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Iwaloye OF, Michaud B, Alloy T, D'Souza N, McKay RML, Morris P, Gura C, Rogers SO. Lake Erie ice is a repository of organisms. Microbiol Resour Announc 2024; 13:e0109423. [PMID: 38411068 PMCID: PMC11008222 DOI: 10.1128/mra.01094-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024] Open
Abstract
Organism abundance and diversity were assessed in Lake Erie ice samples using sequences derived from a combined metagenomic and metatranscriptomic analysis. The 68,417 unique sequences were from Bacteria (77.5%), Eukarya (22.3%), and Archaea (0.2%) and indicated diverse species of organisms from 32 bacterial, 8 eukaryotic, and 2 archaeal taxonomic groups.
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Affiliation(s)
- Opeoluwa F. Iwaloye
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA
| | - Brenna Michaud
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA
| | - Tessa Alloy
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA
| | - Nigel D'Souza
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA
| | - R. Michael L. McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA
| | - Paul Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA
| | - Colby Gura
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA
| | - Scott O. Rogers
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, USA
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2
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Lee YCJ, Javdan B. Ice Cores as a Source for Antimicrobials: From Bioprospecting to Biodesign. BIODESIGN RESEARCH 2023; 5:0024. [PMID: 37928441 PMCID: PMC10623340 DOI: 10.34133/bdr.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023] Open
Abstract
The golden age has passed for antibiotic discovery, and while some antibiotics are currently in various phases of clinical trials in the United States, many pharmaceutical companies have abandoned antibiotic research. With the need for antibiotics, we should expand our horizon for therapeutic mining and can look toward understudied sources such as ice cores. Ice cores contain microorganisms and genetic material that have been frozen in time for thousands of years. The antibiotics used by these organisms are encoded in their genomes, which can be unlocked, identified, and characterized with modern advances in molecular biology, genetic sequencing, various computational approaches, and established natural product discovery pipelines. While synthetic biology can be used in natural product discovery approaches, synthetic biology and bioengineering efforts can also be leveraged in the selection and biodesign of increased compound yields, potency, and stability. Here, we provide the perspective that ice cores can be a source of novel antibiotic compounds and that the tools of synthetic biology can be used to design better antimicrobials.
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Affiliation(s)
| | - Bahar Javdan
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
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3
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Abstract
Hypersaline waters and glacial ice are inhospitable environments that have low water activity and high concentrations of osmolytes. They are inhabited by diverse microbial communities, of which extremotolerant and extremophilic fungi are essential components. Some fungi are specialized in only one of these two environments and can thrive in conditions that are lethal to most other life-forms. Others are generalists, highly adaptable species that occur in both environments and tolerate a wide range of extremes. Both groups efficiently balance cellular osmotic pressure and ion concentration, stabilize cell membranes, remodel cell walls, and neutralize intracellular oxidative stress. Some species use unusual reproductive strategies. Further investigation of these adaptations with new methods and carefully designed experiments under ecologically relevant conditions will help predict the role of fungi in hypersaline and glacial environments affected by climate change, decipher their stress resistance mechanisms and exploit their biotechnological potential.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
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4
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Nikitin DA. Ecological Characteristics of Antarctic Fungi. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2023; 508:32-54. [PMID: 37186046 DOI: 10.1134/s0012496622700120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 05/17/2023]
Abstract
In view of the high responsiveness of polar ecosystems to the global climate change, the research of Antarctic microorganisms has become a topical issue. The unique ecosystems that have developed under the severe climate conditions of the continent lack flowering plants but are dominated by soil mycobiota. In addition to performing their classical ecological functions, Antarctic fungi form the basis of local communities, e.g., endoliths and microbial mats. Furthermore, Antarctic fungi are a major force that mediates transformation of rock minerals in situ and makes biologically significant elements available for other organisms. For these reasons, mycobiota plays a central role in the maintenance of ecological equilibrium in Antarctica. The dominant fungal division on the continent is Ascomycota (77.1%), and not Basidiomycota (9.1%), as it is the case on other continents. For a number of reasons, yeasts and yeast-like micromycetes (mainly basidiomycetes) are more tolerant to extreme conditions in various Antarctic biotopes than filamentous fungi. Substantial evidence suggests that filamentous fungi and yeasts are better adapted to existence in ecosystems with extremely low temperatures than other microorganisms. Due to the long-term isolation of Antarctica from other continents, local biota has been evolving largely independently, which led to emergence of multiple endemic fungal taxa. The presence of eurytopes on the continent is presumably related to the global warming and growing anthropogenic pressure. This review discusses the current state of research on the structure of fungal communities of Antarctic subaerial and subaquatic biotopes, the ecological role of yeast-mycelial dimorphism in Antarctic fungi, the problem of endemism of Antarctic mycobiota, as well as the ecological and physiological adaptations of fungi to low temperatures; it also justifies the relevance of research into secondary metabolites of psychrophilic micromycetes.
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Affiliation(s)
- D A Nikitin
- Dokuchaev Soil Science Institute, 119017, Moscow, Russia.
- Institute of Geography, Russian Academy of Sciences, 119017, Moscow, Russia.
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5
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Prado T, Brandão ML, Fumian TM, Freitas L, Chame M, Leomil L, Magalhães MGP, Degrave WMS, Leite JPG, Miagostovich MP. Virome analysis in lakes of the South Shetland Islands, Antarctica - 2020. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158537. [PMID: 36075413 DOI: 10.1016/j.scitotenv.2022.158537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 05/25/2023]
Abstract
Polar freshwater ecosystems are characterized by a distinct microbiota. However, little is known about viral diversity and abundance, especially regarding the ecology of RNA viruses. We used shotgun metagenomic analysis on samples from Antarctic ecosystems, and report here the characterization of the virome fraction, from different lakes located in the South Shetland Islands (Penguin, Ardley, Deception and King George Island) in the Peninsula Antarctica, in the summer season 2020. DNA viruses (99.4 %) prevailed over RNA viruses (0.6 %) in the lake samples. Six viral orders were identified in the metagenomic libraries: Caudovirales (dsDNA), which was prevalent in most lakes; Picornavirales (ssRNA+); Sobelivirales (ssRNA+); Tolivirales (ssRNA+); Petitvirales (ssDNA) and Baphyvirales (ssDNA), including eight viral families (Herelleviridae, Siphoviridae, Myoviridae, Microviridae, Marnaviridae, Bacilladnaviridae, Barnaviridae and Tombusviridae) and several other, mainly non-classified ssRNA(+) viruses in the lakes of Ardley Island. Bacteriophages (dsDNA) (Herelleviridae family) infecting the phylum Firmicutes and Siphoviridae were predominant in most lakes evaluated. Functional analysis demonstrated a prevalence of unknown proteins (68 %) in the virome. Our prospective study provides virome analysis data from different lakes in the South Shetland Islands, Antarctica, opening exploratory lines for future research related to the biodiversity and viral ecology in this extreme ecosystem.
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Affiliation(s)
- Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil.
| | - Martha Lima Brandão
- FioAntar Project/ VPPIS - Fiocruz, Av Brasil 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Lucas Freitas
- Laboratory of Respiratory Virus and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro CEP 21040-360, Brazil
| | - Marcia Chame
- Institutional Platform for Biodiversity and Wildlife Health, Av Brasil 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Luciana Leomil
- SENAI Innovation Institute for Biosynthetics and Fibers, Technology Center for Chemical and Textile Industry, 4° Andar: Biotecnologia, Rua Fernando de Souza Barros, 120, Parque Tecnológico da UFRJ, Cidade Universitária, Rio de Janeiro CEP 21941-857, Brazil
| | - Maithê Gaspar Pontes Magalhães
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Wim Maurits Sylvain Degrave
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
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Liu Y, Ji M, Yu T, Zaugg J, Anesio AM, Zhang Z, Hu S, Hugenholtz P, Liu K, Liu P, Chen Y, Luo Y, Yao T. A genome and gene catalog of glacier microbiomes. Nat Biotechnol 2022; 40:1341-1348. [PMID: 35760913 DOI: 10.1038/s41587-022-01367-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/19/2022] [Indexed: 12/31/2022]
Abstract
Glaciers represent a unique inventory of microbial genetic diversity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional diversity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.
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Affiliation(s)
- Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China. .,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Tao Yu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Julian Zaugg
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St. Lucia, QLD, Australia
| | - Alexandre M Anesio
- Department of Environmental Science, iClimate, Aarhus University, Roskilde, Denmark
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St. Lucia, QLD, Australia
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Pengfei Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Luo
- University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Tandong Yao
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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de Menezes GCA, Câmara PEAS, Pinto OHB, Convey P, Carvalho-Silva M, Simões JC, Rosa CA, Rosa LH. Fungi in the Antarctic Cryosphere: Using DNA Metabarcoding to Reveal Fungal Diversity in Glacial Ice from the Antarctic Peninsula Region. MICROBIAL ECOLOGY 2022; 83:647-657. [PMID: 34228196 DOI: 10.1007/s00248-021-01792-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
We assessed fungal diversity present in glacial from the Antarctic Peninsula using DNA metabarcoding through high-throughput sequencing (HTS). We detected a total of 353,879 fungal DNA reads, representing 94 genera and 184 taxa, in glacial ice fragments obtained from seven sites in the north-west Antarctic Peninsula and South Shetland Islands. The phylum Ascomycota dominated the sequence diversity, followed by Basidiomycota and Mortierellomycota. Penicillium sp., Cladosporium sp., Penicillium atrovenetum, Epicoccum nigrum, Pseudogymnoascus sp. 1, Pseudogymnoascus sp. 2, Phaeosphaeriaceae sp. and Xylaria grammica were the most dominant taxa, respectively. However, the majority of the fungal diversity comprised taxa of rare and intermediate relative abundance, predominately known mesophilic fungi. High indices of diversity and richness were calculated, along with moderate index of dominance, which varied among the different sampling sites. Only 26 (14%) of the total fungal taxa detected were present at all sampling sites. The identified diversity was dominated by saprophytic taxa, followed by known plant and animal pathogens and a low number of symbiotic fungi. Our data suggest that Antarctic glacial ice may represent a hotspot of previously unreported fungal diversity; however, further studies are required to integrate HTS and culture approaches to confirm viability of the taxa detected.
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Affiliation(s)
- Graciéle Cunha Alves de Menezes
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, , CEP 31270-901, Brazil
| | | | | | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology , University of Johannesburg , Johannesburg, South Africa
| | | | - Jefferson Cardia Simões
- Centro Polar E Climático, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carlos Augusto Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, , CEP 31270-901, Brazil
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, , CEP 31270-901, Brazil.
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8
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Garcia-Lopez E, Moreno A, Bartolomé M, Leunda M, Sancho C, Cid C. Glacial Ice Age Shapes Microbiome Composition in a Receding Southern European Glacier. Front Microbiol 2021; 12:714537. [PMID: 34867842 PMCID: PMC8636055 DOI: 10.3389/fmicb.2021.714537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Glaciers and their microbiomes are exceptional witnesses of the environmental conditions from remote times. Climate change is threatening mountain glaciers, and especially those found in southern Europe, such as the Monte Perdido Glacier (northern Spain, Central Pyrenees). This study focuses on the reconstruction of the history of microbial communities over time. The microorganisms that inhabit the Monte Perdido Glacier were identified using high-throughput sequencing, and the microbial communities were compared along an altitudinal transect covering most of the preserved ice sequence in the glacier. The results showed that the glacial ice age gradient did shape the diversity of microbial populations, which presented large differences throughout the last 2000 years. Variations in microbial community diversity were influenced by glacial conditions over time (nutrient concentration, chemical composition, and ice age). Some groups were exclusively identified in the oldest samples as the bacterial phyla Fusobacteria and Calditrichaeota, or the eukaryotic class Rhodophyceae. Among groups only found in modern samples, the green sulfur bacteria (phylum Chlorobi) stood out, as well as the bacterial phylum Gemmatimonadetes and the eukaryotic class Tubulinea. A patent impact of human contamination was also observed on the glacier microbiome. The oldest samples, corresponding to the Roman Empire times, were influenced by the beginning of mining exploitation in the Pyrenean area, with the presence of metal-tolerant microorganisms. The most recent samples comprise 600-year-old ancient ice in which current communities are living.
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Affiliation(s)
- Eva Garcia-Lopez
- Molecular Evolution Department, Centro de Astrobiologia (CSIC-INTA), Madrid, Spain
| | - Ana Moreno
- Departamento de Procesos Geoambientales y Cambio Global, Instituto Pirenaico de Ecología-CSIC, Zaragoza, Spain
| | - Miguel Bartolomé
- Departamento de Geología, Museo de Ciencias Naturales-CSIC, Madrid, Spain
| | - Maria Leunda
- Oeschger Centre for Climate Change Research, Institute of Plant Sciences, University of Bern, Bern, Switzerland.,Swiss Federal Research Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Carlos Sancho
- Departamento de Ciencias de la Tierra, Universidad de Zaragoza, Zaragoza, Spain
| | - Cristina Cid
- Molecular Evolution Department, Centro de Astrobiologia (CSIC-INTA), Madrid, Spain
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9
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Liu W, Shao W, Wang Q. Does Fear of the New Coronavirus Lead to Low-Carbon Behaviors: The Moderating Effect of Outcome Framing. Risk Manag Healthc Policy 2021; 14:4185-4197. [PMID: 34675713 PMCID: PMC8504551 DOI: 10.2147/rmhp.s320241] [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: 05/17/2021] [Accepted: 08/29/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Air pollution has been found to aggravate the infection and mortality of COVID-19, leading to increasing attention on pro-environmental behaviors. Considering individuals' psychological distance from COVID-19, this research aims to examine the relationship between fear of COVID-19, air pollution concern, and low-carbon behaviors. METHODS Two survey-based studies were conducted in this research. Study 1 consisted of 323 participants and examined the relationships between psychological distance (PD) from COVID-19, fear of COVID-19, air pollution concern, and low-carbon behaviors. Study 2 identified the moderating effect of outcome framing using an intergroup experiment in which 304 participants were randomly assigned to two groups (gain framing vs loss framing). RESULTS The results of Study 1 showed that the closer the PD was, the higher the fear was. Fear of COVID-19 and low-carbon behaviors were positively associated. Additionally, air pollution concern acted as a mediator in their relationship. The results of the moderating effect test in Study 2 showed that fear and air pollution concern led to higher low-carbon behavioral intention within gain framing than within loss framing. CONCLUSION This research revealed that personal fear of public health emergencies will lead to environmental pollution concern and pro-environmental behaviors, and information from the outside plays a moderating role. The results provide implications for policy advocacy of the health and environmental sectors and for guiding people's low-carbon behaviors.
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Affiliation(s)
- Wenlong Liu
- School of Management, Fudan University, Shanghai, People’s Republic of China
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu, People’s Republic of China
| | - Wen Shao
- School of Economics & Management, Southeast University, Nanjing, Jiangsu, People’s Republic of China
| | - Qunwei Wang
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu, People’s Republic of China
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10
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Fungal diversity in the coastal waters of King George Island (maritime Antarctica). World J Microbiol Biotechnol 2021; 37:142. [PMID: 34322842 DOI: 10.1007/s11274-021-03112-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/14/2021] [Indexed: 12/19/2022]
Abstract
Fungi have been reported as common inhabitants of the maritime waters in Antarctica by studies based on culture-dependent methods. More recently, results obtained using DNA sequencing technologies, revealed that fungal diversity worldwide has been underestimated by culture methods. The present study provides the first characterization of fungal communities in the coastal waters of King George Island (maritime Antarctica) using both culture-dependent and high-throughput sequencing (HTS) methods. HTS demostrated a higher level of fungal diversity than the obtained by culture methods. A high prevalence of basidiomycetous yeasts and ascomycetous filamentous fungi was confirmed by both methods, however, Chythriomycota, Rozellomycota, lichenized fungi and Malassezia spp. were detected only by HTS. Correspondingly, members of some genera, such as Metschnikowia, were only found by culture-dependent methods. Our results confirm that culturing and HTS, should be seen as complementary approaches that enable one to obtain a more comprehensive picture of the composition of microbial communities.
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11
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Zhong ZP, Tian F, Roux S, Gazitúa MC, Solonenko NE, Li YF, Davis ME, Van Etten JL, Mosley-Thompson E, Rich VI, Sullivan MB, Thompson LG. Glacier ice archives nearly 15,000-year-old microbes and phages. MICROBIOME 2021; 9:160. [PMID: 34281625 PMCID: PMC8290583 DOI: 10.1186/s40168-021-01106-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/31/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination. RESULTS We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants. CONCLUSIONS Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally. Video Abstract.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Natalie E Solonenko
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Yueh-Fen Li
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Mary E Davis
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ellen Mosley-Thompson
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Geography, Ohio State University, Columbus, OH, USA
| | - Virginia I Rich
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.
- Department of Microbiology, Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA.
| | - Lonnie G Thompson
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA.
- School of Earth Sciences, Ohio State University, Columbus, OH, USA.
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12
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Pedrós-Alió C. Time travel in microorganisms. Syst Appl Microbiol 2021; 44:126227. [PMID: 34252729 DOI: 10.1016/j.syapm.2021.126227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), c/ Darwin 3, 28049 Madrid, Spain.
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13
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Yarzábal LA, Salazar LMB, Batista-García RA. Climate change, melting cryosphere and frozen pathogens: Should we worry…? ENVIRONMENTAL SUSTAINABILITY (SINGAPORE) 2021; 4:489-501. [PMID: 38624658 PMCID: PMC8164958 DOI: 10.1007/s42398-021-00184-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 11/21/2022]
Abstract
Permanently frozen environments (glaciers, permafrost) are considered as natural reservoirs of huge amounts of microorganisms, mostly dormant, including human pathogens. Due to global warming, which increases the rate of ice-melting, approximately 4 × 1021 of these microorganisms are released annually from their frozen confinement and enter natural ecosystems, in close proximity to human settlements. Some years ago, the hypothesis was put forward that this massive release of potentially-pathogenic microbes-many of which disappeared from the face of the Earth thousands and even millions of years ago-could give rise to epidemics. The recent anthrax outbreaks that occurred in Siberia, and the presence of bacterial and viral pathogens in glaciers worldwide, seem to confirm this hypothesis. In that context, the present review summarizes the currently available scientific evidence that allows us to imagine a near future in which epidemic outbreaks, similar to the abovementioned, could occur as a consequence of the resurrection and release of microbes from glaciers and permafrost. Supplementary Information The online version of this article (10.1007/s42398-021-00184-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luis Andrés Yarzábal
- Unidad de Salud y Bienestar, Universidad Católica de Cuenca, Av. Las Américas and Calle Humboldt, Cuenca, Ecuador
- Centro de Investigación, Innovación y Transferencia de Tecnología (CIITT), Universidad Católica de Cuenca, Campus Miracielos, Ricaurte, Ecuador
| | - Lenys M. Buela Salazar
- Unidad de Salud y Bienestar, Universidad Católica de Cuenca, Av. Las Américas and Calle Humboldt, Cuenca, Ecuador
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico
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14
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García-Lopez E, Serrano S, Calvo MA, Peña Perez S, Sanchez-Casanova S, García-Descalzo L, Cid C. Microbial Community Structure Driven by a Volcanic Gradient in Glaciers of the Antarctic Archipelago South Shetland. Microorganisms 2021; 9:microorganisms9020392. [PMID: 33672948 PMCID: PMC7917679 DOI: 10.3390/microorganisms9020392] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 11/26/2022] Open
Abstract
It has been demonstrated that the englacial ecosystem in volcanic environments is inhabited by active bacteria. To know whether this result could be extrapolated to other Antarctic glaciers and to study the populations of microeukaryotes in addition to those of bacteria, a study was performed using ice samples from eight glaciers in the South Shetland archipelago. The identification of microbial communities of bacteria and microeukaryotes using 16S rRNA and 18S rRNA high throughput sequencing showed a great diversity when compared with microbiomes of other Antarctic glaciers or frozen deserts. Even the composition of the microbial communities identified in the glaciers from the same island was different, which may be due to the isolation of microbial clusters within the ice. A gradient in the abundance and diversity of the microbial communities from the volcano (west to the east) was observed. Additionally, a significant correlation was found between the chemical conditions of the ice samples and the composition of the prokaryotic populations inhabiting them along the volcanic gradient. The bacteria that participate in the sulfur cycle were those that best fit this trend. Furthermore, on the eastern island, a clear influence of human contamination was observed on the glacier microbiome.
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15
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First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core. Sci Rep 2021; 11:514. [PMID: 33436712 PMCID: PMC7804186 DOI: 10.1038/s41598-020-79754-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/14/2020] [Indexed: 11/24/2022] Open
Abstract
Despite the unique physiology and metabolic pathways of microbiomes from cold environments providing key evolutionary insights and promising leads for discovering new bioactive compounds, cultivable bacteria entrapped in perennial ice from caves remained a largely unexplored life system. In this context, we obtained and characterized bacterial strains from 13,000-years old ice core of Scarisoara Ice Cave, providing first isolates from perennial ice accumulated in caves since Late Glacial, and first culture-based evidences of bacterial resistome and antimicrobial compounds production. The 68 bacterial isolates belonged to 4 phyla, 34 genera and 56 species, with 17 strains representing putative new taxa. The Gram-negative cave bacteria (Proteobacteria and Bacteroidetes) were more resistant to the great majority of antibiotic classes than the Gram-positive ones (Actinobacteria, Firmicutes). More than 50% of the strains exhibited high resistance to 17 classes of antibiotics. Some of the isolates inhibited the growth of clinically important Gram-positive and Gram-negative resistant strains and revealed metabolic features with applicative potential. The current report on bacterial strains from millennia-old cave ice revealed promising candidates for studying the evolution of environmental resistome and for obtaining new active biomolecules for fighting the antibiotics crisis, and valuable cold-active biocatalysts.
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16
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Sajjad W, Rafiq M, Din G, Hasan F, Iqbal A, Zada S, Ali B, Hayat M, Irfan M, Kang S. Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 735:139275. [PMID: 32480145 DOI: 10.1016/j.scitotenv.2020.139275] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
The present world faces a new threat of ancient microbes and resistomes that are locked in the cryosphere and now releasing upon thawing due to climate change and anthropogenic activities. The cryosphere act as the best preserving place for these microbes and resistomes that stay alive for millions of years. Current reviews extensively discussed whether the resurrection of microbes and resistomes existing in these pristine environments is true or just a hype. Release of these ancient microorganisms and naked DNA is of great concern for society as these microbes can either cause infections directly or they can interact with contemporary microorganisms and affect their fitness, survival, and mutation rate. Moreover, the contemporary microorganisms may uptake the unlocked naked DNA, which might transform non-pathogenic microorganisms into deadly antibiotic-resistant microbes. Additionally, the resurrection of glacial microorganisms can cause adverse effects on ecosystems downstream. The release of glacial pathogens and naked DNA is real and can lead to fatal outbreaks; therefore, we must prepare ourselves for the possible reemergence of diseases caused by these microbes. This study provides a scientific base for the adoption of actions by international cooperation to develop preventive measures.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
| | - Ghufranud Din
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Awais Iqbal
- School of Life Sciences, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, China
| | - Sahib Zada
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Muhammad Hayat
- Institute of Microbial Technology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao Campus, China
| | - Muhammad Irfan
- College of Dentistry, Department of Oral Biology, University of Florida, Gainesville, FL. USA
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
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17
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de Menezes GCA, Porto BA, Amorim SS, Zani CL, de Almeida Alves TM, Junior PAS, Murta SMF, Simões JC, Cota BB, Rosa CA, Rosa LH. Fungi in glacial ice of Antarctica: diversity, distribution and bioprospecting of bioactive compounds. Extremophiles 2020; 24:367-376. [PMID: 32157393 DOI: 10.1007/s00792-020-01161-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/21/2020] [Indexed: 01/21/2023]
Abstract
We identified cultivable fungi present in the glacial ice fragments collected in nine sites across Antarctica Peninsula and assessed their abilities to produce bioactive compounds. Three ice fragments with approximately 20 kg were collected, melted and 3 L filtered through of 0.45 µm sterilized membranes, which were placed on the media Sabouraud agar and minimal medium incubated at 10 °C. We collected 66 isolates classified into 27 taxa of 14 genera. Penicillium palitans, Penicillium sp. 1, Thelebolus balaustiformis, Glaciozyma antarctica, Penicillium sp. 7, Rhodotorula mucilaginosa, and Rhodotorula dairenensis had the highest frequencies. The diversity and richness of the fungal community were high with moderate dominance. Penicillium species were present in all samples, with Penicillium chrysogenum showing the broadest distribution. P. chrysogenum, P. palitans, and Penicillium spp. had trypanocidal, leishmanicidal, and herbicidal activities, with P. chrysogenum having the broadest and highest capability. 1H NMR signals revealed the presence of highly functionalized secondary metabolites in the bioactive extracts. Despite extreme environmental conditions, glacial ice harbours a diverse fungal community, including species never before recorded in the Arctic and Antarctica. Among them, Penicillium taxa may represent wild fungal strains with genetic and biochemical pathways that may produce new secondary bioactive metabolites.
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Affiliation(s)
- Graciéle Cunha Alves de Menezes
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - Bárbara Alves Porto
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - Soraya Sander Amorim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP 31270-901, Brazil
| | | | | | | | | | - Jefferson Cardia Simões
- Centro Polar e Climático, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Carlos Augusto Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP 31270-901, Brazil.
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18
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Sharma Ghimire P, Tripathee L, Zhang Q, Guo J, Ram K, Huang J, Sharma CM, Kang S. Microbial mercury methylation in the cryosphere: Progress and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134150. [PMID: 32380618 DOI: 10.1016/j.scitotenv.2019.134150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 06/11/2023]
Abstract
Mercury (Hg) is one of the most toxic heavy metals, and its cycle is mainly controlled by oxidation-reduction reactions carried out by photochemical or microbial process under suitable conditions. The deposition and accumulation of methylmercury (MeHg) in various ecosystems, including the cryospheric components such as snow, meltwater, glaciers, and ice sheet, and subsequently in the food chain pose serious health concerns for living beings. Unlike the abundance of knowledge about the processes of MeHg production over land and oceans, little is known about the sources and production/degradation rate of MeHg in cryosphere systems. In addition, processes controlling the concentration of Hg and MeHg in the cryosphere remains poorly understood, and filling this scientific gap has been challenging. Therefore, it is essential to study and review the deposition and accumulation by biological, physical, and chemical mechanisms involved in Hg methylation in the cryosphere. This review attempts to address knowledge gaps in understanding processes, especially biotic and abiotic, applicable for Hg methylation in the cryosphere. First, we focus on the variability in Hg concentration and mechanisms of Hg methylation, including physical, chemical, microbial, and biological processes, and transportation in the cryosphere. Then, we elaborate on the mechanism of redox reactions and biotic and abiotic factors controlling Hg methylation and biogeochemistry of Hg in the cryosphere. We also present possible mechanisms of Hg methylation with an emphasis on microbial transformation and molecular function to understand variability in Hg concentration in the cryosphere. Recent advancements in the genetic and physicochemical mechanisms of Hg methylation are also presented. Finally, we summarize and propose a method to study the unsolved issues of Hg methylation in the cryosphere.
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Affiliation(s)
- Prakriti Sharma Ghimire
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; Himalayan Environment Research Institute (HERI), Kathmandu, Nepal
| | - Lekhendra Tripathee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; Himalayan Environment Research Institute (HERI), Kathmandu, Nepal.
| | - Qianggong Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China
| | - Junming Guo
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Kirpa Ram
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Jie Huang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China; Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Chhatra Mani Sharma
- Himalayan Environment Research Institute (HERI), Kathmandu, Nepal; Central Department of Environmental Science, Tribhuvan University, Kathmandu, Nepal
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China.
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19
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Paun VI, Icaza G, Lavin P, Marin C, Tudorache A, Perşoiu A, Dorador C, Purcarea C. Total and Potentially Active Bacterial Communities Entrapped in a Late Glacial Through Holocene Ice Core From Scarisoara Ice Cave, Romania. Front Microbiol 2019; 10:1193. [PMID: 31244788 PMCID: PMC6563852 DOI: 10.3389/fmicb.2019.01193] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/13/2019] [Indexed: 01/20/2023] Open
Abstract
Our understanding of the icy-habitat microbiome is likely limited by a lack of reliable data on microorganisms inhabiting underground ice that has accumulated inside caves. To characterize how environmental variation impacts cave ice microbial community structure, we determined the composition of total and potentially active bacterial communities along a 13,000-year-old ice core from Scarisoara cave (Romania) through 16S rRNA gene Illumina sequencing. An average of 2,546 prokaryotic gDNA operational taxonomic units (OTUs) and 585 cDNA OTUs were identified across the perennial cave ice block and analyzed in relation to the geochemical composition of ice layers. The total microbial community and the putative active fraction displayed dissimilar taxa profiles. The ice-contained microbiome was dominated by Actinobacteria with a variable representation of Proteobacteria, while the putative active microbial community was equally shared between Proteobacteria and Firmicutes. Accordingly, a major presence of Cryobacterium, Lysinomonas, Pedobacter, and Aeromicrobium phylotypes homologous to psychrotrophic and psychrophilic bacteria from various cold environments were noted in the total community, while the prevalent putative active bacteria belonged to Clostridium, Pseudomonas, Janthinobacterium, Stenotrophomonas, and Massilia genera. Variation in the microbial cell density of ice strata with the dissolved organic carbon (DOC) content and the strong correlation of DOC and silicon concentrations revealed a major impact of depositional processes on microbial abundance throughout the ice block. Post-depositional processes appeared to occur mostly during the 4,000–7,000 years BP interval. A major bacterial composition shift was observed in 4,500–5,000-year-old ice, leading to a high representation of Beta- and Deltaproteobacteria in the potentially active community in response to the increased concentrations of DOC and major chemical elements. Estimated metabolic rates suggested the presence of a viable microbial community within the cave ice block, characterized by a maintenance metabolism in most strata and growth capacity in those ice deposits with high microbial abundance and DOC content. This first survey of microbial distribution in perennial cave ice formed since the Last Glacial period revealed a complex potentially active community, highlighting major shifts in community composition associated with geochemical changes that took place during climatic events that occurred about 5,000 years ago, with putative formation of photosynthetic biofilms.
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Affiliation(s)
- Victoria I Paun
- Department of Microbiology, Institute of Biology, Bucharest, Romania
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Paris Lavin
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Constantin Marin
- Laboratory of Hydrogeochemistry, "Emil Racovita" Institute of Speleology, Bucharest, Romania
| | - Alin Tudorache
- Laboratory of Hydrogeochemistry, "Emil Racovita" Institute of Speleology, Bucharest, Romania
| | - Aurel Perşoiu
- Department of Microbiology, Institute of Biology, Bucharest, Romania.,"Emil Racovita" Institute of Speleology, Cluj-Napoca, Romania.,Stefan cel Mare University of Suceava, Suceava, Romania
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology, Bucharest, Romania
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20
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Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Zhan Y, Marsan D, Chen F, Fuhrman JA, Northen TR, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA. Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ 2019; 7:e6902. [PMID: 31119088 PMCID: PMC6511391 DOI: 10.7717/peerj.6902] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/03/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. METHODS Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. RESULTS Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. CONCLUSIONS PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.
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Affiliation(s)
- Simon Roux
- Department of Energy Joint Genome Institute, Walnut Creek, CA, United States of America
| | - Gareth Trubl
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Walnut Creek, CA, United States of America
| | - Nandita Nath
- Department of Energy Joint Genome Institute, Walnut Creek, CA, United States of America
| | - Estelle Couradeau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Nathan A. Ahlgren
- Department of Biology, Clark University, Worcester, MA, United States of America
| | - Yuanchao Zhan
- Institution of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - David Marsan
- Institution of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - Feng Chen
- Institution of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - Jed A. Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Trent R. Northen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, United States of America
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States of America
| | - Virginia I. Rich
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Rex R. Malmstrom
- Department of Energy Joint Genome Institute, Walnut Creek, CA, United States of America
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21
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Zhong ZP, Solonenko NE, Gazitúa MC, Kenny DV, Mosley-Thompson E, Rich VI, Van Etten JL, Thompson LG, Sullivan MB. Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms. Front Microbiol 2018; 9:1094. [PMID: 29910780 PMCID: PMC5992382 DOI: 10.3389/fmicb.2018.01094] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/07/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms in glacier ice provide tens to hundreds of thousands of years archive for a changing climate and microbial responses to it. Analyzing ancient ice is impeded by technical issues, including limited ice, low biomass, and contamination. While many approaches have been evaluated and advanced to remove contaminants on ice core surfaces, few studies leverage modern sequencing to establish in silico decontamination protocols for glacier ice. Here we sought to apply such “clean” sampling techniques with in silico decontamination approaches used elsewhere to investigate microorganisms archived in ice at ∼41 (D41, ∼20,000 years) and ∼49 m (D49, ∼30,000 years) depth in an ice core (GS3) from the summit of the Guliya ice cap in the northwestern Tibetan Plateau. Four “background” controls were established – a co-processed sterile water artificial ice core, two air samples collected from the ice processing laboratories, and a blank, sterile water sample – and used to assess contaminant microbial diversity and abundances. Amplicon sequencing revealed 29 microbial genera in these controls, but quantitative PCR showed that the controls contained about 50–100-times less 16S DNA than the glacial ice samples. As in prior work, we interpreted these low-abundance taxa in controls as “contaminants” and proportionally removed them in silico from the GS3 ice amplicon data. Because of the low biomass in the controls, we also compared prokaryotic 16S DNA amplicons from pre-amplified (by re-conditioning PCR) and standard amplicon sequencing, and found the resulting microbial profiles to be repeatable and nearly identical. Ecologically, the contaminant-controlled ice microbial profiles revealed significantly different microorganisms across the two depths in the GS3 ice core, which is consistent with changing climate, as reported for other glacier ice samples. Many GS3 ice core genera, including Methylobacterium, Sphingomonas, Flavobacterium, Janthinobacterium, Polaromonas, and Rhodobacter, were also abundant in previously studied ice cores, which suggests wide distribution across glacier environments. Together these findings help further establish “clean” procedures for studying low-biomass ice microbial communities and contribute to a baseline understanding of microorganisms archived in glacier ice.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Maria C Gazitúa
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Donald V Kenny
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States
| | - Ellen Mosley-Thompson
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States.,Department of Geography, The Ohio State University, Columbus, OH, United States
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, United States.,Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Lonnie G Thompson
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States.,School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, United States.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
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22
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Managadze GG, Safronova AA, Luchnikov KA, Vorobyova EA, Duxbury NS, Wurz P, Managadze NG, Chumikov AE, Khamizov RK. A New Method and Mass-Spectrometric Instrument for Extraterrestrial Microbial Life Detection Using the Elemental Composition Analyses of Martian Regolith and Permafrost/Ice. ASTROBIOLOGY 2017; 17:448-458. [PMID: 28520473 DOI: 10.1089/ast.2016.1511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We propose a new technique for the detection of microorganisms by elemental composition analyses of a sample extracted from regolith, permafrost, and ice of extraterrestrial bodies. We also describe the design of the ABIMAS instrument, which consists of the onboard time-of-flight laser mass-reflectron (TOF LMR) and the sample preparation unit (SPU) for biomass extraction. This instrument was initially approved to fly on board the ExoMars 2020 lander mission. The instrument can be used to analyze the elemental composition of possible extraterrestrial microbial communities and compare it to that of terrestrial microorganisms. We have conducted numerous laboratory studies to confirm the possibility of biomass identification via the following biomarkers: P/S and Ca/K ratios, and C and N abundances. We underline that only the combination of these factors will allow one to discriminate microbial samples from geological ones. Our technique has been tested experimentally in numerous laboratory trials on cultures of microorganisms and polar permafrost samples as terrestrial analogues for martian polar soils. We discuss various methods of extracting microorganisms and sample preparation. The developed technique can be used to search for and identify microorganisms in different martian samples and in the subsurface of other planets, satellites, comets, and asteroids-in particular, Europa, Ganymede, and Enceladus. Key Words: Mass spectrometry-Life-detection instruments-Biomarkers-Earth Mars-Biomass spectra. Astrobiology 17, 448-458.
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Affiliation(s)
- G G Managadze
- 1 Space Research Institute , Russian Academy of Sciences, Moscow, Russian Federation
| | - A A Safronova
- 1 Space Research Institute , Russian Academy of Sciences, Moscow, Russian Federation
| | - K A Luchnikov
- 1 Space Research Institute , Russian Academy of Sciences, Moscow, Russian Federation
| | - E A Vorobyova
- 1 Space Research Institute , Russian Academy of Sciences, Moscow, Russian Federation
- 2 Soil Science Faculty, Lomonosov Moscow State University , Moscow, Russian Federation
| | - N S Duxbury
- 3 Department of Physics, Astronomy and Computational Sciences, George Mason University , Fairfax, Virginia, USA
- 4 Geology Faculty, Lomonosov Moscow State University , Moscow, Russian Federation
| | - P Wurz
- 5 Physics Institute, University of Bern , Bern, Switzerland
| | - N G Managadze
- 1 Space Research Institute , Russian Academy of Sciences, Moscow, Russian Federation
| | - A E Chumikov
- 1 Space Research Institute , Russian Academy of Sciences, Moscow, Russian Federation
| | - R Kh Khamizov
- 6 Institute of Geological Chemistry , Russian Academy of Sciences, Moscow, Russian Federation
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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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Singh P, Singh SM, Roy U. Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic. J Basic Microbiol 2015; 56:275-85. [PMID: 26567474 DOI: 10.1002/jobm.201500298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 10/18/2015] [Indexed: 11/05/2022]
Abstract
Glacier ice and firn cores have ecological and biotechnological importance. The present study is aimed at characterizing bacteria in crustal ice cores from Svalbard, the Arctic. Counts of viable isolates ranged from 10 to 7000 CFU/ml (mean 803 CFU/ml) while the total bacterial numbers ranged from 7.20 × 10(4) to 2.59 × 10(7) cells ml(-1) (mean 3.12 × 10(6) cells ml(-1) ). Based on 16S rDNA sequence data, the identified species belonged to seven species, namely Bacillus barbaricus, Pseudomonas orientalis, Pseudomonas oryzihabitans, Pseudomonas fluorescens, Pseudomonas syncyanea, Sphingomonas dokdonensis, and Sphingomonas phyllosphaerae, with a sequence similarity ranging between 93.5 and 99.9% with taxa present in the database. The isolates exhibited unique phenotypic properties, and three isolates (MLB-2, MLB-5, and MLB-9) are novel species, yet to be described. To the best of our knowledge, this is the first report on characterization of cultured bacterial communities from Svalbard ice cores. We conclude that high lipase, protease, cellulase, amylase, and urease activities expressed by most of the isolates provide a clue to the potential industrial applications of these organisms. These microbes, producing cold-adapted enzymes may provide an opportunity for biotechnological research.
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Affiliation(s)
- Purnima Singh
- Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, Zuarinagar, Goa-403726, India
| | - Shiv Mohan Singh
- National Centre for Antarctic and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa-403804, India
| | - Utpal Roy
- Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, Zuarinagar, Goa-403726, India
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Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014; 12:87. [PMID: 25387460 PMCID: PMC4228153 DOI: 10.1186/s12915-014-0087-z] [Citation(s) in RCA: 2034] [Impact Index Per Article: 203.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/13/2014] [Indexed: 12/11/2022] Open
Abstract
Background The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. Results In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Conclusions These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0087-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susannah J Salter
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK.
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