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Thweatt JL, Harman CE, Araújo MN, Marlow JJ, Oliver GC, Sabuda MC, Sevgen S, Wilpiszeki RL. Chapter 6: The Breadth and Limits of Life on Earth. ASTROBIOLOGY 2024; 24:S124-S142. [PMID: 38498824 DOI: 10.1089/ast.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.
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Affiliation(s)
- Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - C E Harman
- Planetary Systems Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
- Blue Marble Space Institute of Science, Seattle, Washington, USA
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Ren Z, Ye S, Li H, Huang X, Chen L, Cao S, Chen T. Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau. MICROBIAL ECOLOGY 2023; 86:2756-2769. [PMID: 37542537 DOI: 10.1007/s00248-023-02280-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 Beijing East Road, Nanjing, 210008, China.
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China.
| | - Shudan Ye
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Hongxuan Li
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Xilei Huang
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Luyao Chen
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Shengkui Cao
- School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Tao Chen
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, 768 Jiayuguan W Road, Lanzhou, 730020, China.
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Chan-Yam K, Goordial J, Greer C, Davila A, McKay CP, Whyte LG. Microbial Activity and Habitability of an Antarctic Dry Valley Water Track. ASTROBIOLOGY 2019; 19:757-770. [PMID: 30958705 DOI: 10.1089/ast.2018.1884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Water tracks in the Antarctic Dry Valleys are dark linear features of increased soil moisture that flow downslope over the spring and summer, providing a source of moisture in a cold-arid desert. They are typically sourced from melting snow, ground ice, and deliquescence (Levy et al., 2011 ). This research presents the first in-depth study of the activity potential and diversity of microbial communities of Antarctic water tracks. We investigated whether these water track soils are more habitable to microbial communities by ascertaining the differences in diversity, total and culturable cell counts, and microbial respiratory activity in water track soils compared with the adjacent dry soils in Pearse Valley. Total cell counts ranged from 1.47 × 103 to 4.17 × 105 cells/g dry weight soil. Water track soils had higher total and culturable biomass, in addition to higher microbial activity at 5° and -5°C, compared with adjacent dry soils. Microbial respiration was positively correlated with soil moisture content, but total cell counts and plate counts were not. Surprisingly, microbial community composition did not differ between wet and dry soil communities, and was not related to soil moisture content. The microbial community composition instead appeared to differ spatially based on location and depth. Overall, the data suggest that cold water tracks are more habitable than the surrounding cold-arid soils. Our results suggest that recurring slope lineae, which are dark linear features that grow downslope on Mars over the spring and summer, where liquid water might be a recurring phenomenon, could be sites of astrobiological potential.
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Affiliation(s)
- Kelly Chan-Yam
- 1 Department of Natural Resource Sciences, McGill University, Montreal, Canada
| | - Jacqueline Goordial
- 1 Department of Natural Resource Sciences, McGill University, Montreal, Canada
- 2 Bigelow Laboratory for Ocean Sciences, East Boothbay Harbor, Maine
| | - Charles Greer
- 3 National Research Council of Canada, Montreal, Canada
| | | | | | - Lyle G Whyte
- 1 Department of Natural Resource Sciences, McGill University, Montreal, Canada
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Donhauser J, Frey B. Alpine soil microbial ecology in a changing world. FEMS Microbiol Ecol 2018; 94:5017441. [PMID: 30032189 DOI: 10.1093/femsec/fiy099] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/25/2018] [Indexed: 01/22/2023] Open
Abstract
Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.
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Affiliation(s)
| | - Beat Frey
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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Monteux S, Weedon JT, Blume-Werry G, Gavazov K, Jassey VEJ, Johansson M, Keuper F, Olid C, Dorrepaal E. Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration. ISME JOURNAL 2018; 12:2129-2141. [PMID: 29875436 PMCID: PMC6092332 DOI: 10.1038/s41396-018-0176-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 03/15/2018] [Accepted: 03/28/2018] [Indexed: 12/05/2022]
Abstract
The decomposition of large stocks of soil organic carbon in thawing permafrost might depend on more than climate change-induced temperature increases: indirect effects of thawing via altered bacterial community structure (BCS) or rooting patterns are largely unexplored. We used a 10-year in situ permafrost thaw experiment and aerobic incubations to investigate alterations in BCS and potential respiration at different depths, and the extent to which they are related with each other and with root density. Active layer and permafrost BCS strongly differed, and the BCS in formerly frozen soils (below the natural thawfront) converged under induced deep thaw to strongly resemble the active layer BCS, possibly as a result of colonization by overlying microorganisms. Overall, respiration rates decreased with depth and soils showed lower potential respiration when subjected to deeper thaw, which we attributed to gradual labile carbon pool depletion. Despite deeper rooting under induced deep thaw, root density measurements did not improve soil chemistry-based models of potential respiration. However, BCS explained an additional unique portion of variation in respiration, particularly when accounting for differences in organic matter content. Our results suggest that by measuring bacterial community composition, we can improve both our understanding and the modeling of the permafrost carbon feedback.
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Affiliation(s)
- Sylvain Monteux
- Climate Impacts Research Centre (CIRC), Department of Ecology and Environmental Sciences, Umeå Universitet, 981 07, Abisko, Sweden.
| | - James T Weedon
- Systems Ecology, Department of Ecological Sciences, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands.,PLECO, Department of Biology, University of Antwerp, 2610, Wilrijk, Belgium
| | - Gesche Blume-Werry
- Climate Impacts Research Centre (CIRC), Department of Ecology and Environmental Sciences, Umeå Universitet, 981 07, Abisko, Sweden
| | - Konstantin Gavazov
- Climate Impacts Research Centre (CIRC), Department of Ecology and Environmental Sciences, Umeå Universitet, 981 07, Abisko, Sweden.,Federal Institute for Forest, Snow and Landscape Research WSL, CH-1015, Lausanne, Switzerland
| | - Vincent E J Jassey
- Functional Ecology and Environment Laboratory (ECOLAB), Department of Biology and Geosciences, UMR 6245 Université Toulouse III Paul Sabatier, 31062, Toulouse cedex 09, France
| | - Margareta Johansson
- Department of Physical Geography and Ecosystem Science, Lund Universitet, 223 62, Lund, Sweden
| | - Frida Keuper
- INRA, AgroImpact UR1158, Site Laon, 02000, Barenton Bugny, France
| | - Carolina Olid
- Climate Impacts Research Centre (CIRC), Department of Ecology and Environmental Sciences, Umeå Universitet, 981 07, Abisko, Sweden
| | - Ellen Dorrepaal
- Climate Impacts Research Centre (CIRC), Department of Ecology and Environmental Sciences, Umeå Universitet, 981 07, Abisko, Sweden
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Zhao Y, Song C, Dong H, Luo Y, Wei Y, Gao J, Wu Q, Huang Y, An L, Sheng H. Community structure and distribution of culturable bacteria in soil along an altitudinal gradient of Tianshan Mountains, China. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1396195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Yanting Zhao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Chunli Song
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Hongqiang Dong
- Xinjiang Production & Construction Crops Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Plant Sciences, Tarim University, Alare Xinjiang, PR China
| | - Yang Luo
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Yali Wei
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Jiangli Gao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Qianqian Wu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Yaolong Huang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Lizhe An
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Hongmei Sheng
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, PR China
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Hu W, Zhang Q, Tian T, Cheng G, An L, Feng H. The microbial diversity, distribution, and ecology of permafrost in China: a review. Extremophiles 2015; 19:693-705. [PMID: 25925876 DOI: 10.1007/s00792-015-0749-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/04/2015] [Indexed: 11/29/2022]
Abstract
Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.
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Affiliation(s)
- Weigang Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 °C and hypersaline sediments of a high Arctic permafrost spring. Extremophiles 2014; 19:1-15. [DOI: 10.1007/s00792-014-0703-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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Taş N, Prestat E, McFarland JW, Wickland KP, Knight R, Berhe AA, Jorgenson T, Waldrop MP, Jansson JK. Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. THE ISME JOURNAL 2014; 8:1904-19. [PMID: 24722629 PMCID: PMC4139727 DOI: 10.1038/ismej.2014.36] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/31/2014] [Accepted: 02/07/2014] [Indexed: 11/08/2022]
Abstract
Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG-CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle.
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Affiliation(s)
- Neslihan Taş
- Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emmanuel Prestat
- Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Rob Knight
- Howard Hughes Medical Institute and Departments of Chemistry and Biochemistry and Computer Science, and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | | | | | | | - Janet K Jansson
- Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Genome Institute (JGI), Walnut Creek, CA, USA
- Joint BioEnergy Institute (JBEI), Emeryville, CA, USA
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Hu W, Zhang Q, Li D, Cheng G, Mu J, Wu Q, Niu F, An L, Feng H. Diversity and community structure of fungi through a permafrost core profile from the Qinghai-Tibet Plateau of China. J Basic Microbiol 2014; 54:1331-41. [DOI: 10.1002/jobm.201400232] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/18/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Weigang Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Qi Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Dingyao Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Gang Cheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Jing Mu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Qingbai Wu
- State Key Laboratory of Frozen Soil Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI); Chinese Academy of Sciences; Lanzhou China
| | - Fujun Niu
- State Key Laboratory of Frozen Soil Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI); Chinese Academy of Sciences; Lanzhou China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Huyuan Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
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Abstract
Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.
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Affiliation(s)
- Janet K Jansson
- 1] Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 70A-3317 Berkeley, California 94720, USA. [2] Joint Genome Institute (JGI), 2800 Mitchell Drive, Walnut Creek, California 94598, USA. [3] Joint BioEnergy Institute (JBEI), 5885 Hollis Street, Emeryville, California 94608, USA. [4] Danish Center for Permafrost (CENPERM), University of Copenhagen, Oester Voldgade 10, DK-1350 Copenhagen, Denmark. [5] Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, California 94720-3102, USA
| | - Neslihan Taş
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 70A-3317 Berkeley, California 94720, USA
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Vishnivetskaya TA, Layton AC, Lau MCY, Chauhan A, Cheng KR, Meyers AJ, Murphy JR, Rogers AW, Saarunya GS, Williams DE, Pfiffner SM, Biggerstaff JP, Stackhouse BT, Phelps TJ, Whyte L, Sayler GS, Onstott TC. Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiol Ecol 2013; 87:217-30. [PMID: 24102625 DOI: 10.1111/1574-6941.12219] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/30/2022] Open
Abstract
The total community genomic DNA (gDNA) from permafrost was extracted using four commercial DNA extraction kits. The gDNAs were compared using quantitative real-time PCR (qPCR) targeting 16S rRNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16S rRNA (V3 region) amplified in single or nested PCR. The FastDNA(®) SPIN (FDS) Kit provided the highest gDNA yields and 16S rRNA gene concentrations, followed by MoBio PowerSoil(®) (PS) and MoBio PowerLyzer™ (PL) kits. The lowest gDNA yields and 16S rRNA gene concentrations were from the Meta-G-Nome™ (MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted UniFrac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed β- and γ-Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that gDNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using gDNAs from the three bead-beating lysis extraction kits.
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Steven B, Lionard M, Kuske CR, Vincent WF. High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert. PLoS One 2013; 8:e71489. [PMID: 23967218 PMCID: PMC3742766 DOI: 10.1371/journal.pone.0071489] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/05/2013] [Indexed: 11/18/2022] Open
Abstract
In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.
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Affiliation(s)
- Blaire Steven
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Marie Lionard
- Département de biologie, Université Laval, Québec City, Québec, Canada
- Centre d’Études Nordiques, Université Laval, Québec City, Québec, Canada
| | - Cheryl R. Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Warwick F. Vincent
- Département de biologie, Université Laval, Québec City, Québec, Canada
- Centre d’Études Nordiques, Université Laval, Québec City, Québec, Canada
- * E-mail:
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14
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Goordial J, Lamarche-Gagnon G, Lay CY, Whyte L. Left Out in the Cold: Life in Cryoenvironments. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-94-007-6488-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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15
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Kim HM, Chae N, Jung JY, Lee YK. Isolation of facultatively anaerobic soil bacteria from Ny-Ålesund, Svalbard. Polar Biol 2013. [DOI: 10.1007/s00300-013-1302-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Blanco Y, Prieto-Ballesteros O, Gómez MJ, Moreno-Paz M, García-Villadangos M, Rodríguez-Manfredi JA, Cruz-Gil P, Sánchez-Román M, Rivas LA, Parro V. Prokaryotic communities and operating metabolisms in the surface and the permafrost of Deception Island (Antarctica). Environ Microbiol 2012; 14:2495-510. [PMID: 22564293 DOI: 10.1111/j.1462-2920.2012.02767.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this study we examined the microbial community composition and operating metabolisms on the surface and in the permafrost of Deception Island, (Antarctica) with an on site antibody microarray biosensor. Samples (down to a depth of 4.2 m) were analysed with LDChip300 (Life Detector Chip), an immunosensor containing more than 300 antibodies targeted to bacterial and archaeal antigens. The immunograms showed positive antigen-antibody reactions in all surface samples (lichens, pyroclasts) and the top layer of the permafrost. The results indicated the presence of exopolysaccharides, bacteria belonging to the Alpha-, Delta- and Gammaproteobacteria, Bacteroidetes, Gram-positive Actinobacteria and Firmicutes, as well as archaeal species, most probably Methanobacterium spp. Positive reactions with antibodies to proteins and peptides revealed the presence of nitrogen fixation (NifHD, GlnB, HscA), methanogenic (McrB), iron homeostasis and iron scavenging (ferritins and DPS proteins) proteins, as well as ABC transporters, which indicated that these processes were operating at the time of sampling. These results were validated with other molecular ecology techniques such as oligonucleotide microarrays, 16S bacterial rRNA gene sequence analysis, aerobic viable counts and microscopy. Molecular ecology results showed a differentiated pattern along the depth of the drill, being the top active layer the most diverse, with Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes and the phototrophs Cyanobacteria and Chloroflexi as dominant groups. Actinobacteria and Firmicutes were dominant in depths from 0.5 to 2 m, and Betaproteobacteria from 3 to 4.2 m. The geochemical analysis revealed the presence of low molecular weight organic acids (acetate, formate) which could be used by microorganisms as energy sources for sulfate, nitrate and metal reduction under anaerobic conditions.
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Affiliation(s)
- Yolanda Blanco
- Departments of Molecular Evolution Planetology and Habitability Instrumentation, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
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Wilhelm RC, Radtke KJ, Mykytczuk NCS, Greer CW, Whyte LG. Life at the wedge: the activity and diversity of arctic ice wedge microbial communities. ASTROBIOLOGY 2012; 12:347-360. [PMID: 22519974 DOI: 10.1089/ast.2011.0730] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The discovery of polygonal terrain on Mars underlain by ice heightens interest in the possibility that this water-bearing habitat may be, or may have been, a suitable habitat for extant life. The possibility is supported by the recurring detection of terrestrial microorganisms in subsurface ice environments, such as ice wedges found beneath tundra polygon features. A characterization of the microbial community of ice wedges from the high Arctic was performed to determine whether this ice environment can sustain actively respiring microorganisms and to assess the ecology of this extreme niche. We found that ice wedge samples contained a relatively abundant number of culturable cells compared to other ice habitats (∼10(5) CFU·mL(-1)). Respiration assays in which radio-labeled acetate and in situ measurement of CO(2) flux were used suggested low levels of microbial activity, though more sensitive techniques are required to confirm these findings. Based on 16S rRNA gene pyrosequencing, bacterial and archaeal ice wedge communities appeared to reflect surrounding soil communities. Two Pseudomonas sp. were the most abundant taxa in the ice wedge bacterial library (∼50%), while taxa related to ammonia-oxidizing Thaumarchaeota occupied 90% of the archaeal library. The tolerance of a variety of isolates to salinity and temperature revealed characteristics of a psychrotolerant, halotolerant community. Our findings support the hypothesis that ice wedges are capable of sustaining a diverse, plausibly active microbial community. As such, ice wedges, compared to other forms of less habitable ground ice, could serve as a reservoir for life on permanently cold, water-scarce, ice-rich extraterrestrial bodies and are therefore of interest to astrobiologists and ecologists alike. .
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Affiliation(s)
- Roland C Wilhelm
- Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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Microbial diversity and activity in hypersaline high Arctic spring channels. Extremophiles 2012; 16:177-91. [PMID: 22246205 DOI: 10.1007/s00792-011-0417-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022]
Abstract
Lost Hammer (LH) spring is a unique hypersaline, subzero, perennial high Arctic spring arising through thick permafrost. In the present study, the microbial and geochemical characteristics of the LH outflow channels, which remain unfrozen at ≥-18°C and are more aerobic/less reducing than the spring source were examined and compared to the previously characterized spring source environment. LH channel sediments contained greater microbial biomass (~100-fold) and greater microbial diversity reflected by the 16S rRNA clone libraries. Phylotypes related to methanogenesis, methanotrophy, sulfur reduction and oxidation were detected in the bacterial clone libraries while the archaeal community was dominated by phylotypes most closely related to THE ammonia-oxidizing Thaumarchaeota. The cumulative percent recovery of (14)C-acetate mineralization in channel sediment microcosms exceeded ~30% and ~10% at 5 and -5°C, respectively, but sharply decreased at -10°C (≤1%). Most bacterial isolates (Marinobacter, Planococcus, and Nesterenkonia spp.) were psychrotrophic, halotolerant, and capable of growth at -5°C. Overall, the hypersaline, subzero LH spring channel has higher microbial diversity and activity than the source, and supports a variety of niches reflecting the more dynamic and heterogeneous channel environment.
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Prasad S, Manasa P, Buddhi S, Singh SM, Shivaji S. Antagonistic interaction networks among bacteria from a cold soil environment. FEMS Microbiol Ecol 2011; 78:376-85. [DOI: 10.1111/j.1574-6941.2011.01171.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 07/07/2011] [Accepted: 07/07/2011] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sathish Prasad
- Centre for Cellular and Molecular Biology; Hyderabad; India
| | - Poorna Manasa
- Centre for Cellular and Molecular Biology; Hyderabad; India
| | - Sailaja Buddhi
- Centre for Cellular and Molecular Biology; Hyderabad; India
| | - Shiv Mohan Singh
- National Centre for Antarctic & Ocean Research; Ministry of Earth Sciences; Government of India; Vasco-da-Gama; Goa; India
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Hinsa-Leasure SM, Bhavaraju L, Rodrigues JLM, Bakermans C, Gilichinsky DA, Tiedje JM. Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample. FEMS Microbiol Ecol 2010; 74:103-13. [PMID: 20695892 DOI: 10.1111/j.1574-6941.2010.00945.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME JOURNAL 2010; 4:1206-14. [DOI: 10.1038/ismej.2010.41] [Citation(s) in RCA: 238] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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