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Sannino C, Qi W, Rüthi J, Stierli B, Frey B. Distinct taxonomic and functional profiles of high Arctic and alpine permafrost-affected soil microbiomes. ENVIRONMENTAL MICROBIOME 2023; 18:54. [PMID: 37328770 DOI: 10.1186/s40793-023-00509-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Global warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze-thaw cycles occurring in permafrost-affected soils, and mainly in the seasonally active top layers, modify microbial communities and consequently ecosystem processes. Although taxonomic responses of the microbiomes in permafrost-affected soils have been widely documented, studies about how the microbial genetic potential, especially pathways involved in C and N cycling, changes between active-layer soils and permafrost soils are rare. Here, we used shotgun metagenomics to analyze the microbial and functional diversity and the metabolic potential of permafrost-affected soil collected from an alpine site (Val Lavirun, Engadin area, Switzerland) and a High Arctic site (Station Nord, Villum Research Station, Greenland). The main goal was to discover the key genes abundant in the active-layer and permafrost soils, with the purpose to highlight the potential role of the functional genes found. RESULTS We observed differences between the alpine and High Arctic sites in alpha- and beta-diversity, and in EggNOG, CAZy, and NCyc datasets. In the High Arctic site, the metagenome in permafrost soil had an overrepresentation (relative to that in active-layer soil) of genes involved in lipid transport by fatty acid desaturate and ABC transporters, i.e. genes that are useful in preventing microorganisms from freezing by increasing membrane fluidity, and genes involved in cell defense mechanisms. The majority of CAZy and NCyc genes were overrepresented in permafrost soils relative to active-layer soils in both localities, with genes involved in the degradation of carbon substrates and in the degradation of N compounds indicating high microbial activity in permafrost in response to climate warming. CONCLUSIONS Our study on the functional characteristics of permafrost microbiomes underlines the remarkably high functional gene diversity of the High Arctic and temperate mountain permafrost, including a broad range of C- and N-cycling genes, and multiple survival and energetic metabolisms. Their metabolic versatility in using organic materials from ancient soils undergoing microbial degradation determine organic matter decomposition and greenhouse gas emissions upon permafrost thawing. Attention to their functional genes is therefore essential to predict potential soil-climate feedbacks to the future warmer climate.
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Affiliation(s)
- Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Joel Rüthi
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland.
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Napoli A, Coleine C, Ulrich NJ, Moeller R, Billi D, Selbmann L. Snow Surface Microbial Diversity at the Detection Limit within the Vicinity of the Concordia Station, Antarctica. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010113. [PMID: 36676062 PMCID: PMC9863605 DOI: 10.3390/life13010113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/17/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023]
Abstract
The Concordia Research Station provides a unique location for preparatory activities for future human journey to Mars, to explore microbial diversity at subzero temperatures, and monitor the dissemination of human-associated microorganisms within the pristine surrounding environment. Amplicon sequencing was leveraged to investigate the microbial diversity of surface snow samples collected monthly over a two-year period, at three distances from the Station (10, 500, and 1000 m). Even when the extracted total DNA was below the detection limit, 16S rRNA gene sequencing was successfully performed on all samples, while 18S rRNA was amplified on 19 samples out of 51. No significant relationships were observed between microbial diversity and seasonality (summer or winter) or distance from the Concordia base. This suggested that if present, the anthropogenic impact should have been below the detectable limit. While harboring low microbial diversity, the surface snow samples were characterized by heterogeneous microbiomes. Ultimately, our study corroborated the use of DNA sequencing-based techniques for revealing microbial presence in remote and hostile environments, with implications for Planetary Protection during space missions and for life-detection in astrobiology relevant targets.
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Affiliation(s)
- Alessandro Napoli
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- Ph.D. Program in Cellular and Molecular Biology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
| | - Nikea J. Ulrich
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Ralf Moeller
- Aerospace Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), 28359 Cologne, Germany
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg (BRSU), 53359 Rheinbach, Germany
- Correspondence: (R.M.); (D.B.)
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (R.M.); (D.B.)
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), 16128 Genoa, Italy
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van Soest MAJ, Anderson NJ, Bol R, Dixon LR, Haygarth PM. Grazing and topography control nutrient pools in low Arctic soils of Southwest Greenland. EUROPEAN JOURNAL OF SOIL SCIENCE 2022; 73:e13278. [PMID: 36248184 PMCID: PMC9541922 DOI: 10.1111/ejss.13278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/18/2022] [Accepted: 06/29/2022] [Indexed: 06/16/2023]
Abstract
Soil nutrient pools in the dry low Arctic are likely to be released under climatic change and this bioavailability has the potential to increase both terrestrial and aquatic productions. As well as the direct effect of warming, external disturbances such as nutrient deposition and grazing can also drive ecosystem change. This study in the low Arctic Kangerlussuaq area of southwest Greenland compared soil nutrient pools in terms of both topographic position on a catena and by soil depth in two small catchments with contrasting muskox abundance. We tested the hypotheses that there were differences between soil carbon (C), nitrogen (N) and phosphorus (P) across a soil catena (ridge - slope - valley) and by soil depth (litter - 0-5 cm - 25-30 cm) for the two sites (SS17b, muskox present, versus - SS85, no muskox). Total C and N concentrations of soils were on average lower at SS17b compared to SS85. Moreover, the soil N concentration increased downslope in the catena with higher amounts in the valleys compared to the slopes and ridges. Soil P concentration (0.70 g P kg-1) was similar between catchments; however, litter P content was substantially different. The difference in soil nutrients between the two catchments was most likely due to the presence of muskox at SS17b, and hence grazing associated processes (defecation, altered microbiology and nutrient cycling). This study emphasises the heterogeneity of arctic landscapes and need for ecosystem specific research. Highlights Soil nutrient pools in two low-arctic catchments in Greenland were compared.Grazing and dung inputs by muskox affect soil nutrient pools in Greenland.Soil P stores in Kangerlussuaq are similar to intensively managed farmland in Europe.The heterogeneity of arctic landscapes and need for ecosystem-specific research are emphasised.
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Affiliation(s)
- Maud A. J. van Soest
- Geography & EnvironmentLoughborough UniversityLoughboroughUK
- Present address:
Centre for Ecology and Hydrology, Environment Centre WalesBangorUK
| | - N. John Anderson
- Geography & EnvironmentLoughborough UniversityLoughboroughUK
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | - Roland Bol
- Institute of Bio and Geosciences, Agrosphere (IBG‐3), Forschungszentrum Jülich GmbHJülichGermany
- School of Natural Sciences, Environment Centre WalesBangor UniversityBangorUK
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D'Alò F, Baldrian P, Odriozola I, Morais D, Větrovský T, Zucconi L, Ripa C, Cannone N, Malfasi F, Onofri S. Composition and functioning of the soil microbiome in the highest altitudes of the Italian Alps and potential effects of climate change. FEMS Microbiol Ecol 2022; 98:6541846. [PMID: 35238906 DOI: 10.1093/femsec/fiac025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/04/2022] [Accepted: 03/01/2022] [Indexed: 11/14/2022] Open
Abstract
As the European Alps are experiencing a strong climate warming; this study analyzed the soil microbiome at different altitudes and among different vegetation types at the Stelvio Pass (Italian Alps), aiming to i) characterize the composition and functional potential of the microbiome of soils and their gene expression during the peak vegetative stage; ii) explore the potential short-term (using open top chambers) and long-term (space-for-time substitutions) effects of increasing temperature on the alpine soil microbiome. We found that the functional potential of the soil microbiome and its expression differed among vegetation types. Microbial α-diversity increased along the altitudinal gradient. At lower altitude, shrubland had the highest proportion of fungi, which was correlated with higher amounts of CAZymes, specific for degrading fungal biomass and recalcitrant plant biopolymers. Subalpine upward vegetation shift could lead a possible loss of species of alpine soils. Shrub encroachment may accelerate higher recalcitrant C decomposition and reduce total ecosystem C storage, increasing the efflux of CO2 to the atmosphere with a positive feedback to warming. Five years of warming had no effect on the composition and functioning of microbial communities, indicating that longer-term warming experiments are needed to investigate the effects of temperature increases on the soil microbiome.
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Affiliation(s)
- Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Caterina Ripa
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Nicoletta Cannone
- Department of Science and High Technology, Insubria University, Via Valleggio, 11, 21100 Como (CO), Italy
| | - Francesco Malfasi
- Department of Science and High Technology, Insubria University, Via Valleggio, 11, 21100 Como (CO), Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
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Cary C, Cowan DA, McMinn A, Häggblom MM. Editorial: Thematic issue on polar and alpine microbiology. FEMS Microbiol Ecol 2020; 96:5875089. [PMID: 32697840 DOI: 10.1093/femsec/fiaa136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato - Te Whare Wānanga o Waikato, Hamilton 3240, New Zealand
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield 0028, Pretoria, South Africa
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, College of Science and Engineering, University of Tasmania, Battery Point, Tasmania, Australia
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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