed for other Himalayan and non-polar cold habitats. A total of 40 strains of bacteria were isolated from the above three soil samples and based on the morphology 20 bacterial strains were selected for further characterization. The 20 bacteria belonged to 12 different genera. All the isolates were psychro-, halo- and alkalitolerant. Amylase and urease activities were detected in majority of the strains but lipase and protease activities were not detected. Long chain, saturated, unsaturated and branched fatty acids were predominant in the psychrotolerant bacteria.
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Pradhan S, Srinivas TNR, Pindi PK, Kishore KH, Begum Z, Singh PK, Singh AK, Pratibha MS, Yasala AK, Reddy GSN, Shivaji S. Bacterial biodiversity from Roopkund Glacier, Himalayan mountain ranges, India. Extremophiles 2010; 14:377-95. [PMID: 20505964 DOI: 10.1007/s00792-010-0318-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
Abstract
The bacterial diversity of two soil samples collected from the periphery of the Roopkund glacial lake and one soil sample from the surface of the Roopkund Glacier in the Himalayan ranges was determined by constructing three 16S rRNA gene clone libraries. The three clone libraries yielded a total of 798 clones belonging to 25 classes. Actinobacteria was the most predominant class (>10% of the clones) in the three libraries. In the library from the glacial soil, class Betaproteobacteria (24.2%) was the most predominant. The rarefaction analysis indicated coverage of 43.4 and 41.2% in the samples collected from the periphery of the lake thus indicating a limited bacterial diversity covered; at the same time, the coverage of 98.4% in the glacier sample indicated most of the diversity was covered. Further, the bacterial diversity in the Roopkund glacier soil was low, but was comparable with the bacterial diversity of a few other glaciers. The results of principal component analysis based on the 16S rRNA gene clone library data, percentages of OTUs and biogeochemical data revealed that the lake soil samples were different from the glacier soil sample and the biogeochemical properties affected the diversity of microbial communities in the soil samples.
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Affiliation(s)
- Suman Pradhan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
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Xiang SR, Shang TC, Chen Y, Jing ZF, Yao T. Changes in diversity and biomass of bacteria along a shallow snow pit from Kuytun 51 Glacier, Tianshan Mountains, China. ACTA ACUST UNITED AC 2009. [DOI: 10.1029/2008jg000864] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Xiang SR, Shang TC, Chen Y, Yao TD. Deposition and postdeposition mechanisms as possible drivers of microbial population variability in glacier ice. FEMS Microbiol Ecol 2009; 70:9-20. [PMID: 19796140 DOI: 10.1111/j.1574-6941.2009.00759.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Shu-Rong Xiang
- Institute of the Tibetan Plateau Research, Chinese Academy of Science (CAS), Beijing, China.
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16
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Miteva V, Teacher C, Sowers T, Brenchley J. Comparison of the microbial diversity at different depths of the GISP2 Greenland ice core in relationship to deposition climates. Environ Microbiol 2009; 11:640-56. [DOI: 10.1111/j.1462-2920.2008.01835.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Zhang X, Ma X, Wang N, Yao T. New subgroup of Bacteroidetes and diverse microorganisms in Tibetan plateau glacial ice provide a biological record of environmental conditions. FEMS Microbiol Ecol 2009; 67:21-9. [PMID: 19049497 DOI: 10.1111/j.1574-6941.2008.00604.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Xiaojun Zhang
- School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China
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18
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Liu Y, Yao T, Jiao N, Kang S, Zeng Y, Huang S. Microbial community structure in moraine lakes and glacial meltwaters, Mount Everest. FEMS Microbiol Lett 2007; 265:98-105. [PMID: 17107422 DOI: 10.1111/j.1574-6968.2006.00477.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The bacterial diversity and abundance in two moraine lakes and two glacial meltwaters (5140, 5152, 5800 and 6350 m above sea level, respectively) in the remote Mount Everest region were examined through 16S rRNA gene clone library and flow cytometry approaches. In total, 247 clones were screened by RFLP and 60 16S rRNA gene sequences were obtained, belonging to the following groups: Proteobacteria (8% alpha subdivision, 21% beta subdivision, and 1% gamma subdivision), Cytophaga-Flavobacteria-Bacteroides (CFB) (54%), Actinobacteria (4%), Planctomycetes (2%), Verrucomicrobia (2%), Fibrobacteres (1%) and Eukaryotic chroloplast (3%), respectively. The high dominance of CFB distinguished the Mount Everest waters from other mountain lakes. The highest bacterial abundance and diversity occurred in the open moraine lake at 5152 m, and the lowest in the glacial meltwater at 6350 m. Low temperature at high altitude is considered to be critical for component dominancy. At the same altitude, nutrient availability plays a role in regulating population structure. Our results also show that the bacteria in Mount Everest may be derived from different sources.
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Affiliation(s)
- Yongqin Liu
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, China
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19
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Xiang S, Yao T, An L, Xu B, Wang J. 16S rRNA sequences and differences in bacteria isolated from the Muztag Ata glacier at increasing depths. Appl Environ Microbiol 2005; 71:4619-27. [PMID: 16085856 PMCID: PMC1183274 DOI: 10.1128/aem.71.8.4619-4627.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small subunit 16S rRNA sequences, growth temperatures, and phylogenetic relationships have been established for 129 bacterial isolates recovered under aerobic growth conditions from different regions of a 22-m ice core from the Muztag Ata Mountain glacier on the Pamirs Plateau (China). Only 11% were psychrophiles (grew at 2 degrees C or -2 degrees C up to approximately 20 degrees C), although the majority (82%) were psychrotolerant (grew at 2 degrees C or -2 degrees C up to 37 degrees C). The majority of the isolates had 16S rRNA sequences similar to previously determined sequences, ranging from 85% to 100% identical to database sequences. Based on their 16S rRNA sequences, 42.6% of the isolates were high-G+C (HGC) gram-positive bacteria, 23.3% were gamma-Proteobacteria, 14.7% were alpha-Proteobacteria, 14.7% were Flavobacteria, and 4.7% were low-G+C (LGC) gram-positive bacteria. There were clear differences in the depth distribution, with Proteobacteria, HGC/Cytophaga-Flavobacterium-Bacteroides (CFB), Proteobacteria, LGC/CFB/HGC, Cryobacterium psychrophilum, HGC/CFB, Proteobacteria/HGC/CFB, and HGC/CFB being the predominant isolates from ice that originated from 2.7 to 3.8, 6.2, 7.5, 8.3, 9.0, 9.7, 12.5, and 15.3 m below the surface, respectively. This layered distribution of bacterial isolates presumably reflects both differences in bacteria inhabiting the glacier's surface, differences in bacteria deposited serendipitously on the glacier's surface by wind and snowfall, and nutrient availability within the ice.
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Affiliation(s)
- Shurong Xiang
- Institute of Tibetan Plateau Research, Chinese Academy of Science, Beijing, People's Republic of China
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Xiang S, Yao T, An L, Wu G, Xu B, Ma X, Li Z, Wang J, Yu W. Vertical quantitative and dominant population distribution of the bacteria isolated from the Muztagata ice core. ACTA ACUST UNITED AC 2005. [DOI: 10.1360/02yd0210] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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