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Ali A, Vishnivetskaya TA, Chauhan A. Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches. Braz J Microbiol 2024; 55:2437-2452. [PMID: 38758507 PMCID: PMC11405653 DOI: 10.1007/s42770-024-01365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.
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Affiliation(s)
- Ahmad Ali
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India
| | | | - Archana Chauhan
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India.
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Hao Y, Song Y, Li X, Li M, Wei X, Guo S, Hu Y. Progressive melting of surface water and unequal discharge of different DOM components profoundly perturb soil biochemical cycling. WATER RESEARCH 2024; 266:122360. [PMID: 39236504 DOI: 10.1016/j.watres.2024.122360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/21/2024] [Accepted: 08/28/2024] [Indexed: 09/07/2024]
Abstract
Freeze-thaw (FT) events profoundly perturb the biochemical processes of soil and water in mid- and high-latitude regions, especially the riparian zones that are often recognized as the hotspots of soil-water interactions and thus one of the most sensitive ecosystems to future climate change. However, it remains largely unknown how the heterogeneously composed and progressively discharged meltwater affect the biochemical cycling of the neighbor soil. In this study, stream water from a valley in the Chinese Loess Plateau was frozen at -10°C for 12 hours, and the meltwater (at +10°C) progressively discharged at three stages (T1 ∼ T3) was respectively added to rewet the soil collected from the same stream bed (Soil+T1 ∼ Soil+T3). Our results show that: (1) Approximately 65% of the total dissolved organic carbon and 53% of the total NO3--N were preferentially discharged at the first stage T1, with enrichment ratios of 1.60 ∼ 1.94. (2) The dissolved organic matter discharged at T1 was noticeably more biodegradable with significantly lower SUVA254 but higher HIX, and also predominated with humic-like, dissolved microbial metabolite-like, and fulvic acid-like components. (3) After added to the soil, the meltwater discharged at T1 (e.g., Soil+T1) significantly accelerated the mineralization of soil organic carbon with 2.4 ∼ 8.07-folded k factor after fitted into the first-order kinetics equation, triggering 125 ∼ 152% more total CO2 emissions. Adding T1 also promoted significantly more accumulation of soil microbial biomass carbon after 15 days of incubation, especially on the FT soil. Overall, the preferential discharge of the nutrient-enriched meltwater with more biodegradable DOM components at the initial melting stage significantly promoted the microbial growth and respiratory activities in the recipient soil, and triggered sizable CO2 emission pulses. This reveals a common but long-ignored phenomenon in cold riparian zones, where progressive freeze-thaw can partition and thus shift the DOM compositions in stream water over melting time, and in turn profoundly perturb the biochemical cycles of the neighbor soil body.
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Affiliation(s)
- Yongli Hao
- State Key Lab of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil & Water Conservation Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuan Song
- State Key Lab of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil & Water Conservation Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianwen Li
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Ming Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Xiaorong Wei
- State Key Lab of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil & Water Conservation Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shengli Guo
- State Key Lab of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil & Water Conservation Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaxian Hu
- State Key Lab of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil & Water Conservation Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Fasaeiyan N, Jung S, Boudreault R, Arenson LU, Maghoul P. A review on mathematical modeling of microbial and plant induced permafrost carbon feedback. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 939:173144. [PMID: 38768718 DOI: 10.1016/j.scitotenv.2024.173144] [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: 01/08/2024] [Revised: 03/11/2024] [Accepted: 05/09/2024] [Indexed: 05/22/2024]
Abstract
This review paper analyses the significance of microbial activity in permafrost carbon feedback (PCF) and emphasizes the necessity for enhanced modeling tools to appropriately predict carbon fluxes associated with permafrost thaw. Beginning with an overview of experimental findings, both in situ and laboratory, it stresses the key role of microbes and plants in PCF. The research investigates several modeling techniques, starting with current models of soil respiration and plant-microorganism interactions built outside of the context of permafrost, and then moving on to specific models dedicated to PCF. The review of the current literature reveals the complex nature of permafrost ecosystems, where various geophysical factors have considerable effects on greenhouse gas emissions. Soil properties, plant types, and time scales all contribute to carbon dynamics. Process-based models are widely used for simulating greenhouse gas production, transport, and emissions. While these models are beneficial at capturing soil respiration complexity, adjusting them to the unique constraints of permafrost environments often calls for novel process descriptions for proper representation. Understanding the temporal coherence and time delays between surface soil respiration and subsurface carbon production, which are controlled by numerous parameters such as soil texture, water content, and temperature, remains a challenge. This review highlights the need for comprehensive models that integrate thermo-hydro-biogeochemical processes to understand permafrost system dynamics in the context of changing climatic circumstances. Furthermore, it emphasizes the need for rigorous validation procedures to reduce model complexity biases.
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Affiliation(s)
- Niloofar Fasaeiyan
- Sustainable Infrastructure and Geoengineering Lab (SIGLab), Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Sophie Jung
- Sustainable Infrastructure and Geoengineering Lab (SIGLab), Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Richard Boudreault
- Sustainable Infrastructure and Geoengineering Lab (SIGLab), Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | | | - Pooneh Maghoul
- Sustainable Infrastructure and Geoengineering Lab (SIGLab), Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, QC, Canada.
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Liu G, Sun J, Xie P, Guo C, Zhu K, Tian K. Climate warming enhances microbial network complexity by increasing bacterial diversity and fungal interaction strength in litter decomposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168444. [PMID: 37949122 DOI: 10.1016/j.scitotenv.2023.168444] [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: 09/20/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Microbial communities are important drivers of plant litter decomposition; however, the mechanisms of microbial co-occurrence networks and their network interaction dynamics in response to climate warming in wetlands remain unclear. Here, we conducted a 1.5-year warming experiment on the bacterial and fungal communities involved in litter decomposition in a typical wetland. The results showed that warming accelerated the decomposition of litter and had a greater effect on the diversity of bacteria than on that of fungi. Dominant bacterial communities, such as Bacteroidia, Alphaproteobacteria, and Actinobacteria, and dominant fungal communities, such as Leotiomycetes and Sordariomycetes, showed significant positive correlations with lignin and cellulose. Co-occurrence networks revealed that the average path length and betweenness centrality under warming conditions increased in the bacterial community but decreased in the fungal community. Both bacterial and fungal networks in the 2.0 °C warming treatment had the highest ratio of positive links (58.53 % and 98.14 %), indicating that moderate warming can promote the positive correlations and symbiotic relationships observed in the microbial community. This also suggests that small-world characteristics and weak-link advantages accelerate diffusion, and scale-free features facilitate propagation in microbial communities in response to climate warming. Logistic growth and Lotka-Volterra competition models revealed that climate warming enhances microbial network complexity mainly by increasing bacterial diversity and fungal interaction strength in litter decomposition. However, the symbiotic relationship decreased slightly under 4.0 °C warming, indicating that climate warming is a random attack rather than a targeted attack, and the microbial network has strong resistance to random attack, as shown by the highly robust dynamic performance of the microbial network in litter decomposition. Overall, the microbial community in litter decomposition responded to climate warming and shifted its network interactions, leading to further changes in emergent network topology and dynamics, thus accelerating litter decomposition in wetlands.
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Affiliation(s)
- Guodong Liu
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China; Key Laboratory of Lake Nansi Wetland Ecological and Environmental Protection, Rizhao 276826, China.
| | - Jinfang Sun
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China; Key Laboratory of Lake Nansi Wetland Ecological and Environmental Protection, Rizhao 276826, China.
| | - Peng Xie
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Chao Guo
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Kaixiang Zhu
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Kun Tian
- National Plateau Wetlands Research Center/Southwest Forestry University, Kunming 650224, China
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Varliero G, Lebre PH, Adams B, Chown SL, Convey P, Dennis PG, Fan D, Ferrari B, Frey B, Hogg ID, Hopkins DW, Kong W, Makhalanyane T, Matcher G, Newsham KK, Stevens MI, Weigh KV, Cowan DA. Biogeographic survey of soil bacterial communities across Antarctica. MICROBIOME 2024; 12:9. [PMID: 38212738 PMCID: PMC10785390 DOI: 10.1186/s40168-023-01719-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/11/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs. RESULTS Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs. CONCLUSIONS Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.
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Affiliation(s)
- Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Pedro H Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton, VA, 3800, Australia
| | - Peter Convey
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006, South Africa
- Biodiversity of Antarctic and Sub-Antarctic Ecosystems (BASE), Santiago, Chile
| | - Paul G Dennis
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW, 2052, Australia
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - David W Hopkins
- SRUC - Scotland's Rural College, West Mains Road, Edinburgh, EH9 3JG, Scotland, UK
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Thulani Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Gwynneth Matcher
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kevin K Newsham
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark I Stevens
- Securing Antarctica's Environmental Future, Earth and Biological Sciences, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Katherine V Weigh
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa.
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Wang X, Song C, Chen N, Qiao T, Wang S, Jiang J, Du Y. Gas storage of peat in autumn and early winter in permafrost peatland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165548. [PMID: 37454856 DOI: 10.1016/j.scitotenv.2023.165548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
The carbon (C) balance of permafrost peatlands in autumn and winter, which affects the annual C budget estimation, has become a hotspot of studies on peatlands C cycle. This study combined the static chamber method, in situ soil profile measurements, and incubation experiments to investigate release and storage of C during autumn and early winter in a permafrost peatland in the Da Xing'an Mountains, Northeast China. Our results showed that the peak values of CH4 fluxes (30 August 2016) lagged behind those of CO2 fluxes (24 July 2016). At the onset of soil freezing, CH4 fluxes slightly increased, while CO2 fluxes decreased. During soil freezing in autumn, gases were found to be mainly stored in the soil as dissolved CH4 and CO2 and dissolved C concentrations (CH4, CO2, and DOC (dissolved organic carbon)) increased with depth. DOC concentrations were closely related to dissolved C gases, implying that the stored dissolved C gases might be derived from DOC decomposition. The CO2: CH4 ratio decreased sharply from the freezing of the surface layer to the total freezing of the soil, indicating larger CH4 storage in totally frozen soil. The incubation experiments also showed larger CH4 storage in the frozen soils and the stored C gases could influence the assessment of C emissions during thawing. These findings have important implications for clarifying the gas storage of permafrost peatland in autumn and early winter. The results may also clarify the key link of C emissions between the growing season and the nongrowing season.
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Affiliation(s)
- Xianwei Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; Dalian University of Technology, Dalian 116024, China.
| | - Ning Chen
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Tianhua Qiao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Shujie Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy Sciences, Beijing 100049, China
| | - Jingyi Jiang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yu Du
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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Miner KR, Hollis JR, Miller CE, Uckert K, Douglas TA, Cardarelli E, Mackelprang R. Earth to Mars: A Protocol for Characterizing Permafrost in the Context of Climate Change as an Analog for Extraplanetary Exploration. ASTROBIOLOGY 2023; 23:1006-1018. [PMID: 37566539 PMCID: PMC10510695 DOI: 10.1089/ast.2022.0155] [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: 12/08/2022] [Accepted: 07/02/2023] [Indexed: 08/13/2023]
Abstract
Abstract Permafrost is important from an exobiology and climate change perspective. It serves as an analog for extraplanetary exploration, and it threatens to emit globally significant amounts of greenhouse gases as it thaws due to climate change. Viable microbes survive in Earth's permafrost, slowly metabolizing and transforming organic matter through geologic time. Ancient permafrost microbial communities represent a crucial resource for gaining novel insights into survival strategies adopted by extremotolerant organisms in extraplanetary analogs. We present a proof-of-concept study on ∼22 Kya permafrost to determine the potential for coupling Raman and fluorescence biosignature detection technology from the NASA Mars Perseverance rover with microbial community characterization in frozen soils, which could be expanded to other Earth and off-Earth locations. Besides the well-known utility for biosignature detection and identification, our results indicate that spectral mapping of permafrost could be used to rapidly characterize organic carbon characteristics. Coupled with microbial community analyses, this method has the potential to enhance our understanding of carbon degradation and emissions in thawing permafrost. Further, spectroscopy can be accomplished in situ to mitigate sample transport challenges and in assessing and prioritizing frozen soils for further investigation. This method has broad-range applicability to understanding microbial communities and their associations with biosignatures and soil carbon and mineralogic characteristics relevant to climate science and astrobiology.
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Affiliation(s)
- Kimberley R. Miner
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Charles E. Miller
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Kyle Uckert
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Emily Cardarelli
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Mishra A, Singh L, Singh D. Unboxing the black box-one step forward to understand the soil microbiome: A systematic review. MICROBIAL ECOLOGY 2023; 85:669-683. [PMID: 35112151 PMCID: PMC9957845 DOI: 10.1007/s00248-022-01962-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.
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Affiliation(s)
- Apurva Mishra
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, 201002, India
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Lal Singh
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Dharmesh Singh
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstrasse 30, 81675, Munich, Bavaria, Germany.
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Wang X, Yu Z, Shen G, Cheng H, Tao S. Distribution of microbial communities in seasonally frozen soil layers on the Tibetan Plateau and the driving environmental factors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:1919-1937. [PMID: 35925461 DOI: 10.1007/s11356-022-22283-7] [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: 02/17/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Large stocks of carbon and nitrogen stored in permafrost regions can potentially feed back to global biogeochemical cycles under climate warming. To understand the response of microbial communities to environmental changes, this study investigated the spatial distribution of bacterial communities in the upper layers (0-10, 10-20, and 20-30 cm) of seasonally frozen soil on the Tibetan Plateau and their relationships with the environmental factors. A total of 135 soil samples were collected from the soils at depths of 0-10, 10-20, and 20-30 cm in the Lhasa River and Nyang River basins, and the diversity and composition of bacterial communities in them were identified by high-throughput 16S rRNA gene sequencing. Bacterial diversity changed significantly with soil depth in the Nyang River basin (p < 0.001), while no obvious change was found in the Lhasa River basin. The whole bacterial composition exhibited small variations across different soil layers (p > 0.05). The relative abundance of aerobic bacteria, Sphingomonas and Arthrobacter, decreased with soil depth, while that of the other aerobic, facultative anaerobic, and anaerobic bacteria did not exhibit this trend. Soil pH was the key driving edaphic factor of the whole bacterial composition in all three depth layers, while vegetation also had an important influence on bacterial composition. Arthrobacter, Bradyrhizobium, and Bacillus had obvious correlations with soil nutrients or vegetation, while the other species were not significantly correlated with any environmental factors. Structural equation modeling revealed that vegetation and mean annual temperature had a key direct impact on the bacterial diversity and composition, respectively. Climate also indirectly affected bacterial communities, mainly through shaping soil pH and vegetation. These results indicate that the soil depth has a different impact on the bacterial α-diversity, whole bacterial composition, and specific taxa in the 0-30-cm surface layers of seasonally frozen soil, which were mainly determined by various environmental factors.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
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10
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Poppeliers SWM, Hefting M, Dorrepaal E, Weedon JT. Functional microbial ecology in arctic soils: the need for a year-round perspective. FEMS Microbiol Ecol 2022; 98:6824434. [PMID: 36368693 PMCID: PMC9701097 DOI: 10.1093/femsec/fiac134] [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: 03/31/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.
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Affiliation(s)
- Sanne W M Poppeliers
- Corresponding author: Department of Biology, Utrecht University, 3584 CH, The Netherlands. E-mail:
| | - Mariet Hefting
- Department of Biology, Utrecht University, 3584 CH, The Netherlands
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Umea University, SE-981 07, Abisko, Sweden
| | - James T Weedon
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
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11
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Response of Carbon Emissions and the Bacterial Community to Freeze-Thaw Cycles in a Permafrost-Affected Forest-Wetland Ecotone in Northeast China. Microorganisms 2022; 10:microorganisms10101950. [PMID: 36296226 PMCID: PMC9609725 DOI: 10.3390/microorganisms10101950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
Climate warming can affect freeze–thaw cycle (FTCs) patterns in northern high-latitude regions and may affect permafrost carbon emissions. The response of carbon release and microbial communities to FTCs has not been well characterized. Here, we conducted laboratory incubation experiments to investigate the relationships among carbon emissions, bacterial community, and soil variables in a permafrost-affected forest–wetland ecotone in Northeast China. The emission rates of CO2 and CH4 increased during the FTCs. FTC amplitude, FTC frequency, and patch type had significant effects on carbon emissions. FTCs increased the contents of soil DOC, NH4+-N, and NO3−-N but reduced bacterial alpha diversity. CO2 emissions were mainly affected by bacterial alpha diversity and composition, and the inorganic nitrogen content was the important factor affecting CH4 emissions. Our findings indicated that FTCs could significantly regulate CO2 and CH4 emissions by reducing bacterial community diversity and increasing the concentration of available soil substrates. Our findings shed new light on the microorganism-substrate mechanisms regulating the response patterns of the soil carbon cycle to FTCs in permafrost regions.
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12
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Wang X, Ren Y, Yu Z, Shen G, Cheng H, Tao S. Effects of environmental factors on the distribution of microbial communities across soils and lake sediments in the Hoh Xil Nature Reserve of the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156148. [PMID: 35609688 DOI: 10.1016/j.scitotenv.2022.156148] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Comparison of microbial community diversity and composition of terrestrial and aquatic ecosystems in undisturbed regions could expand our understanding on the mechanisms of microbial community assembly and ecosystem responses to environmental change. This study investigated the spatial distribution of bacterial community diversity and composition in the lakeshore soils and lake sediments from one of the best preserved nature reserves, Hoh Xil on the Qinghai-Tibetan Plateau, and explored the corresponding environmental drivers. A total of 36 sediment and soil samples were collected from six alpine lakes and the corresponding shore zones, and their bacterial community structure was identified by high-throughput 16S rRNA gene sequencing. Significant difference (p < 0.05) in diversity and composition of bacterial communities between the soils and sediments was observed. Heterogeneous selection played a dominant role in shaping the spatial variations of bacterial communities between the soils and sediments. Results of canonical correspondence analysis showed that the difference in composition of bacterial communities at OTU level between the soils and sediments was mainly determined by the mean annual temperature, salinity, and contents of total organic carbon and total nitrogen. Structural equation modeling revealed that salinity played a significantly direct role in soil bacterial composition, while mean annual temperature indirectly affected the bacterial composition mainly through changing soil salinity. In contrast, the sediment bacterial composition was directly influenced primarily by the contents of total organic carbon and total nitrogen, while pH also had an important indirect effect on sediment bacterial composition. These results shed light on the distribution patterns of bacterial communities between lakeshore soils and lake sediments in high-altitude permafrost regions, and the major ecological processes and environmental drivers that shaped their bacterial communities, and provide insight into the mechanisms underlying microbial community assembly in such regions.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yuxuan Ren
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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13
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da Silva TH, Queres Gomes EC, Gonçalves VN, da Costa MC, Valério AD, de Assis Santos D, Johann S, Convey P, Rosa CA, Rosa LH. Does maritime Antarctic permafrost harbor environmental fungi with pathogenic potential? Fungal Biol 2022; 126:488-497. [DOI: 10.1016/j.funbio.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/02/2022] [Accepted: 04/12/2022] [Indexed: 11/04/2022]
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14
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Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals. CRYSTALS 2022. [DOI: 10.3390/cryst12030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.
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15
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Perez-Mon C, Stierli B, Plötze M, Frey B. Fast and persistent responses of alpine permafrost microbial communities to in situ warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150720. [PMID: 34610405 DOI: 10.1016/j.scitotenv.2021.150720] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Global warming in mid-latitude alpine regions results in permafrost thawing, together with greater availability of carbon and nutrients in soils and frequent freeze-thaw cycles. Yet it is unclear how these multifactorial changes will shape the 1 m-deep permafrost microbiome in the future, and how this will in turn modulate microbially-mediated feedbacks between mountain soils and climate (e.g. soil CO2 emissions). To unravel the responses of the alpine permafrost microbiome to in situ warming, we established a three-year experiment in a permafrost monitoring summit in the Alps. Specifically, we simulated conditions of warming by transplanting permafrost soils from a depth of 160 cm either to the active-layer topsoils in the north-facing slope or in the warmer south-facing slope, near the summit. qPCR-based and amplicon sequencing analyses indicated an augmented microbial abundance in the transplanted permafrost, driven by the increase in copiotrophic prokaryotic taxa (e.g. Noviherbaspirillum and Massilia) and metabolically versatile psychrotrophs (e.g. Tundrisphaera and Granulicella); which acclimatized to the changing environment and potentially benefited from substrates released upon thawing. Metabolically restricted Patescibacteria lineages vastly decreased with warming, as reflected in the loss of α-diversity in the transplanted soils. Ascomycetous sapro-pathotrophs (e.g. Tetracladium) and a few lichenized fungi (e.g. Aspicilia) expanded in the transplanted permafrost, particularly in soils transplanted to the warmer south-facing slope, replacing basidiomycetous yeasts (e.g. Glaciozyma). The transplantation-induced loosening of microbial association networks in the permafrost could potentially indicate lesser cooperative interactions between neighboring microorganisms. Broader substrate-use microbial activities measured in the transplanted permafrost could relate to altered soil C dynamics. The three-year simulated warming did not, however, enhance heterotrophic respiration, which was limited by the carbon-depleted permafrost conditions. Collectively, our quantitative findings suggest the vulnerability of the alpine permafrost microbiome to warming, which might improve predictions on microbially-modulated transformations of mountain soil ecosystems under the future climate.
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Affiliation(s)
- Carla Perez-Mon
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Michael Plötze
- Institute for Geotechnical Engineering, ETH Zurich, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
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16
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Lu XM, Jiang XQ, Liu XP. Response process and adaptation mechanism of estuarine benthic microbiota to polyvinyl chloride microplastics with and without phthalates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150693. [PMID: 34599949 DOI: 10.1016/j.scitotenv.2021.150693] [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: 07/16/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
This study aimed to explore the response mechanisms of the microbiota in estuarine sediments amended with polyvinyl chloride (PVC) microplastics (MPs) with and without phthalates (PAEs) through a 60-day microcosm experiment. The results indicated that addition of MPs increased the porosity of the sediment. However, the sediment porosity decreased with the length of the amendment period. Following amendment with MPs containing PAEs, the sediment PAE content increased over time. The addition of MPs without PAEs increased the relative abundance of the dominant phyla of bacteria (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes) and eukaryotes (Ascomycota, Bacillariophyta, Chordata, and Streptophyta), whereas the relative abundance decreased over time following the addition of MPs containing PAEs. The PAEs released from MPs had greater effects on these phyla than the MPs themselves. The dominant bacteria were more sensitive to MPs than the dominant eukaryotes. After a 60-day amendment with MPs containing PAEs, the bacterial and eukaryotic species numbers were lower by 5.4% and 3.4%, respectively, the relative abundance of certain genes involved in metabolism was lower, and the relative abundance of stress-related genes was higher. These findings provide insight into the microbial response and adaptation mechanisms in estuarine environments polluted with MPs.
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Affiliation(s)
- Xiao-Ming Lu
- School of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350118, China.
| | - Xiao-Qiang Jiang
- School of Urban Operations Management, Shanghai Urban Construction Vocational College, Shanghai 200438, China
| | - Xue-Ping Liu
- School of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350118, China
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17
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Gao D, Liu Z, Bai E. Effects of in situ freeze-thaw cycles on winter soil respiration in mid-temperate plantation forests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148567. [PMID: 34175599 DOI: 10.1016/j.scitotenv.2021.148567] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/30/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
As an important factor regulating soil carbon cycle, freeze-thaw cycle significantly affects winter soil respiration in temperate regions. However, few in situ studies have been carried out to evaluate the effect of freeze-thaw cycle on soil respiration. Here, a field experiment was conducted to explore the response of winter soil respiration to freeze-thaw cycle and the underlying mechanisms in larch and Chinese pine plantation forests in a mid-temperate region. These results indicated that CO2 emissions during the freeze-thaw period accounted for 18.89-18.94% and 0.79-1.00% of the cumulative winter CO2 emissions and the annual soil CO2 emissions, respectively. Soil respiration rates during the thawing phase were 1.54-3.95 times higher than those during the freezing phase, which was mainly due to the increase of soil microbial biomass upon thawing. This effect declined during the second freeze-thaw cycle compared to the first freeze-thaw cycle due to the exhaustion of resources for microbes. The different responses of soil CO2 flux to freeze-thaw cycle between the two types of forests were mainly because of the difference in the thickness of litter layer, which plays an important role in regulating soil temperature and enzyme activity. These results suggest the intensity and frequency of freeze-thaw cycle strongly affect soil carbon emissions during the freeze-thaw cycle period. Therefore, these factors should be considered in laboratory studies and model simulations under climate change scenarios.
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Affiliation(s)
- Decai Gao
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China
| | - Ziping Liu
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China.
| | - Edith Bai
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun 130024, China.
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18
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Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. MICROBIOME 2021; 9:208. [PMID: 34663463 PMCID: PMC8522061 DOI: 10.1186/s40168-021-01154-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/19/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). RESULTS We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. CONCLUSIONS Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jose Liquet-Gonzalez
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark P Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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19
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Perez-Mon C, Qi W, Vikram S, Frossard A, Makhalanyane T, Cowan D, Frey B. Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps). Microb Genom 2021; 7:000558. [PMID: 33848236 PMCID: PMC8208683 DOI: 10.1099/mgen.0.000558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.
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Affiliation(s)
- Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Carla Perez-Mon,
| | - Weihong Qi
- Functional Genomics Center of the University of Zurich and the ETH Zurich, Zurich, Switzerland
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Thulani Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Beat Frey,
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20
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Compost Samples from Different Temperature Zones as a Model to Study Co-occurrence of Thermophilic and Psychrophilic Bacterial Population: a Metagenomics Approach. Curr Microbiol 2021; 78:1903-1913. [PMID: 33786643 DOI: 10.1007/s00284-021-02456-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
In this study, using a metagenomic approach, we explore the bacterial diversity of compost sites categorized based on their ambient temperatures. The two sites were Reckong Peo in the lower Himalayas and Tambaram in the southern region of the country, namely, CPR and CT. Following assembly of the raw reads from shotgun metagenomics, similarity hits were generated using NCBI BLAST + and SILVA database. A total of 1463 and 1483 species were annotated from CPR and CT. A species-level annotation was performed using a python-based literature search pipeline revealing their growth characteristics. Thermophiles Thermomonospora curvata and Thermus scotoductus were among the prominent species in CT. CPR too was seen abundant with Acidothermus cellulolyticus and Moorella thermoacetica, constituting 10% of the population. Nearly 3% of the identified species in the site CPR were psychrophilic. Although found higher in CPR, psychrophilic species were identified in CT too. Flavobacterium and Psychrobacter spp. were present in both sites without any significant changes in their relative distribution contrary to the thermophilic species abundance (z = - 4.3). Akin to the sequenced samples, database-derived metagenomes also showed similar distribution of thermophiles and psychrophiles. Identifying such peculiar prevalence of extremophiles can be central to understanding extended growth temperatures.
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21
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Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil. Microorganisms 2021; 9:microorganisms9030609. [PMID: 33809442 PMCID: PMC8000410 DOI: 10.3390/microorganisms9030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.
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22
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Zhu C, Miller M, Lusskin N, Bergk Pinto B, Maccario L, Häggblom M, Vogel T, Larose C, Bromberg Y. Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds. Microbiologyopen 2020; 9:e1100. [PMID: 32762019 PMCID: PMC7520998 DOI: 10.1002/mbo3.1100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes active in extreme cold are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold-specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of 20 snow samples collected in early and late spring in Svalbard, Norway using mi-faser, our read-based computational microbiome function annotation tool. Our results reveal a more diverse microbiome functional capacity and activity in the early- vs. late-spring samples. We also find that functional dissimilarity between the same-sample metagenomes and metatranscriptomes is significantly higher in early than late spring samples. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant (or dead) organisms, while late spring samples reflect a new, metabolically active community. We further show that the abundance of sequencing reads mapping to the fatty acid synthesis-related microbial pathways in late spring metagenomes and metatranscriptomes is significantly correlated with the organic acid levels measured in these samples. Similarly, the organic acid levels correlate with the pathway read abundances of geraniol degradation and inversely correlate with those of styrene degradation, suggesting a possible nutrient change. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures.
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Affiliation(s)
- Chengsheng Zhu
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
| | - Maximilian Miller
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
| | - Nicholas Lusskin
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
| | - Benoît Bergk Pinto
- Environmental Microbial GenomicsLaboratoire AmpereEcole Centrale de LyonCNRS UMR 5005Université de LyonEcullyFrance
| | - Lorrie Maccario
- Environmental Microbial GenomicsLaboratoire AmpereEcole Centrale de LyonCNRS UMR 5005Université de LyonEcullyFrance
- Section of MicrobiologyCopenhagen UniversityCopenhagen ØDenmark
| | - Max Häggblom
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
| | - Timothy Vogel
- Environmental Microbial GenomicsLaboratoire AmpereEcole Centrale de LyonCNRS UMR 5005Université de LyonEcullyFrance
| | - Catherine Larose
- Environmental Microbial GenomicsLaboratoire AmpereEcole Centrale de LyonCNRS UMR 5005Université de LyonEcullyFrance
| | - Yana Bromberg
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
- Department of GeneticsHuman Genetics InstituteRutgers UniversityPiscatawayNJUSA
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Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples. Sci Rep 2020; 10:14295. [PMID: 32868827 PMCID: PMC7459103 DOI: 10.1038/s41598-020-71234-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
This study aims to act as a methodological guide for contamination monitoring, decontamination, and DNA extraction for peaty and silty permafrost samples with low biomass or difficult to extract DNA. We applied a biological tracer, either only in the field or both in the field and in the lab, via either spraying or painting. Spraying in the field followed by painting in the lab resulted in a uniform layer of the tracer on the core sections. A combination of bleaching, washing, and scraping resulted in complete removal of the tracer leaving sufficient material for DNA extraction, while other widely used decontamination methods did not remove all detectable tracer. In addition, of four widely used commercially available DNA extraction kits, only a modified ZymoBIOMICS DNA Microprep kit was able to acquire PCR amplifiable DNA. Permafrost chemical parameters, age, and soil texture did not have an effect on decontamination efficacy; however, the permafrost type did influence DNA extraction. Based on these findings, we developed recommendations for permafrost researchers to acquire contaminant-free DNA from permafrost with low biomass.
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24
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Sub-Surface Carbon Stocks in Northern Taiga Landscapes Exposed in the Batagay Megaslump, Yana Upland, Yakutia. LAND 2020. [DOI: 10.3390/land9090305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The most massive and fast-eroding thaw slump of the Northern Hemisphere located in the Yana Uplands of Northern Yakutia was investigated to assess in detail the cryogenic inventory and carbon pools of two distinctive Ice Complex stratigraphic units and the uppermost cover deposits. Differentiating into modern and Holocene near-surface layers (active layer and shielding layer), highest total carbon contents were found in the active layer (18.72 kg m−2), while the shielding layer yielded a much lower carbon content of 1.81 kg m−2. The late Pleistocene upper Ice Complex contained 10.34 kg m−2 total carbon, and the mid-Pleistocene lower Ice Complex 17.66 kg m−2. The proportion of organic carbon from total carbon content is well above 70% in all studied units with 94% in the active layer, 73% in the shielding layer, 83% in the upper Ice Complex and 79% in the lower Ice Complex. Inorganic carbon is low in the overall structure of the deposits.
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25
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Brin LD, Goyer C, Zebarth BJ, Burton DL, Chantigny MH. Linking changes in snow cover with microbial nitrogen cycling functional gene abundance and expression in agricultural soil. FEMS Microbiol Ecol 2020; 95:5511778. [PMID: 31167230 DOI: 10.1093/femsec/fiz073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/04/2019] [Indexed: 11/12/2022] Open
Abstract
In eastern Canada, climate change-related warming and increased precipitation may alter winter snow cover, with potential consequences for soil conditions, nitrogen (N) cycling, and microbes. We conducted a 2-year field study aimed at determining the influence of snow removal, snow accumulation, and ambient snow in a potato-barley crop system on the abundance and expression of denitrifier (nirS, nirK, nosZ) and nitrifier (ammonium oxidizing archaeal (AOA) and bacterial (AOB) amoA) genes. Denitrifier and nitrifier abundance and expression results were compared to N2O production, soil atmosphere accumulation, and surface fluxes. In the first winter, nirK abundance was lowest while AOB abundance was greatest in snow accumulation treatments. In the second winter, greatest abundances were observed in the ambient snow treatment, which had greatest N2O accumulation and spring thaw fluxes, suggesting a link between microbial populations and biogeochemical functioning. Treatment effects on gene expression were limited, but greatest AOA, AOB, and nosZ expression was measured near 0°C and above 15°C, indicating that activity was promoted by freeze-thaw conditions and at summer temperatures. Overall, effects of changing snow depth on denitrifier and nitrifier abundance were not solely due to change in soil temperature, but also to soil moisture and/or interactions between these parameters.
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Affiliation(s)
- Lindsay D Brin
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Claudia Goyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Bernie J Zebarth
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - David L Burton
- Department of Environmental Sciences, Dalhousie University, Agricultural Campus, PO Box 550, Truro, Nova Scotia, B2N 5E3, Canada
| | - Martin H Chantigny
- Québec Research and Development Centre, Agriculture and Agri-Food Canada, 2560 Hochelaga Boulevard, Québec, Québec, G1V 2J3, Canada
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26
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Perez-Mon C, Frey B, Frossard A. Functional and Structural Responses of Arctic and Alpine Soil Prokaryotic and Fungal Communities Under Freeze-Thaw Cycles of Different Frequencies. Front Microbiol 2020; 11:982. [PMID: 32523565 PMCID: PMC7261861 DOI: 10.3389/fmicb.2020.00982] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Ongoing climate change involves increasing snow scarcity, which results in more frequent freeze-thaw cycles (FTCs) in polar and alpine soils. Although repeated FTCs have been shown to alter the structure and functions of soil microbial communities, a thorough understanding on the influence of FTCs frequency on polar and especially alpine soil microbiomes is still elusive. Here, we investigated the impact of repeated weekly vs. daily FTC frequencies on the structure and functions of prokaryotic and fungal communities from north- and south-exposed soils from two mountain ridges, one in the Arctic and one in the High-Alps. FTCs affected prokaryotic communities more strongly than fungal communities, where mainly cold-tolerant and opportunistic fungi (e.g., Mrakia, Mortierella) were responsive. Prokaryotic communities were more affected by weekly FTCs than by daily FTCs. Daily FTCs favored fast-growing bacteria (e.g., Arthrobacter), while oligotrophic and largely uncultured taxa (e.g., Verrucomicrobia) benefited from weekly FTCs. FTCs negatively affected microbial respiration but had minor impacts on C-, N- and P-acquiring enzymatic activities. Plausible pre-adaptation of the microbial communities to naturally occurring frequent FTCs at their site of origin did not show a clear influence on the microbial responses to the tested FTCs. Altogether, our study provides an integrative overview on potential structural and functional changes of soil microbial communities in polar and alpine regions in response to the projected increase in FTCs; therefore advancing our understanding on the impact of climate change in these rapidly changing ecosystems.
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Affiliation(s)
- Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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27
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da Silva TH, Silva DAS, de Oliveira FS, Schaefer CEGR, Rosa CA, Rosa LH. Diversity, distribution, and ecology of viable fungi in permafrost and active layer of Maritime Antarctica. Extremophiles 2020; 24:565-576. [PMID: 32405812 DOI: 10.1007/s00792-020-01176-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/27/2020] [Indexed: 01/20/2023]
Abstract
We evaluated the diversity and distribution of viable fungi present in permafrost and active layers obtained from three islands of Maritime Antarctica. A total of 213 fungal isolates were recovered from the permafrost, and 351 from the active layer, which were identified in 58 taxa; 27 from permafrost and 31 from the active layer. Oidiodendron, Penicillium, and Pseudogymnoascus taxa were the most abundant in permafrost. Bionectriaceae, Helotiales, Mortierellaceae, and Pseudeurotium were the most abundant in the active layer. Only five shared both substrates. The yeast Mrakia blollopis represented is the first reported on Antarctic permafrost. The fungal diversity detected was moderate to high, and composed of cosmopolitan, cold-adapted, and endemic taxa, reported as saprobic, mutualistic, and parasitic species. Our results demonstrate that permafrost shelters viable fungi across the Maritime Antarctica, and that they are contrasting to the overlying active layer. We detected important fungal taxa represented by potential new species, particularly, those genetically close to Pseudogymnoascus destructans, which can cause extinction of bats in North America and Eurasia. The detection of viable fungi trapped in permafrost deserves further studies on the extension of its fungal diversity and its capability to expand from permafrost to other habitats in Antarctica, and elsewhere.
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Affiliation(s)
- Thamar Holanda da Silva
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Fábio Soares de Oliveira
- Departamento de Geografia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Luiz Henrique Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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28
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Edwards A, Cameron KA, Cook JM, Debbonaire AR, Furness E, Hay MC, Rassner SM. Microbial genomics amidst the Arctic crisis. Microb Genom 2020; 6:e000375. [PMID: 32392124 PMCID: PMC7371112 DOI: 10.1099/mgen.0.000375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
The Arctic is warming - fast. Microbes in the Arctic play pivotal roles in feedbacks that magnify the impacts of Arctic change. Understanding the genome evolution, diversity and dynamics of Arctic microbes can provide insights relevant for both fundamental microbiology and interdisciplinary Arctic science. Within this synthesis, we highlight four key areas where genomic insights to the microbial dimensions of Arctic change are urgently required: the changing Arctic Ocean, greenhouse gas release from the thawing permafrost, 'biological darkening' of glacial surfaces, and human activities within the Arctic. Furthermore, we identify four principal challenges that provide opportunities for timely innovation in Arctic microbial genomics. These range from insufficient genomic data to develop unifying concepts or model organisms for Arctic microbiology to challenges in gaining authentic insights to the structure and function of low-biomass microbiota and integration of data on the causes and consequences of microbial feedbacks across scales. We contend that our insights to date on the genomics of Arctic microbes are limited in these key areas, and we identify priorities and new ways of working to help ensure microbial genomics is in the vanguard of the scientific response to the Arctic crisis.
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Affiliation(s)
- Arwyn Edwards
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Karen A. Cameron
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Joseph M. Cook
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Aliyah R. Debbonaire
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Eleanor Furness
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Melanie C. Hay
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Sara M.E. Rassner
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
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29
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Soil Water Contents Control the Responses of Dissolved Nitrogen Pools and Bacterial Communities to Freeze-Thaw in Temperate Soils. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6867081. [PMID: 32258137 PMCID: PMC7086428 DOI: 10.1155/2020/6867081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/30/2020] [Accepted: 02/26/2020] [Indexed: 11/18/2022]
Abstract
Background Freeze-thaw influences soil-dissolved nitrogen (N) pools due to variations in bacterial communities in temperate regions. The availability of soil water is important to soil biogeochemical cycles under frozen conditions. However, it is unclear how soil water content (SWC) mediates the effects of freeze-thaw on soil-dissolved N pools and bacterial communities. Method In this study, freeze-thaw microcosms were incubated at three levels of SWC, including 10% (air-dried soils), 15% (natural SWC), and 30% (wet soils). In addition to measuring soil-dissolved N pools, variations in bacterial communities were examined using high-throughput sequencing. Results and Conclusions. Total dissolved N (TDN), NO3 --N, NH4 +-N, microbial biomass N (MBN), and net N mineralization rate (NNMR) were significantly influenced by SWC, freeze-thaw, and their interaction (NH4 +-N excluded). N immobilization was inhibited under both low and high SWC, which was accompanied by varied bacterial community composition. However, only higher SWC substantially modified the freeze-thaw effects on the soil-dissolved N pools, characterized by a decrease in N mineralization (especially for the content of NO3 --N and NNMR) and an increase in N immobilization (MBN). These scenarios could be significantly correlated to variations in bacterial community composition based on redundancy analysis, especially by species belonging to Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.
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30
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Arctic Greening Caused by Warming Contributes to Compositional Changes of Mycobiota at the Polar Urals. FORESTS 2019. [DOI: 10.3390/f10121112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The long-term influence of climate change on spatio-temporal dynamics of the Polar mycobiota was analyzed on the eastern macro slope of the Polar Urals (Sob River valley and Mountain Slantsevaya) over a period of 60 years. The anthropogenic impact is minimal in the study area. Effects of environmental warming were addressed as changes in treeline and forest communities (greening of the vegetation). With warming, permafrost is beginning to thaw, and as it thaws, it decomposes. Therefore, we also included depth of soil thawing and litter decomposition in our study. Particular attention was paid to the reaction of aphyllophoroid fungal communities concerning these factors. Our results provide evidence for drastic changes in the mycobiota due to global warming. Fungal community composition followed changes of the vegetation, which was transforming from forest-tundra to northern boreal type forests during the last 60 years. Key fungal groups of the ongoing borealization and important indicator species are discussed. Increased economic activity in the area may lead to deforestation, destruction of swamps, and meadows. However, this special environment provides important services such as carbon sequestration, soil formation, protecting against flood risks, and filtering of air. In this regard, we propose to include the studied territory in the Polarnouralsky Natural Park.
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31
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Gadkari PS, McGuinness LR, Männistö MK, Kerkhof LJ, Häggblom MM. Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing. FEMS Microbiol Ecol 2019; 96:5645228. [DOI: 10.1093/femsec/fiz192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Arctic soils store vast amounts of carbon and are subject to intense climate change. While the effects of thaw on the composition and activities of Arctic tundra microorganisms has been examined extensively, little is known about the consequences of temperature fluctuations within the subzero range in seasonally frozen or permafrost soils. This study identified tundra soil bacteria active at subzero temperatures using stable isotope probing (SIP). Soils from Kilpisjärvi, Finland, were amended with 13C-cellobiose and incubated at 0, −4 and −16°C for up to 40 weeks. 16S rRNA gene sequence analysis of 13C-labelled DNA revealed distinct subzero-active bacterial taxa. The SIP experiments demonstrated that diverse bacteria, including members of Candidatus Saccharibacteria, Melioribacteraceae, Verrucomicrobiaceae, Burkholderiaceae, Acetobacteraceae, Armatimonadaceae and Planctomycetaceae, were capable of synthesising 13C-DNA at subzero temperatures. Differences in subzero temperature optima were observed, for example, with members of Oxalobacteraceae and Rhizobiaceae found to be more active at 0°C than at −4°C or −16°C, whereas Melioribacteriaceae were active at all subzero temperatures tested. Phylogeny of 13C-labelled 16S rRNA genes from the Melioribacteriaceae, Verrucomicrobiaceae and Candidatus Saccharibacteria suggested that these taxa formed subzero-active clusters closely related to members from other cryo-environments. This study demonstrates that subzero temperatures impact active bacterial community composition and activity, which may influence biogeochemical cycles.
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Affiliation(s)
- Preshita S Gadkari
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
| | - Lora R McGuinness
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Minna K Männistö
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Max M Häggblom
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
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32
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Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon. ISME JOURNAL 2019; 13:2901-2915. [PMID: 31384013 DOI: 10.1038/s41396-019-0485-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 04/17/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023]
Abstract
The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.
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33
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Luláková P, Perez-Mon C, Šantrůčková H, Ruethi J, Frey B. High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures. Front Microbiol 2019; 10:668. [PMID: 31001236 PMCID: PMC6456652 DOI: 10.3389/fmicb.2019.00668] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/18/2019] [Indexed: 02/01/2023] Open
Abstract
The response of microbial communities to the predicted rising temperatures in alpine regions might be an important part of the ability of these ecosystems to deal with climate change. Soil microbial communities might be significantly affected by elevated temperatures, which influence the functioning of soils within high-alpine ecosystems. To evaluate the potential of the permafrost microbiome to adapt to short-term moderate and extreme warming, we set up an incubation experiment with permafrost and active soil layers from northern and southern slopes of a high-alpine mountain ridge on Muot da Barba Peider in the Swiss Alps. Soils were acclimated to increasing temperatures (4–40°C) for 26 days before being exposed to a heat shock treatment of 40°C for 4 days. Alpha-diversity in all soils increased slightly under gradual warming, from 4 to 25°C, but then dropped considerably at 40°C. Similarly, heat shock induced strong changes in microbial community structures and functioning in the active layer of soils from both northern and southern slope aspects. In contrast, permafrost soils showed only minor changes in their microbial community structures and no changes in their functioning, except regarding specific respiration activity. Shifts in microbial community structures with increasing temperature were significantly more pronounced for bacteria than for fungi, regardless of the soil origin, suggesting higher resistance of high-alpine fungi to short-term warming. Firmicutes, mainly represented by Tumebacillus and Alicyclobacillaceae OTUs, increased strongly at 40°C in active layer soils, reaching almost 50% of the total abundance. In contrast, Saccharibacteria decreased significantly with increasing temperature across all soil samples. Overall, our study highlights the divergent responses of fungal and bacterial communities to increased temperature. Fungi were highly resistant to increased temperatures compared to bacteria, and permafrost communities showed surprisingly low response to rising temperature. The unique responses were related to both site aspect and soil origin indicating that distinct differences within high-alpine soils may be driven by substrate limitation and legacy effects of soil temperatures at the field site.
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Affiliation(s)
- Petra Luláková
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Hana Šantrůčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Joel Ruethi
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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34
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Margesin R, Collins T. Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge. Appl Microbiol Biotechnol 2019; 103:2537-2549. [PMID: 30719551 PMCID: PMC6443599 DOI: 10.1007/s00253-019-09631-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 11/28/2022]
Abstract
Microorganisms in cold ecosystems play a key ecological role in their natural habitats. Since these ecosystems are especially sensitive to climate changes, as indicated by the worldwide retreat of glaciers and ice sheets as well as permafrost thawing, an understanding of the role and potential of microbial life in these habitats has become crucial. Emerging technologies have added significantly to our knowledge of abundance, functional activity, and lifestyles of microbial communities in cold environments. The current knowledge of microbial ecology in glacial habitats and permafrost, the most studied habitats of the cryosphere, is reported in this review.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, 6020, Innsbruck, Austria.
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal
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35
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Schostag M, Priemé A, Jacquiod S, Russel J, Ekelund F, Jacobsen CS. Bacterial and protozoan dynamics upon thawing and freezing of an active layer permafrost soil. ISME JOURNAL 2019; 13:1345-1359. [PMID: 30692629 DOI: 10.1038/s41396-019-0351-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/17/2018] [Accepted: 12/23/2018] [Indexed: 11/09/2022]
Abstract
The active layer of soil overlaying permafrost in the Arctic is subjected to annual changes in temperature and soil chemistry, which we hypothesize to affect the overall soil microbial community. We investigated changes in soil microorganisms at different temperatures during warming and freezing of the active layer soil from Svalbard, Norway. Soil community data were obtained by direct shotgun sequencing of total extracted RNA. No changes in soil microbial communities were detected when warming from -10 to -2 °C or when freezing from -2 to -10 °C. In contrast, within a few days we observed changes when warming from -2 to +2 °C with a decrease in fungal rRNA and an increase in several OTUs belonging to Gemmatimonadetes, Bacteroidetes and Betaproteobacteria. Even more substantial changes occurred when incubating at 2 °C for 16 days, with declines in total fungal potential activity and decreases in oligotrophic members from Actinobacteria and Acidobacteria. Additionally, we detected an increase in transcriptome sequences of bacterial phyla Bacteriodetes, Firmicutes, Betaproteobacteria and Gammaproteobacteria-collectively presumed to be copiotrophic. Furthermore, we detected an increase in putative bacterivorous heterotrophic flagellates, likely due to predation upon the bacterial community via grazing. Although this grazing activity may explain relatively large changes in the bacterial community composition, no changes in total 16S rRNA gene copy number were observed and the total RNA level remained stable during the incubation. Together, these results are showing the first comprehensive ecological evaluation across prokaryotic and eukaryotic microbial communities on thawing and freezing of soil by application of the TotalRNA technique.
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Affiliation(s)
- Morten Schostag
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Anders Priemé
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,INRA Dijon, UMR1347 Agroécologie, Dijon, France
| | - Jakob Russel
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Suhr Jacobsen
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark. .,Geological Survey of Denmark and Greenland, Copenhagen, Denmark. .,Department of Environmental Science, Aarhus University, Roskilde, Denmark.
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36
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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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37
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Müller O, Bang-Andreasen T, White RA, Elberling B, Taş N, Kneafsey T, Jansson JK, Øvreås L. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates. Environ Microbiol 2018; 20:4328-4342. [PMID: 29971895 DOI: 10.1111/1462-2920.14348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/28/2022]
Abstract
Thawing permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO2 production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities are structured in permafrost and a better understanding of how they respond to thaw.
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Affiliation(s)
- Oliver Müller
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway
| | - Toke Bang-Andreasen
- Department of Environmental Science, Aarhus University, DK-4000, Roskilde, Denmark.,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | | | - Bo Elberling
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Neslihan Taş
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Janet K Jansson
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway.,University Center in Svalbard, UNIS, N-9171, Longyearbyen, Norway
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38
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Effect of Freeze-Thaw on a Midtemperate Soil Bacterial Community and the Correlation Network of Its Members. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8412429. [PMID: 30050943 PMCID: PMC6040300 DOI: 10.1155/2018/8412429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/17/2018] [Indexed: 11/17/2022]
Abstract
Freeze-thaw (FT) events can influence soil functions. However, the overall impact of FTs on soil bacterial communities, especially in temperate regions, remains unclear. In this study, soil samples were collected from a midtemperate region in the northeast of China, and three incubation tests were then designed with varied FT amplitudes (i.e., at a freezing temperature of −15, −9, and −3°C, respectively), frequencies of FT cycles (i.e., under one, six, and 15 FT cycles, respectively) and soil water content (SWC) values (i.e., at 10 and 30% SWC, respectively). High-throughput sequencing of 16S rRNA gene amplicons was performed and the functional profile was further predicted based on these data, in addition to examinations of bulk microbial properties. Data analyses suggested that, first of all, the FT amplitude significantly influenced the bulk microbial properties and bacterial community (composition and function); certain taxa showed a nonlinear response to the three amplitudes. Next, compared to a single FTC, multiple FT cycles had only minor effects on the bacterial functional capabilities, although the bulk microbial properties changed significantly after multiple FT cycles. In addition, the bacterial response to FTs was influenced by the SWC, characterized by the significantly different bacterial community structures (composition and function) and the opposite trends of enzyme activities. Finally, RDA plots and a correlation network assembled data from all soil samples across the three tests and suggested that bacterial response trajectories changed because some species were influenced mainly by other species (i.e., biotic environment) during FT processes.
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39
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Perfumo A, Banat IM, Marchant R. Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications. Trends Biotechnol 2018; 36:277-289. [PMID: 29428461 DOI: 10.1016/j.tibtech.2017.10.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 11/17/2022]
Abstract
Approximately 80% of the Earth's biosphere is cold, at an average temperature of 5°C, and is populated by a diversity of microorganisms that are a precious source of molecules with high biotechnological potential. Biosurfactants from cold-adapted organisms can interact with multiple physical phases - water, ice, hydrophobic compounds, and gases - at low and freezing temperatures and be used in sustainable (green) and low-energy-impact (cold) products and processes. We review the biodiversity of microbial biosurfactants produced in cold habitats and provide a perspective on the most promising future applications in environmental and industrial technologies. Finally, we encourage exploring the cryosphere for novel types of biosurfactants via both culture screening and functional metagenomics.
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Affiliation(s)
- Amedea Perfumo
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.
| | - Ibrahim M Banat
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, UK
| | - Roger Marchant
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, UK
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40
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Penczykowski RM, Connolly BM, Barton BT. Winter is changing: Trophic interactions under altered snow regimes. FOOD WEBS 2017. [DOI: 10.1016/j.fooweb.2017.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Tecon R, Or D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 2017; 41:599-623. [PMID: 28961933 PMCID: PMC5812502 DOI: 10.1093/femsre/fux039] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
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Affiliation(s)
- Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
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42
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Bore EK, Apostel C, Halicki S, Kuzyakov Y, Dippold MA. Microbial Metabolism in Soil at Subzero Temperatures: Adaptation Mechanisms Revealed by Position-Specific 13C Labeling. Front Microbiol 2017; 8:946. [PMID: 28611748 PMCID: PMC5447017 DOI: 10.3389/fmicb.2017.00946] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/11/2017] [Indexed: 11/13/2022] Open
Abstract
Although biogeochemical models designed to simulate carbon (C) and nitrogen (N) dynamics in high-latitude ecosystems incorporate extracellular parameters, molecular and biochemical adaptations of microorganisms to freezing remain unclear. This knowledge gap hampers estimations of the C balance and ecosystem feedback in high-latitude regions. To analyze microbial metabolism at subzero temperatures, soils were incubated with isotopomers of position-specifically 13C-labeled glucose at three temperatures: +5 (control), -5, and -20°C. 13C was quantified in CO2, bulk soil, microbial biomass, and dissolved organic carbon (DOC) after 1, 3, and 10 days and also after 30 days for samples at -20°C. Compared to +5°C, CO2 decreased 3- and 10-fold at -5 and -20°C, respectively. High 13C recovery in CO2 from the C-1 position indicates dominance of the pentose phosphate pathway at +5°C. In contrast, increased oxidation of the C-4 position at subzero temperatures implies a switch to glycolysis. A threefold higher 13C recovery in microbial biomass at -5 than +5°C points to synthesis of intracellular compounds such as glycerol and ethanol in response to freezing. Less than 0.4% of 13C was recovered in DOC after 1 day, demonstrating complete glucose uptake by microorganisms even at -20°C. Consequently, we attribute the fivefold higher extracellular 13C in soil than in microbial biomass to secreted antifreeze compounds. This suggests that with decreasing temperature, intracellular antifreeze protection is complemented by extracellular mechanisms to avoid cellular damage by crystallizing water. The knowledge of sustained metabolism at subzero temperatures will not only be useful for modeling global C dynamics in ecosystems with periodically or permanently frozen soils, but will also be important in understanding and controlling the adaptive mechanisms of food spoilage organisms.
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Affiliation(s)
- Ezekiel K. Bore
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
| | - Carolin Apostel
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
- Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
| | - Sara Halicki
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
| | - Yakov Kuzyakov
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
- Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
- Institute of Environmental Sciences, Kazan Federal UniversityKazan, Russia
| | - Michaela A. Dippold
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
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43
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Kashuba E, Dmitriev AA, Kamal SM, Melefors O, Griva G, Römling U, Ernberg I, Kashuba V, Brouchkov A. Ancient permafrost staphylococci carry antibiotic resistance genes. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017; 28:1345574. [PMID: 28959177 PMCID: PMC5614383 DOI: 10.1080/16512235.2017.1345574] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/14/2017] [Indexed: 10/26/2022]
Abstract
Background: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years. Objective: To cultivate bacterial strains from permafrost. Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40-60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences. Results: Genomic sequence analysis revealed the close relation of the isolated ancient bacteria to the modern bacteria of this species. Moreover, several genes associated with resistance to different groups of antibiotics were found in the S. hominis MMP2 genome. Conclusions: These findings supports a hypothesis that antibiotic resistance has an ancient origin. The enrichment of cultivated bacterial communities with ancient permafrost strains is essential for the analysis of bacterial evolution and antibiotic resistance.
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Affiliation(s)
- Elena Kashuba
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Laboratory of Cancer Genetics, R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NASU, Kyiv, Ukraine
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Shady Mansour Kamal
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, New Cairo, Egypt
| | - Ojar Melefors
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Gennady Griva
- Siberian Branch of RAS, Institute of the Earth Cryosphere, Tyumen, Russia
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Vladimir Kashuba
- Department of Molecular Oncogenetics, Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Anatoli Brouchkov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, Russia
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44
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Elster J, Margesin R, Wagner D, Häggblom M. Editorial: Polar and Alpine Microbiology—Earth's cryobiosphere. FEMS Microbiol Ecol 2016; 93:fiw221. [DOI: 10.1093/femsec/fiw221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 11/12/2022] Open
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