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Wicaksono WA, Mora M, Bickel S, Berg C, Kühn I, Cernava T, Berg G. Rhizosphere assembly alters along a chronosequence in the Hallstätter glacier forefield (Dachstein, Austria). FEMS Microbiol Ecol 2024; 100:fiae005. [PMID: 38271603 PMCID: PMC10858390 DOI: 10.1093/femsec/fiae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/07/2023] [Accepted: 01/24/2024] [Indexed: 01/27/2024] Open
Abstract
Rhizosphere microbiome assembly is essential for plant health, but the temporal dimension of this process remains unexplored. We used a chronosequence of 150 years of the retreating Hallstätter glacier (Dachstein, Austria) to disentangle this exemplarily for the rhizosphere of three pioneer alpine plants. Time of deglaciation was an important factor shaping the rhizosphere microbiome. Microbiome functions, i.e. nutrient uptake and stress protection, were carried out by ubiquitous and cosmopolitan bacteria. The rhizosphere succession along the chronosequence was characterized by decreasing microbial richness but increasing specificity of the plant-associated bacterial community. Environmental selection is a critical factor in shaping the ecosystem, particularly in terms of plant-driven recruitment from the available edaphic pool. A higher rhizosphere microbial richness during early succession compared to late succession can be explained by the occurrence of cold-acclimated bacteria recruited from the surrounding soils. These taxa might be sensitive to changing habitat conditions that occurred at the later stages. A stronger influence of the plant host on the rhizosphere microbiome assembly was observed with increased time since deglaciation. Overall, this study indicated that well-adapted, ubiquitous microbes potentially support pioneer plants to colonize new ecosystems, while plant-specific microbes may be associated with the long-term establishment of their hosts.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Maximilian Mora
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Samuel Bickel
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Christian Berg
- Institute of Plant Sciences, University of Graz, Graz 8010, Austria
| | - Ingolf Kühn
- Department of Community Ecology, Helmholtz Centre for Environmental Research—UFZ, Halle 06120, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle–Wittenberg, Halle 06099, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig 04103, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Potsdam 14469, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam 14469, Germany
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Purcell AM, Dijkstra P, Hungate BA, McMillen K, Schwartz E, van Gestel N. Rapid growth rate responses of terrestrial bacteria to field warming on the Antarctic Peninsula. ISME J 2023; 17:2290-2302. [PMID: 37872274 PMCID: PMC10689830 DOI: 10.1038/s41396-023-01536-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
Ice-free terrestrial environments of the western Antarctic Peninsula are expanding and subject to colonization by new microorganisms and plants, which control biogeochemical cycling. Measuring growth rates of microbial populations and ecosystem carbon flux is critical for understanding how terrestrial ecosystems in Antarctica will respond to future warming. We implemented a field warming experiment in early (bare soil; +2 °C) and late (peat moss-dominated; +1.2 °C) successional glacier forefield sites on the western Antarctica Peninsula. We used quantitative stable isotope probing with H218O using intact cores in situ to determine growth rate responses of bacterial taxa to short-term (1 month) warming. Warming increased the growth rates of bacterial communities at both sites, even doubling the number of taxa exhibiting significant growth at the early site. Growth responses varied among taxa. Despite that warming induced a similar response for bacterial relative growth rates overall, the warming effect on ecosystem carbon fluxes was stronger at the early successional site-likely driven by increased activity of autotrophs which switched the ecosystem from a carbon source to a carbon sink. At the late-successional site, warming caused a significant increase in growth rate of many Alphaproteobacteria, but a weaker and opposite gross ecosystem productivity response that decreased the carbon sink-indicating that the carbon flux rates were driven more strongly by the plant communities. Such changes to bacterial growth and ecosystem carbon cycling suggest that the terrestrial Antarctic Peninsula can respond fast to increases in temperature, which can have repercussions for long-term elemental cycling and carbon storage.
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Affiliation(s)
- Alicia M Purcell
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Kelly McMillen
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Natasja van Gestel
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
- TTU Climate Center, Texas Tech University, Lubbock, TX, USA
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Feng M, Varliero G, Qi W, Stierli B, Edwards A, Robinson S, van der Heijden MGA, Frey B. Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential. Environ Microbiol 2023; 25:3116-3138. [PMID: 37688461 DOI: 10.1111/1462-2920.16497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.
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Affiliation(s)
- Maomao Feng
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Serina Robinson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Plant-Soil Interactions, Agroscope, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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Wu X, Zhang W, Liu G, Chen T, Li Z. Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China. Microorganisms 2023; 11:2871. [PMID: 38138015 PMCID: PMC10745509 DOI: 10.3390/microorganisms11122871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by "Nitrosospira cluster ME", while the AOA community was dominated by "the soil and sediment 1". Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat.
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Affiliation(s)
- Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Zhongqin Li
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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Hay MC, Mitchell AC, Soares AR, Debbonaire AR, Mogrovejo DC, Els N, Edwards A. Metagenome-assembled genomes from High Arctic glaciers highlight the vulnerability of glacier-associated microbiota and their activities to habitat loss. Microb Genom 2023; 9. [PMID: 37937832 DOI: 10.1099/mgen.0.001131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
The rapid warming of the Arctic is threatening the demise of its glaciers and their associated ecosystems. Therefore, there is an urgent need to explore and understand the diversity of genomes resident within glacial ecosystems endangered by human-induced climate change. In this study we use genome-resolved metagenomics to explore the taxonomic and functional diversity of different habitats within glacier-occupied catchments. Comparing different habitats within such catchments offers a natural experiment for understanding the effects of changing habitat extent or even loss upon Arctic microbiota. Through binning and annotation of metagenome-assembled genomes (MAGs) we describe the spatial differences in taxon distribution and their implications for glacier-associated biogeochemical cycling. Multiple taxa associated with carbon cycling included organisms with the potential for carbon monoxide oxidation. Meanwhile, nitrogen fixation was mediated by a single taxon, although diverse taxa contribute to other nitrogen conversions. Genes for sulphur oxidation were prevalent within MAGs implying the potential capacity for sulphur cycling. Finally, we focused on cyanobacterial MAGs, and those within cryoconite, a biodiverse microbe-mineral granular aggregate responsible for darkening glacier surfaces. Although the metagenome-assembled genome of Phormidesmis priestleyi, the cyanobacterium responsible for forming Arctic cryoconite was represented with high coverage, evidence for the biosynthesis of multiple vitamins and co-factors was absent from its MAG. Our results indicate the potential for cross-feeding to sustain P. priestleyi within granular cryoconite. Taken together, genome-resolved metagenomics reveals the vulnerability of glacier-associated microbiota to the deletion of glacial habitats through the rapid warming of the Arctic.
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Affiliation(s)
- Melanie C Hay
- Department of Life Sciences (DLS), Aberystwyth University, Wales, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
- Department of Geography and Earth Sciences (DGES), Aberystwyth University, Wales, UK
- Present address: Department of Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - Andrew C Mitchell
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
- Department of Geography and Earth Sciences (DGES), Aberystwyth University, Wales, UK
| | - Andre R Soares
- Department of Life Sciences (DLS), Aberystwyth University, Wales, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
- Department of Geography and Earth Sciences (DGES), Aberystwyth University, Wales, UK
- Present address: Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Aliyah R Debbonaire
- Department of Life Sciences (DLS), Aberystwyth University, Wales, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
| | - Diana C Mogrovejo
- Dr. Brill + Partner GmbH Institut für Hygiene und Mikrobiologie, Hamburg, Germany
| | - Nora Els
- Department of Lake and Glacier Research, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Arwyn Edwards
- Department of Life Sciences (DLS), Aberystwyth University, Wales, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
- Department of Arctic Biology, University Centre in Svalbard (UNIS), Longyearbyen, Svalbard and Jan Mayen
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Ortiz-Rivero J, Garrido-Benavent I, Heiðmarsson S, de los Ríos A. Moss and Liverwort Covers Structure Soil Bacterial and Fungal Communities Differently in the Icelandic Highlands. Microb Ecol 2023; 86:1893-1908. [PMID: 36802019 PMCID: PMC10497656 DOI: 10.1007/s00248-023-02194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Cryptogamic covers extend over vast polar tundra regions and their main components, e.g., bryophytes and lichens, are frequently the first visible colonizers of deglaciated areas. To understand their role in polar soil development, we analyzed how cryptogamic covers dominated by different bryophyte lineages (mosses and liverworts) influence the diversity and composition of edaphic bacterial and fungal communities as well as the abiotic attributes of underlying soils in the southern part of the Highlands of Iceland. For comparison, the same traits were examined in soils devoid of bryophyte covers. We measured an increase in soil C, N, and organic matter contents coupled with a lower pH in association with bryophyte cover establishment. However, liverwort covers showed noticeably higher C and N contents than moss covers. Significant changes in diversity and composition of bacterial and fungal communities were revealed between (a) bare and bryophyte-covered soils, (b) bryophyte covers and the underlying soils, and (c) moss and liverworts covers. These differences were more obvious for fungi than bacteria, and involved different lineages of saprotrophic and symbiotic fungi, which suggests a certain specificity of microbial taxa to particular bryophyte groups. In addition, differences observed in the spatial structure of the two bryophyte covers may be also responsible for the detected differences in microbial community diversity and composition. Altogether, our findings indicate that soil microbial communities and abiotic attributes are ultimately affected by the composition of the most conspicuous elements of cryptogamic covers in polar regions, which is of great value to predict the biotic responses of these ecosystems to future climate change.
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Affiliation(s)
- Javier Ortiz-Rivero
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), C/ Serrano 115 dpdo, E-28045 Madrid, Spain
| | - Isaac Garrido-Benavent
- Departament de Botànica i Geologia, Fac. CC. Biològiques, Universitat de València, C/ Doctor Moliner 50, E-46100 Burjassot, Valencia Spain
| | - Starri Heiðmarsson
- Icelandic Institute of Natural History, Akureyri Division, Borgir Nordurslod, 600 Akureyri, Iceland
- Present address: Northwest Iceland Nature Research Centre, Aðalgötu 2, 550 Sauðárkrókur, Iceland
| | - Asunción de los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), C/ Serrano 115 dpdo, E-28045 Madrid, Spain
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Mashamaite L, Lebre PH, Varliero G, Maphosa S, Ortiz M, Hogg ID, Cowan DA. Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient. Front Microbiol 2023; 14:1203216. [PMID: 37555066 PMCID: PMC10406297 DOI: 10.3389/fmicb.2023.1203216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. METHODS We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. RESULTS AND DISCUSSION Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.
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Affiliation(s)
- Lefentse Mashamaite
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Max Ortiz
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Clemson University Genomics & Bioinformatics Facility, Clemson University, Clemson, SC, United States
| | - Ian D. Hogg
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Klarenberg IJ, Keuschnig C, Salazar A, Benning LG, Vilhelmsson O. Moss and underlying soil bacterial community structures are linked to moss functional traits. Ecosphere 2023. [DOI: 10.1002/ecs2.4447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Affiliation(s)
- Ingeborg J. Klarenberg
- Natural Resource Sciences University of Akureyri Akureyri Iceland
- Faculty of Life and Environmental Sciences University of Iceland Reykjavík Iceland
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam Netherlands
| | - Christoph Keuschnig
- Environmental Microbial Genomics Laboratoire Ampère, CNRS, École Centrale de Lyon Écully France
- German Research Centre for Geosciences (GFZ) Interface Geochemistry Potsdam Germany
| | - Alejandro Salazar
- Faculty of Environmental and Forest Sciences Agricultural University of Iceland Reykjavík Iceland
| | - Liane G. Benning
- German Research Centre for Geosciences (GFZ) Interface Geochemistry Potsdam Germany
- Department of Earth Sciences Free University of Berlin Berlin Germany
| | - Oddur Vilhelmsson
- Natural Resource Sciences University of Akureyri Akureyri Iceland
- BioMedical Center University of Iceland Reykjavík Iceland
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Rola K, Rożek K, Chowaniec K, Błaszkowski J, Gielas I, Stanek M, Wietrzyk-Pełka P, Węgrzyn M, Fałowska P, Dziurowicz P, Nicia P, Bejger R, Zadrożny P, Pliszko A, Zalewska-Gałosz J, Zubek S. Vascular plant and cryptogam abundance as well as soil chemical properties shape microbial communities in the successional gradient of glacier foreland soils. Sci Total Environ 2023; 860:160550. [PMID: 36460115 DOI: 10.1016/j.scitotenv.2022.160550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
In the glacier forelands, microbes play a fundamental role in soil development and shaping the vegetation structure. Such ecosystems represent various stages of soil development and are, therefore, an excellent place to study the interrelationship between soil, plants, and microorganisms. The aim of the study was to assess the effects of vegetation and soil physicochemical properties developing after glacier retreat on soil microbial communities. Specifically, abundance, species richness and the composition of arbuscular mycorrhizal fungi (AMF), as well as microbial biomass and community structure in soils were compared between plots established in 800-meter transects of three glacier forelands in northern Sweden. The cover of vascular plants and cryptogams, soil C content, AMF spore density and species richness, AMF biomass indicators, total microbial biomass, and bacterial phospholipid fatty acids (PLFA) were significantly and positively related to the distance from the glacier terminus. On the other hand, macronutrient concentrations and pH decreased along with increasing distance. No significant impact of the distance from the glacier terminus on the ratio fungal/bacterial PLFA was observed. Moreover, we found a significant effect of both glacier and the distance from the glacier terminus on the microbial community structure. AMF species richness and spore density in the glacier forelands were generally low, which is probably due to a limited supply of inoculum in primary successional ecosystems. Most microbial biochemical markers and AMF parameters were positively associated with the number of arbuscular mycorrhizal plant species and vascular plant and lichen cover as well as C content in soil, whereas negatively with soil macronutrients and pH. This could be related to an increase in plant cover and a decrease in soil nutrient levels as plant succession progresses. Our results showed that vegetation, soil C content, and microbial communities are interlinked and exhibit concordant patterns along successional gradients.
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Affiliation(s)
- Kaja Rola
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland.
| | - Katarzyna Rożek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Karolina Chowaniec
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Janusz Błaszkowski
- Department of Environmental Management, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434 Szczecin, Poland
| | - Igor Gielas
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Małgorzata Stanek
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Paulina Wietrzyk-Pełka
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Michał Węgrzyn
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Patrycja Fałowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Patrycja Dziurowicz
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Paweł Nicia
- Department of Soil Science and Agrophysics, University of Agriculture in Krakow, Al. Mickiewicza 21, 31-120 Kraków, Poland
| | - Romualda Bejger
- Department of Bioengineering, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Paweł Zadrożny
- Department of Soil Science and Agrophysics, University of Agriculture in Krakow, Al. Mickiewicza 21, 31-120 Kraków, Poland
| | - Artur Pliszko
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Joanna Zalewska-Gałosz
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Szymon Zubek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
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Purkamo L, Ó Dochartaigh B, MacDonald A, Cousins C. Following the flow-Microbial ecology in surface- and groundwaters in the glacial forefield of a rapidly retreating glacier in Iceland. Environ Microbiol 2022; 24:5840-5858. [PMID: 35706139 DOI: 10.1111/1462-2920.16104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 06/07/2022] [Accepted: 06/12/2022] [Indexed: 01/12/2023]
Abstract
The retreat of glaciers in response to climate change has major impacts on the hydrology and ecosystems of glacier forefield catchments. Microbes are key players in ecosystem functionality, supporting the supply of ecosystem services that glacier systems provide. The interaction between surface and groundwaters in glacier forefields has only recently gained much attention, and how these interactions influence the microbiology is still unclear. Here, we identify the microbial communities in groundwater from shallow (<15 m deep) boreholes in a glacial forefield floodplain ('sandur') aquifer at different distances from the rapidly retreating Virkisjökull glacier, Iceland, and with varying hydraulic connectivity with the glacial meltwater river that flows over the sandur. Groundwater communities are shown to differ from those in nearby glacial and non-glacial surface water communities. Groundwater-meltwater interactions and groundwater flow dynamics affect the microbial community structure, leading to different microbial communities at different sampling points in the glacier forefield. Groundwater communities differ from those in nearby glacial and non-glacial surface waters. Functional potential for microbial nitrogen and methane cycling was detected, although the functional gene copy numbers of specific groups were low.
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Affiliation(s)
- Lotta Purkamo
- Geological Survey of Finland, Espoo, Finland.,School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
| | | | | | - Claire Cousins
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
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11
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Pothula SK, Adams BJ. Community assembly in the wake of glacial retreat: A meta-analysis. Glob Chang Biol 2022; 28:6973-6991. [PMID: 36087341 DOI: 10.1111/gcb.16427] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Ecosystems shaped by retreating glaciers provide a unique opportunity to study the order and timing of biotic colonization, and how this influences the structure of successive ecological communities. In the last century glaciers across most of the cryosphere have receded at an unprecedented pace. Many studies have been published from different parts of the world testing hypotheses about how soil ecosystems are responding to rapid, contemporary deglaciation events. To better understand and draw general conclusions about how soil ecosystems respond to deglaciation, we conducted a global meta-analysis of 95 published articles focused on the succession of various organisms and soil physicochemical properties in glacier forefields along the chronosequence. Our global synthesis reveals that key soil properties and the abundance and richness of biota follow two conspicuous patterns: (1) some taxa demonstrate a persistent increase in abundance and richness over the entire chronosequence, (2) other taxa increase in abundance and richness during the first 50 years of succession, then gradually decline 50 years onward. The soil properties and soil organisms that are intimately tied to vegetation follow the first pattern, consistent with the idea that aboveground patterns of vegetation can drive patterns of belowground biodiversity. The second pattern may be due to an initial increase and subsequent decline in available nutrients and habitat suitability caused by increased biotic interactions, including resource competition among soil biota. A consensus view of the patterns of historical and contemporary soil ecosystem responses to deglaciation provides a better understanding of the processes that generate these patterns and informs predictions of ongoing and future responses to environmental changes.
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Affiliation(s)
| | - Byron J Adams
- Department of Biology, Brigham Young University, Provo, Utah, USA
- Evolutionary Ecology Laboratories, Brigham Young University, Provo, Utah, USA
- Life Science Museum, Brigham Young University, Provo, Utah, USA
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12
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Vimercati L, Bueno de Mesquita CP, Johnson BW, Mineart D, DeForce E, Vimercati Molano Y, Ducklow H, Schmidt SK. Dynamic trophic shifts in bacterial and eukaryotic communities during the first 30 years of microbial succession following retreat of an Antarctic glacier. FEMS Microbiol Ecol 2022; 98:6762214. [PMID: 36251461 DOI: 10.1093/femsec/fiac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 01/21/2023] Open
Abstract
We examined microbial succession along a glacier forefront in the Antarctic Peninsula representing ∼30 years of deglaciation to contrast bacterial and eukaryotic successional dynamics and abiotic drivers of community assembly using sequencing and soil properties. Microbial communities changed most rapidly early along the chronosequence, and co-occurrence network analysis showed the most complex topology at the earliest stage. Initial microbial communities were dominated by microorganisms derived from the glacial environment, whereas later stages hosted a mixed community of taxa associated with soils. Eukaryotes became increasingly dominated by Cercozoa, particularly Vampyrellidae, indicating a previously unappreciated role for cercozoan predators during early stages of primary succession. Chlorophytes and Charophytes (rather than cyanobacteria) were the dominant primary producers and there was a spatio-temporal sequence in which major groups became abundant succeeding from simple ice Chlorophytes to Ochrophytes and Bryophytes. Time since deglaciation and pH were the main abiotic drivers structuring both bacterial and eukaryotic communities. Determinism was the dominant assembly mechanism for Bacteria, while the balance between stochastic/deterministic processes in eukaryotes varied along the distance from the glacier front. This study provides new insights into the unexpected dynamic changes and interactions across multiple trophic groups during primary succession in a rapidly changing polar ecosystem.
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Affiliation(s)
- Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| | - Clifton P Bueno de Mesquita
- DOE Joint Genome Institute Lawrence Berkeley National Laboratory 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Ben W Johnson
- Department of Geological and Atmospheric Sciences 253 Science Hall 2237 Osborn Drive Ames, Iowa 50011-3212, United States
| | - Dana Mineart
- Department of Geological and Atmospheric Sciences 253 Science Hall 2237 Osborn Drive Ames, Iowa 50011-3212, United States
| | - Emelia DeForce
- Integrative Oceanography Division Scripps Institution of Oceanography 9500 Gilman Drive La Jolla, CA 92093 5, United States
| | - Ylenia Vimercati Molano
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| | - Hugh Ducklow
- Lamont-Doherty Earth Observatory P.O. Box 1000 61 Route 9W Palisades, NY 10964-1000, United States
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
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13
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Tian C, Lv Y, Yang Z, Zhang R, Zhu Z, Ma H, Li J, Zhang Y. Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard. Microb Ecol 2022:10.1007/s00248-022-02116-3. [PMID: 36239777 DOI: 10.1007/s00248-022-02116-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.
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Affiliation(s)
- Chen Tian
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yongxin Lv
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhifeng Yang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Ruifeng Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Zhuoyi Zhu
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Hongmei Ma
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Jing Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yu Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China.
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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14
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Peck C, Jackobs F, Smith E. The PortaLyzer, a DIY tool that allows environmental DNA extraction in the field. HardwareX 2022; 12:e00373. [PMID: 36393914 PMCID: PMC9644035 DOI: 10.1016/j.ohx.2022.e00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
The PortaLyzer is a portable homemade device that allows researchers to perform bead-beating steps commonly found in environmental DNA (eDNA) extraction protocols in the field without access to power. This allows researchers to preserve in situ organism abundance by beginning eDNA extraction quickly. The PortaLyzer is composed of a variable speed, battery-powered multi-tool and a vortexer adapter plate. We used the PortaLyzer, in conjunction with the Qiagen DNEasy PowerSoil Pro kit, to successfully field process samples taken from the forelands of the Sólheimajökull and Kvíárjökull glaciers in Iceland, as well as soil samples acquired from a prairie in Indiana. Additionally, we provide evidence that samples held in Buffer CD2 of the DNEasy PowerSoil Pro Kit may be transported to traditional lab spaces and processed up to one month after the initial protocol steps, and still provide an equivalent DNA quality and abundance yield as those processed the same day. These improvements to DNA extraction protocols give researchers more flexibility while sampling, shipping and processing eDNA samples.
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15
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Zhang J, Ma A, Zhou H, Chen X, Zhou X, Liu G, Zhuang X, Qin X, Priemé A, Zhuang G. Unexpected high carbon losses in a continental glacier foreland on the Tibetan Plateau. ISME Commun 2022; 2:68. [PMID: 37938688 PMCID: PMC9723710 DOI: 10.1038/s43705-022-00148-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/19/2022] [Accepted: 06/28/2022] [Indexed: 10/21/2023]
Abstract
Closely related with microbial activities, soil developments along the glacier forelands are generally considered a carbon sink; however, those of continental glacier forelands remain unclear. Continental glaciers are characterized by dry conditions and low temperature that limit microbial growth. We investigated the carbon characteristics along a chronosequence of the Laohugou Glacier No. 12 foreland, a typical continental glacier on the Tibetan Plateau, by analyzing soil bacterial community structure and microbial carbon-related functional potentials. We found an unexpected carbon loss in which soil organic carbon decreased from 22.21 g kg-1 to 10.77 g kg-1 after receding 50 years. Structural equation modeling verified the important positive impacts from bacterial community. Lower carbon fixation efficiency along the chronosequence was supported by less autotrophic bacteria and carbon fixation genes relating to the reductive tricarboxylic acid cycle. Lower carbon availability and higher carbon requirements were identified by an increasing bacterial copy number and a shift of the dominant bacterial community from Proteobacteria and Bacteroidetes (r-strategists) to Actinobacteria and Acidobacteria (K-strategists). Our findings show that the carbon loss of continental glacier foreland was significantly affected by the changes of bacterial community, and can help to avoid overestimating the carbon sink characteristics of glacier forelands in climate models.
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Affiliation(s)
- Jiejie Zhang
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101400, China
- Sino-Danish Center for Education and Research, Beijing, 101400, China
| | - Anzhou Ma
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hanchang Zhou
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianke Chen
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101400, China
- Sino-Danish Center for Education and Research, Beijing, 101400, China
| | - Xiaorong Zhou
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guohua Liu
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuliang Zhuang
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang Qin
- Qilian Shan Station of Glaciology and Eco-environment, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Anders Priemé
- Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Center for Permafrost, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Guoqiang Zhuang
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Xing T, Liu P, Ji M, Deng Y, Liu K, Wang W, Liu Y. Sink or Source: Alternative Roles of Glacier Foreland Meadow Soils in Methane Emission Is Regulated by Glacier Melting on the Tibetan Plateau. Front Microbiol 2022; 13:862242. [PMID: 35387086 PMCID: PMC8977769 DOI: 10.3389/fmicb.2022.862242] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Glacier foreland soils have long been considered as methane (CH4) sinks. However, they are flooded by glacial meltwater annually during the glacier melting season, altering their redox potential. The impacts of this annual flooding on CH4 emission dynamics and methane-cycling microorganisms are not well understood. Herein, we measured in situ methane flux in glacier foreland soils during the pre-melting and melting seasons on the Tibetan Plateau. In addition, high-throughput sequencing and qPCR were used to investigate the diversity, taxonomic composition, and the abundance of methanogenic archaea and methanotrophic bacteria. Our results showed that the methane flux ranged from -10.11 to 4.81 μg·m-2·h-1 in the pre-melting season, and increased to 7.48-22.57 μg·m-2·h-1 in the melting season. This indicates that glacier foreland soils change from a methane sink to a methane source under the impact of glacial meltwater. The extent of methane flux depends on methane production and oxidation conducted by methanogens and methanotrophs. Among all the environmental factors, pH (but not moisture) is dominant for methanogens, while both pH and moisture are not that strong for methanotrophs. The dominant methanotrophs were Methylobacter and Methylocystis, whereas the methanogens were dominated by methylotrophic Methanomassiliicoccales and hydrogenotrophic Methanomicrobiales. Their distributions were also affected by microtopography and environmental factor differences. This study reveals an alternative role of glacier foreland meadow soils as both methane sink and source, which is regulated by the annual glacial melt. This suggests enhanced glacial retreat may positively feedback global warming by increasing methane emission in glacier foreland soils in the context of climate change.
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Affiliation(s)
- Tingting Xing
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing, China.,Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Wenqiang Wang
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
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17
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Ma A, Zhang J, Liu G, Zhuang X, Zhuang G. Cryosphere Microbiome Biobanks for Mountain Glaciers in China. Sustainability 2022; 14:2903. [DOI: 10.3390/su14052903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The glaciers in China have an important role as one of the most climate-sensitive constituents of the Tibetan Plateau which is known as the Asian Water Tower. Although the cryosphere is one of the most extreme environments for organisms, the soils of the glacier foreland harbor surprisingly rich microbiomes. A large amount of accelerated glacier retreat accompanied by global warming will not only raise the sea level, but it will also lead to the massive release of a considerable amount of carbon stored in these glaciers. The responses of glacier microbiomes could alter the biogeochemical cycle of carbon and have a complex impact on climate change. Thus, understanding present-day and future glacier microbiome changes is crucial to assess the feedback on climate change and the impacts on ecosystems. To this end, we discuss here the diversity and biogeochemical functions of the microbiomes in Chinese mountain glacier ecosystems.
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18
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Pérez CA, Kim M, Aravena JC, Silva W. Diazotrophic activity and denitrification in two long-term chronosequences of maritime Antarctica. Sci Total Environ 2022; 809:152234. [PMID: 34896140 DOI: 10.1016/j.scitotenv.2021.152234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
The main goals of this study were to identify whether key processes involved in microbial soil nitrogen transformations, such as diazotrophic activity and denitrification, the chemical properties of limiting elements in the soil, and microbial community structure, differ in the different successional stages of two long term chronosequences in maritime Antarctica. Moreover, we expect the rates of diazotrophic activity and denitrification to be stimulated by increases in air temperature and moisture. To answer these questions, we selected three stages in the succession (early, mid and late) in each of two well established chronosequences: three raised beaches in Ardley Island; and the Barton Peninsula, which includes two cosmogenically dated sites and the forefield of the Fourcade glacier. In the Ardley chronosequence, higher diazotrophic activity was found in the older successional stages, concomitant with an increase in the abundance of Cyanobacteria. In the Barton chronosequence, Cyanobacteria were only present and abundant (Microcoleus) in the early successional stage, coinciding with the highest diazotrophic activity. Denitrification in the Barton chronosequence tended to be highest at the mid successional sites, associated with the highest abundance of Rhodanobacter. In the Ardley chronosequence, the lowest abundance of Rhodanobacter was linked to lower denitrification rates in the mid successional stage. In the Ardley chronosequence, significant positive effects of passive warming and water addition on diazotrophic activity were detected in the first and the second years of the study respectively. In the Barton chronosequence on the other hand, there was no response to either passive warming or water addition, probably a manifestation of the higher nutrient limitation in this site. Denitrification showed no response to either warming or water addition. Thus, the response of microbial nitrogen transformations to global change is highly dependent on the environmental setting, such as soil origin, age and climate regime.
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Affiliation(s)
- Cecilia A Pérez
- Institute of Ecology and Biodiversity (IEB), Las Palmeras, 3425 Santiago, Chile.
| | - Mincheol Kim
- Korea Polar Research Institute (KOPRI), Incheon 21990, Republic of Korea
| | - Juan Carlos Aravena
- Centro de Investigación Gaia Antártica (CIGA), Universidad de Magallanes, Punta Arenas, Chile
| | - Wladimir Silva
- Institute of Ecology and Biodiversity (IEB), Las Palmeras, 3425 Santiago, Chile
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19
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OUP accepted manuscript. FEMS Microbiol Ecol. [DOI: 10.1093/femsec/fiac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/22/2021] [Accepted: 03/17/2022] [Indexed: 11/14/2022] Open
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20
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Sengupta A, Volkmann THM, Danczak RE, Stegen JC, Dontsova K, Abramson N, Bugaj AS, Volk MJ, Matos KA, Meira-Neto AA, Barberán A, Neilson JW, Maier RM, Chorover J, Troch PA, Meredith LK. Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System. Front Microbiol 2021; 12:754698. [PMID: 34887842 PMCID: PMC8650109 DOI: 10.3389/fmicb.2021.754698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.
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Affiliation(s)
- Aditi Sengupta
- Department of Biology, California Lutheran University, Thousand Oaks, CA, United States.,Biosphere 2, University of Arizona, Tucson, AZ, United States
| | | | - Robert E Danczak
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - James C Stegen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Katerina Dontsova
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Nate Abramson
- Department of Geosciences, University of Arizona, Tucson, AZ, United States
| | - Aaron S Bugaj
- Biosphere 2, University of Arizona, Tucson, AZ, United States
| | - Michael J Volk
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | | | - Antonio A Meira-Neto
- Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Julia W Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Raina M Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Jon Chorover
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Peter A Troch
- Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, United States
| | - Laura K Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
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21
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Kumar V, Kumar S, Singh D. Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies. Extremophiles 2021; 26:3. [PMID: 34878610 DOI: 10.1007/s00792-021-01252-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/13/2021] [Indexed: 12/31/2022]
Abstract
Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.
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Liu J, Kong W, Xia P, Zhu C, Li X. Prokaryotic Community Succession in Bulk and Rhizosphere Soils Along a High-Elevation Glacier Retreat Chronosequence on the Tibetan Plateau. Front Microbiol 2021; 12:736407. [PMID: 34690976 PMCID: PMC8531754 DOI: 10.3389/fmicb.2021.736407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023] Open
Abstract
Early colonization and succession of soil microbial communities are essential for soil development and nutrient accumulation. Herein we focused on the changes in pioneer prokaryotic communities in rhizosphere and bulk soils along the high-elevation glacier retreat chronosequence, the northern Himalayas, Tibetan Plateau. Rhizosphere soils showed substantially higher levels of total organic carbon, total nitrogen, ammonium, and nitrate than bulk soils. The dominant prokaryotes were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Crenarchaeota, Bacteroidetes, and Planctomycetes, which totally accounted for more than 75% in relative abundance. The dominant genus Candidatus Nitrososphaera occurred at each stage of the microbial succession. The richness and evenness of soil prokaryotes displayed mild succession along chronosequene. Linear discriminant analysis effect size (LEfSe) analysis demonstrated that Proteobacteria (especially Alphaproteobacteria) and Actinobacteria were significantly enriched in rhizosphere soils compared with bulk soils. Actinobacteria, SHA_109, and Thermoleophilia; Betaproteobacteria and OP1.MSBL6; and Planctomycetia and Verrucomicrobia were separately enriched at each of the three sample sites. The compositions of prokaryotic communities were substantially changed with bulk and rhizosphere soils and sampling sites, indicating that the communities were dominantly driven by plants and habitat-specific effects in the deglaciated soils. Additionally, the distance to the glacier terminus also played a significant role in driving the change of prokaryotic communities in both bulk and rhizosphere soils. Soil C/N ratio exhibited a greater effect on prokaryotic communities in bulk soils than rhizosphere soils. These results indicate that plants, habitat, and glacier retreat chronosequence collectively control prokaryotic community composition and succession.
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Affiliation(s)
- Jinbo Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Pinhua Xia
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang, China
| | - Chunmao Zhu
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Japan
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Varliero G, Anesio AM, Barker GLA. A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems. Front Microbiol 2021; 12:627437. [PMID: 34621246 PMCID: PMC8491546 DOI: 10.3389/fmicb.2021.627437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.
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Affiliation(s)
- Gilda Varliero
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Gary L. A. Barker
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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Krauze P, Wagner D, Yang S, Spinola D, Kühn P. Influence of prokaryotic microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica. Sci Rep 2021; 11:13135. [PMID: 34162928 PMCID: PMC8222374 DOI: 10.1038/s41598-021-92205-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/02/2021] [Indexed: 02/05/2023] Open
Abstract
Compared to the 1970s, the edge of the Ecology Glacier on King George Island, maritime Antarctica, is positioned more than 500 m inwards, exposing a large area of new terrain to soil-forming processes and periglacial climate for more than 40 years. To gain information on the state of soil formation and its interplay with microbial activity, three hyperskeletic Cryosols (vegetation cover of 0-80%) deglaciated after 1979 in the foreland of the Ecology Glacier and a Cambic Cryosol (vegetation cover of 100%) distal to the lateral moraine deglaciated before 1956 were investigated by combining soil chemical and microbiological methods. In the upper part of all soils, a decrease in soil pH was observed, but only the Cambic Cryosol showed a clear direction of pedogenic and weathering processes, such as initial silicate weathering indicated by a decreasing Chemical Index of Alteration with depth. Differences in the development of these initial soils could be related to different microbial community compositions and vegetation coverage, despite the short distance among them. We observed-decreasing with depth-the highest bacterial abundances and microbial diversity at vegetated sites. Multiple clusters of abundant amplicon sequence variants were found depending on the site-specific characteristics as well as a distinct shift in the microbial community structure towards more similar communities at soil depths > 10 cm. In the foreland of the Ecology Glacier, the main soil-forming processes on a decadal timescale are acidification and accumulation of soil organic carbon and nitrogen, accompanied by changes in microbial abundances, microbial community compositions, and plant coverage, whereas quantifiable silicate weathering and the formation of pedogenic oxides occur on a centennial to a millennial timescale after deglaciation.
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Affiliation(s)
- Patryk Krauze
- GFZ, German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, 14473, Potsdam, Germany.
| | - Dirk Wagner
- GFZ, German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, 14473, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, 14476, Potsdam, Germany
| | - Sizhong Yang
- GFZ, German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, 14473, Potsdam, Germany
| | - Diogo Spinola
- Department of Geosciences, Research Area Geography, Laboratory of Soil Science and Geoecology, Eberhard Karls University Tübingen, 72070, Tübingen, Germany
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, 99775-6160, USA
| | - Peter Kühn
- Department of Geosciences, Research Area Geography, Laboratory of Soil Science and Geoecology, Eberhard Karls University Tübingen, 72070, Tübingen, Germany
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Hu W, Schmidt SK, Sommers P, Darcy JL, Porazinska DL. Multiple‐trophic patterns of primary succession following retreat of a high‐elevation glacier. Ecosphere 2021. [DOI: 10.1002/ecs2.3400] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Weiming Hu
- Department of Entomology and Nematology University of Florida Gainesville Florida32611USA
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
| | - John L. Darcy
- Anschutz Medical Campus University of Colorado, Denver Denver Colorado80204USA
| | - Dorota L. Porazinska
- Department of Entomology and Nematology University of Florida Gainesville Florida32611USA
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
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26
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Franzetti A, Pittino F, Gandolfi I, Azzoni RS, Diolaiuti G, Smiraglia C, Pelfini M, Compostella C, Turchetti B, Buzzini P, Ambrosini R. Early ecological succession patterns of bacterial, fungal and plant communities along a chronosequence in a recently deglaciated area of the Italian Alps. FEMS Microbiol Ecol 2021; 96:5894918. [PMID: 32815995 DOI: 10.1093/femsec/fiaa165] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/12/2020] [Indexed: 12/31/2022] Open
Abstract
In this study, the early ecological succession patterns of Forni Glacier (Ortles-Cevedale group, Italian Alps) forefield along an 18-year long chronosequence (with a temporal resolution of 1 year) has been reported. Bacterial and fungal community structures were inferred by high-throughput sequencing of 16S rRNA gene and ITS, respectively. In addition, the occurrence of both herbaceous and arboreous plants was also recorded at each plot. A significant decrease of alpha-diversity in more recently deglaciated areas was observed for both bacteria and plants. Time since deglaciation and pH affected the structure of both fungal and bacterial communities. Pioneer plants could be a major source of colonization for both bacterial and fungal communities. Consistently, some of the most abundant bacterial taxa and some of those significantly varying with pH along the chronosequence (Polaromonas, Granulicella, Thiobacillus, Acidiferrobacter) are known to be actively involved in rock-weathering processes due to their chemolithotrophic metabolism, thus suggesting that the early phase of the chronosequence could be mainly shaped by the biologically controlled bioavailability of metals and inorganic compounds. Fungal communities were dominated by ascomycetous filamentous fungi and basidiomycetous yeasts. Their role as cold-adapted organic matter decomposers, due to their heterotrophic metabolism, was suggested.
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Affiliation(s)
- A Franzetti
- Department of Earth and Environmental Sciences (DISAT) - University of Milano-Bicocca, Milano, Italy
| | - F Pittino
- Department of Earth and Environmental Sciences (DISAT) - University of Milano-Bicocca, Milano, Italy
| | - I Gandolfi
- Department of Earth and Environmental Sciences (DISAT) - University of Milano-Bicocca, Milano, Italy
| | - R S Azzoni
- Department of Environmental Science and Policy, University of Milano, Milano, Italy
| | - G Diolaiuti
- Department of Environmental Science and Policy, University of Milano, Milano, Italy
| | - C Smiraglia
- Department of Earth Science "Ardito Desio", University of Milano, Milano, Italy
| | - M Pelfini
- Department of Earth Science "Ardito Desio", University of Milano, Milano, Italy
| | - C Compostella
- Department of Earth Science "Ardito Desio", University of Milano, Milano, Italy
| | - B Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - P Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - R Ambrosini
- Department of Environmental Science and Policy, University of Milano, Milano, Italy
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27
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Sanyal A, Antony R, Ganesan P, Thamban M. Metabolic activity and bioweathering properties of yeasts isolated from different supraglacial environments of Antarctica and Himalaya. Antonie Van Leeuwenhoek 2020; 113:2243-2258. [PMID: 33219409 DOI: 10.1007/s10482-020-01496-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/29/2020] [Indexed: 11/26/2022]
Abstract
Yeasts have been frequently isolated from cold habitats, but their contribution to essential ecological processes such as the mineralization of organic matter in these environments is less known. Here, the diversity, metabolic capability, and extracellular enzyme profiles of yeasts from snow, blue ice and cryoconite hole environments from East Antarctica and cryoconite holes from a glacier in Western Himalaya were determined. Eighty-six yeast strains isolated were affiliated to the genera Glaciozyma, Goffeauzyma, Mrakia, Phenoliferia, and Rhodotorula. Variations in the abundance, diversity, physiological properties, extracellular enzyme and carbon substrate utilization patterns of the isolated yeasts, reflect the specific environmental conditions from which they were isolated. Overall, 20-90% of the yeasts across all habitat types and geographical locations produced extracellular enzymes to degrade proteins, esters, carbohydrates, pectin, cellulose, lignin, and tannin. About 10 and 29% of the yeasts also exhibited ability to solubilize rock-minerals like phosphate and silicate, respectively. Additionally, selected isolates were able to metabolize 28-93% of the carbon substrates comprising different compound classes on Biolog YT plates. Overall, the ability of yeasts to use diverse organic compounds prevalent on the glacier surface, points to their ecological significance in the decomposition of organic matter, cycling of nutrients, and in the weathering of minerals in supraglacial environments. Moreover, their wide metabolic capabilities suggest that they can colonize new niches and environments when meltwater export during the summer that enables links with surrounding ecosystems.
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Affiliation(s)
- Aritri Sanyal
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India.
| | - Runa Antony
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India
| | - Preethika Ganesan
- Department of Applied Microbiology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, 632014, India
- Department of Food Science, School of Chemical Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Meloth Thamban
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India
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Sun X, Xu R, Dong Y, Li F, Tao W, Kong T, Zhang M, Qiu L, Wang X, Sun W. Investigation of the Ecological Roles of Putative Keystone Taxa during Tailing Revegetation. Environ Sci Technol 2020; 54:11258-11270. [PMID: 32786562 DOI: 10.1021/acs.est.0c03031] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metal contamination released from tailings is a global environmental concern. Although phytoremediation is a promising remediation method, its practice is often impeded by the adverse tailing geochemical conditions, which suppress biological activities. The ecosystem services provided by indigenous microorganisms could alter environmental conditions and facilitate revegetation in tailings. During the process, the keystone taxa of the microbial community are assumed an essential role in regulating the community composition and functions. The identity and the environmental functions of the keystone taxa during tailing revegetation, however, remain unelucidated. The current study compared the microbial community composition and interactions of two contrasting stibnite (Sb2S3) tailings, one revegetated and one unvegetated. The microbial interaction networks and keystone taxa were significantly different in the two tailings. Similar keystone taxa were also identified in other revegetated tailings, but not in their corresponding unvegetated tailings. Metagenome-assembled genomes (MAGs) indicated that the keystone taxa in the revegetated tailing may use both organic and inorganic energy sources (e.g., sulfur, arsenic, and antimony). They could also facilitate plant growth since a number of plant-growth-promoting genes, including phosphorus solubilization and siderophore production genes, were encoded. The current study suggests that keystone taxa may play important roles in tailing revegetation by providing nutrients, such as P and Fe, and promoting plant growth.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Wan Tao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Lang Qiu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Xiaoyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
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29
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Santos JAD, Meyer E, Sette LD. Fungal Community in Antarctic Soil Along the Retreating Collins Glacier (Fildes Peninsula, King George Island). Microorganisms 2020; 8:E1145. [PMID: 32751125 DOI: 10.3390/microorganisms8081145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 01/17/2023] Open
Abstract
Glacial retreat is one of the most conspicuous signs of warming in Antarctic regions. Glacier soils harbor an active microbial community of decomposers, and under the continuous retraction of glaciers, the soil starts to present a gradient of physical, chemical, and biological factors reflecting regional changes over time. Little is known about the biological nature of fungi in Antarctic glacier soils. In this sense, this work aimed at studying the behavior of fungal community structure from samples of glacier soil collected after glacial retreat (Collins Glacier). A total of 309 fungi distributed in 19 genera were obtained from eleven soil samples. Representatives of the genera Pseudogymnoascus (Ascomycota) and Mortierella (Mortierellomycota) were the most abundant isolates in all samples. The data revealed the presence of filamentous fungi belonging to the phylum Basidiomycota, rarely found in Antarctica. Analysis of the generalized linear models revealed that the distance from the glacier as well as phosphorus and clay were able to modify the distribution of fungal species. Environmental variations proved to have influenced the genera Pseudogymnoascus and Pseudeutorium.
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Cameron KA, Müller O, Stibal M, Edwards A, Jacobsen CS. Glacial microbiota are hydrologically connected and temporally variable. Environ Microbiol 2020; 22:3172-3187. [PMID: 32383292 DOI: 10.1111/1462-2920.15059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/15/2020] [Accepted: 05/02/2020] [Indexed: 11/29/2022]
Abstract
Glaciers are melting rapidly. The concurrent export of microbial assemblages alongside glacial meltwater is expected to impact the ecology of adjoining ecosystems. Currently, the source of exported assemblages is poorly understood, yet this information may be critical for understanding how current and future glacial melt seasons may influence downstream environments. We report on the connectivity and temporal variability of microbiota sampled from supraglacial, subglacial and periglacial habitats and water bodies within a glacial catchment. Sampled assemblages showed evidence of being biologically connected through hydrological flowpaths, leading to a meltwater system that accumulates prokaryotic biota as it travels downstream. Temporal changes in the connected assemblages were similarly observed. Snow assemblages changed markedly throughout the sample period, likely reflecting changes in the surrounding environment. Changes in supraglacial meltwater assemblages reflected the transition of the glacial surface from snow-covered to bare-ice. Marked snowmelt across the surrounding periglacial environment resulted in the flushing of soil assemblages into the riverine system. In contrast, surface ice within the ablation zone and subglacial meltwaters remained relatively stable throughout the sample period. Our results are indicative that changes in snow and ice melt across glacial environments will influence the abundance and diversity of microbial assemblages transported downstream.
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Affiliation(s)
- Karen A Cameron
- Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK.,Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, 1350, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, 1350, Denmark.,School of Geographical and Earth Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Oliver Müller
- Department of Biological Sciences, University of Bergen, Bergen, 5006, Norway
| | - Marek Stibal
- Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, 1350, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, 1350, Denmark.,Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Arwyn Edwards
- Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK
| | - Carsten Suhr Jacobsen
- Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, 1350, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, 1350, Denmark.,Department of Environmental Science, Aarhus University, Roskilde, 4000, Denmark
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31
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Sun X, Kong T, Häggblom MM, Kolton M, Li F, Dong Y, Huang Y, Li B, Sun W. Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings. Environ Sci Technol 2020; 54:6082-6093. [PMID: 32216300 DOI: 10.1021/acs.est.9b07835] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.
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Affiliation(s)
- Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Tianle Kong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Max Kolton
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqing Huang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
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Fickert T. Common Patterns and Diverging Trajectories in Primary Succession of Plants in Eastern Alpine Glacier Forelands. Diversity 2020; 12:191. [DOI: 10.3390/d12050191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper deals with the vegetation development in four glacier forelands, aligned along a distance of 250 km from West to East in the siliceous Eastern Central Alps. The study employs a chronosequence approach, which assumes a temporal sequence in vegetation development by spatially different sites regarding time since deglaciation. The chronosequences cover the area between Little Ice Age (LIA) maximum glacier extent around 1850, and the current glacier terminus. Despite some shortcomings, chronosequences allow the identification of general patterns of primary succession of plants as a function of site age and local environmental conditions, e.g., changes in species richness, ground cover, plant functional traits, and community structure. While there is no shortage of chronosequence studies in glacier forelands of the Alps, a straightforward comparison aimed at the deduction of general successional trajectories is tricky, due to different procedures of vegetation sampling and data analyses. The comparative examination by a standardized sampling and analyzing protocol of four glacier forelands in the Eastern Central Alps presented here proves the existence of several common patterns in primary succession, but also diverging successional trajectories from West to East. While the pioneer stage in all glacier forelands is similar both floristically and structurally, from the early successional stage onwards, differences increase, leading to different phases in the late successional stage, which is shrub dominated throughout in the westernmost study site, herb–grass–dwarfshrub dominated throughout in the easternmost study site, and divided into an earlier herb–grass–dwarfshrub phase and a later shrub phase in the two study sites in between.
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Canini F, Zucconi L, Pacelli C, Selbmann L, Onofri S, Geml J. Vegetation, pH and Water Content as Main Factors for Shaping Fungal Richness, Community Composition and Functional Guilds Distribution in Soils of Western Greenland. Front Microbiol 2019; 10:2348. [PMID: 31681213 PMCID: PMC6797927 DOI: 10.3389/fmicb.2019.02348] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/26/2019] [Indexed: 01/29/2023] Open
Abstract
Fungi are the most abundant and one of the most diverse components of arctic soil ecosystems, where they are fundamental drivers of plant nutrient acquisition and recycling. Nevertheless, few studies have focused on the factors driving the diversity and functionality of fungal communities associated with these ecosystems, especially in the scope of global warming that is particularly affecting Greenland and is leading to shrub expansion, with expected profound changes of soil microbial communities. We used soil DNA metabarcoding to compare taxonomic and functional composition of fungal communities in three habitats [bare ground (BG), biological soil crusts (BSC), and vascular vegetation (VV) coverage] in Western Greenland. Fungal richness increased with the increasing complexity of the coverage, but BGs and BSCs samples showed the highest number of unique OTUs. Differences in both fungal community composition and distribution of functional guilds identified were correlated with edaphic factors (mainly pH and water content), in turn connected with the different type of coverage. These results suggest also possible losses of diversity connected to the expansion of VV and possible interactions among the members of different functional guilds, likely due to the nutrient limitation, with potential effects on elements recycling.
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Affiliation(s)
- Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Biodiversity Dynamics, Naturalis Biodiversity Center, Leiden, Netherlands
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Claudia Pacelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Section of Mycology, Italian National Antarctic Museum (MNA), Genoa, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - József Geml
- Biodiversity Dynamics, Naturalis Biodiversity Center, Leiden, Netherlands
- Faculty of Science, Leiden University, Leiden, Netherlands
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Ren Z, Gao H. Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia. PeerJ 2019; 7:e7715. [PMID: 31576247 PMCID: PMC6753927 DOI: 10.7717/peerj.7715] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/21/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.
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Affiliation(s)
- Ze Ren
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Hongkai Gao
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, China.,School of Geographic Sciences, East China Normal University, Shanghai, China
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35
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Wadham JL, Hawkings JR, Tarasov L, Gregoire LJ, Spencer RGM, Gutjahr M, Ridgwell A, Kohfeld KE. Ice sheets matter for the global carbon cycle. Nat Commun 2019; 10:3567. [PMID: 31417076 PMCID: PMC6695407 DOI: 10.1038/s41467-019-11394-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 07/09/2019] [Indexed: 11/09/2022] Open
Abstract
The cycling of carbon on Earth exerts a fundamental influence upon the greenhouse gas content of the atmosphere, and hence global climate over millennia. Until recently, ice sheets were viewed as inert components of this cycle and largely disregarded in global models. Research in the past decade has transformed this view, demonstrating the existence of uniquely adapted microbial communities, high rates of biogeochemical/physical weathering in ice sheets and storage and cycling of organic carbon (>104 Pg C) and nutrients. Here we assess the active role of ice sheets in the global carbon cycle and potential ramifications of enhanced melt and ice discharge in a warming world.
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Affiliation(s)
- J L Wadham
- University of Bristol, Bristol, BS8 1TH, UK.
| | - J R Hawkings
- National High Magnetic Field Lab and Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, 32306, USA
- German Research Centre for Geosciences GFZ, 14473, Potsdam, Germany
| | - L Tarasov
- Memorial University, St. John's, NF, A1B 3X9, Canada
| | | | - R G M Spencer
- National High Magnetic Field Lab and Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | | | - A Ridgwell
- University of California, Riverside, CA, 94720, USA
| | - K E Kohfeld
- Simon Fraser University, Burnaby, BC, 8888, Canada
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36
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Shen JP, Li ZM, Hu HW, Zeng J, Zhang LM, Du S, He JZ. Distribution and Succession Feature of Antibiotic Resistance Genes Along a Soil Development Chronosequence in Urumqi No.1 Glacier of China. Front Microbiol 2019; 10:1569. [PMID: 31354668 PMCID: PMC6629927 DOI: 10.3389/fmicb.2019.01569] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 06/24/2019] [Indexed: 01/03/2023] Open
Abstract
Primary succession of plant and microbial communities in the glacier retreating foreland has been extensively studied, but shifts of antibiotic resistance genes (ARGs) with the glacier retreating due to global warming remain elusive. Unraveling the diversity and succession features of ARGs in pristine soil during glacier retreating could contribute to a mechanistic understanding of the evolution and development of soil resistome. In this study, we quantified the abundance and diversity of ARGs along a 50-year soil development chronosequence by using a high-throughput quantitative PCR (HT-qPCR) technique. A total of 24 ARGs and two mobile genetic elements (MGEs) were detected from all the glacier samples, and the numbers of detected ARGs showed a unimodal pattern with an increasing trend at the early stage (0∼8 years) but no significant change at later stages (17∼50 years). The oprJ and mexF genes encoding multidrug resistance were the only two ARGs that were detected across all the succession ages, and the mexF gene showed an increasing trend along the succession time. Structural equation models indicated the predominant role of the intI1 gene encoding the Class 1 integron-integrase in shaping the variation of ARG profiles. These findings suggested the presence of ARGs in pristine soils devoid of anthropogenic impacts, and horizontal gene transfer mediated by MGEs may contribute to the succession patterns of ARGs during the initial soil formation stage along the chronosequence.
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Affiliation(s)
- Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zong-Ming Li
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Jun Zeng
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
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37
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Buongiorno J, Herbert LC, Wehrmann LM, Michaud AB, Laufer K, Røy H, Jørgensen BB, Szynkiewicz A, Faiia A, Yeager KM, Schindler K, Lloyd KG. Complex Microbial Communities Drive Iron and Sulfur Cycling in Arctic Fjord Sediments. Appl Environ Microbiol 2019; 85:e00949-19. [PMID: 31076435 DOI: 10.1128/AEM.00949-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 11/20/2022] Open
Abstract
Glacial retreat is changing biogeochemical cycling in the Arctic, where glacial runoff contributes iron for oceanic shelf primary production. We hypothesize that in Svalbard fjords, microbes catalyze intense iron and sulfur cycling in low-organic-matter sediments. This is because low organic matter limits sulfide generation, allowing iron mobility to the water column instead of precipitation as iron monosulfides. In this study, we tested this with high-depth-resolution 16S rRNA gene libraries in the upper 20 cm at two sites in Van Keulenfjorden, Svalbard. At the site closer to the glaciers, iron-reducing Desulfuromonadales, iron-oxidizing Gallionella and Mariprofundus, and sulfur-oxidizing Thiotrichales and Epsilonproteobacteria were abundant above a 12-cm depth. Below this depth, the relative abundances of sequences for sulfate-reducing Desulfobacteraceae and Desulfobulbaceae increased. At the outer station, the switch from iron-cycling clades to sulfate reducers occurred at shallower depths (∼5 cm), corresponding to higher sulfate reduction rates. Relatively labile organic matter (shown by δ13C and C/N ratios) was more abundant at this outer site, and ordination analysis suggested that this affected microbial community structure in surface sediments. Network analysis revealed more correlations between predicted iron- and sulfur-cycling taxa and with uncultured clades proximal to the glacier. Together, these results suggest that complex microbial communities catalyze redox cycling of iron and sulfur, especially closer to the glacier, where sulfate reduction is limited due to low availability of organic matter. Diminished sulfate reduction in upper sediments enables iron to flux into the overlying water, where it may be transported to the shelf.IMPORTANCE Glacial runoff is a key source of iron for primary production in the Arctic. In the fjords of the Svalbard archipelago, glacial retreat is predicted to stimulate phytoplankton blooms that were previously restricted to outer margins. Decreased sediment delivery and enhanced primary production have been hypothesized to alter sediment biogeochemistry, wherein any free reduced iron that could potentially be delivered to the shelf will instead become buried with sulfide generated through microbial sulfate reduction. We support this hypothesis with sequencing data that showed increases in the relative abundance of sulfate reducing taxa and sulfate reduction rates with increasing distance from the glaciers in Van Keulenfjorden, Svalbard. Community structure was driven by organic geochemistry, suggesting that enhanced input of organic material will stimulate sulfate reduction in interior fjord sediments as glaciers continue to recede.
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38
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Mania I, Gorra R, Colombo N, Freppaz M, Martin M, Anesio AM. Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System. Microb Ecol 2019; 78:70-84. [PMID: 30317429 DOI: 10.1007/s00248-018-1272-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow. RG surface material and neighbouring soil have been included in the analysis to better elucidate relationships among different habitats.Our results showed that different habitats harboured different, well-separated microbial assemblages. Across the pond, the main variations in community composition (e.g. Thaumarchaeota and Cyanobacteria relative abundance) and porewater geochemistry (pH, DOC, TDN and NH4+) were not directly linked to RG proximity, but to differences in water depth. Some microbial markers potentially linked to the presence of meltwater inputs from the RG have been recognised, although the RG seems to have a greater influence on the pond microbial communities due to its contribution in terms of sedimentary material.
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Affiliation(s)
- I Mania
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy.
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK.
| | - R Gorra
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - N Colombo
- Department of Earth Sciences, University of Turin, Via Valperga Caluso 35, 10125, Torino, Italy
- Department of Geography and Environmental Studies, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - M Freppaz
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - M Martin
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - A M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Department of Environmental Sciences, Aarhus University, 4000, Roskilde, Denmark
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39
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Nash MV, Anesio AM, Barker G, Tranter M, Varliero G, Eloe-Fadrosh EA, Nielsen T, Turpin-Jelfs T, Benning LG, Sánchez-Baracaldo P. Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol 2019; 94:5036517. [PMID: 29901729 PMCID: PMC6054269 DOI: 10.1093/femsec/fiy114] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/11/2018] [Indexed: 11/30/2022] Open
Abstract
Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonisation in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled contigs. The low number of recovered genes highlights the need for deeper sequencing in some diverse samples, to uncover the complete microbial populations. A key group of forefield diazotrophs, found throughout the forefields, was identified using a nifH phylogeny, associated with nifH Cluster I and III. Sequences related most closely to groups including Alphaproteobacteria, Betaproteobacteria, Cyanobacteria and Firmicutes. Using multiple nif genes in a Last Common Ancestor analysis revealed a diverse range of diazotrophs across the forefields. Key organisms identified across the forefields included Nostoc, Geobacter, Polaromonas and Frankia. Nitrogen fixers that are symbiotic with plants were also identified, through the presence of root associated diazotrophs, which fix nitrogen in return for reduced carbon. Additional nitrogen fixers identified in forefield soils were metabolically diverse, including fermentative and sulphur cycling bacteria, halophiles and anaerobes.
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Affiliation(s)
- Maisie V Nash
- School of Geographical Sciences, University of Bristol, UK
| | | | - Gary Barker
- School of Life Sciences, University of Bristol, UK
| | - Martyn Tranter
- School of Geographical Sciences, University of Bristol, UK
| | | | | | - Torben Nielsen
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, US
| | | | - Liane G Benning
- GFZ German Research Centre for Geosciences, Telegrafenenberg, 14473 Potsdam, Germany.,School of Earth and Environment, University of Leeds, LS2 9JT, Leeds, UK.,Department of Earth Sciences, Free University of Berlin, Malteserstr, 74-100, Building A, 12249, Berlin, Germany
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40
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Šantl-Temkiv T, Gosewinkel U, Starnawski P, Lever M, Finster K. Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states. FEMS Microbiol Ecol 2019; 94:4898009. [PMID: 29481623 DOI: 10.1093/femsec/fiy031] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/21/2018] [Indexed: 01/18/2023] Open
Abstract
The Arctic is undergoing dramatic climatic changes that cause profound transformations in its terrestrial ecosystems and consequently in the microbial communities that inhabit them. The assembly of these communities is affected by aeolian deposition. However, the abundance, diversity, sources and activity of airborne microorganisms in the Arctic are poorly understood. We studied bacteria in the atmosphere over southwest Greenland and found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity. The communities consisted of 1.3×103 ± 1.0×103 cells m-3, which were aerosolized from local terrestrial environments or transported from marine, glaciated and terrestrial surfaces over long distances. On average, airborne bacterial cells displayed a high activity potential, reflected in the high 16S rRNA copy number (590 ± 300 rRNA cell-1), that correlated positively with water vapor pressure. We observed that bacterial clades differed in their activity potential. For instance, a high activity potential was seen for Rubrobacteridae and Clostridiales, while a low activity potential was observed for Proteobacteria. Of those bacterial families that harbor ice-nucleation active species, which are known to facilitate freezing and may thus be involved in cloud and rain formation, cells with a high activity potential were rare in air, but were enriched in rain.
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Affiliation(s)
- Tina Šantl-Temkiv
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark.,Department of Bioscience, Microbiology Section, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Piotr Starnawski
- Centre for Geomicrobiology, Aarhus University, 116 Ny Munkegade, 8000 Aarhus, Denmark
| | - Mark Lever
- Centre for Geomicrobiology, Aarhus University, 116 Ny Munkegade, 8000 Aarhus, Denmark.,ETH Zürich, Department of Environmental Systems Science, Universitätsstrasse 16, 8092 Zurich, Switzerland
| | - Kai Finster
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark.,Department of Bioscience, Microbiology Section, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
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41
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Pessi IS, Pushkareva E, Lara Y, Borderie F, Wilmotte A, Elster J. Marked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic. Microb Ecol 2019; 77:136-147. [PMID: 29796758 DOI: 10.1007/s00248-018-1203-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10-20 years since deglaciation), mid (30-50 years), and late (80-100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa.
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Affiliation(s)
- Igor S Pessi
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium.
- Department of Microbiology, University of Helsinki, P.O. Box 56 (Viikinkaari 9), 00014, Helsinki, Finland.
| | - Ekaterina Pushkareva
- Centre for Polar Ecology, University of South Bohemia, Na Zlaté Stoce 3, 37005, České Budějovice, Czech Republic
| | - Yannick Lara
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
- UR Geology - Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Allée du Six Août14, B18, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Fabien Borderie
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
- Laboratoire Chrono-environnement, UMR 6249 CNRS Université Bourgogne Franche-Comté UsC INRA, Campus La Bouloie, Route de Gray 16, 25030, Besançon, France
| | - Annick Wilmotte
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Josef Elster
- Centre for Polar Ecology, University of South Bohemia, Na Zlaté Stoce 3, 37005, České Budějovice, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, 37982, Třeboň, Czech Republic
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Pandey A, Yarzábal LA. Bioprospecting cold-adapted plant growth promoting microorganisms from mountain environments. Appl Microbiol Biotechnol 2018; 103:643-657. [PMID: 30465306 DOI: 10.1007/s00253-018-9515-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
Mountain soils are challenging environments for all kinds of living things, including plants and microorganisms. Many cold-adapted microorganisms colonizing these extreme soils play important roles as promoters of plant growth and development; for that reason, they are called collectively plant growth-promoting microorganisms (PGPM). Even though there is seldom doubt concerning the usefulness of PGPM to develop eco-friendly bioinoculants, including biofertilizers and biocontrollers, a series of aspects need to be addressed in order to make this technology field-applicable. Among these aspects, the ecological and rhizosphere competences of PGPM are of paramount importance, particularly when considering the development of bioinoculants, well suited for the intensification of mountainous agricultural production. Studies on native, cold-adapted PGPM conducted in the Indian Himalayan region (IHR) and the Tropical Andes (TA) lead nowadays the research in this field. Noticeably, some common themes are emerging. For instance, soils in these mountain environments are colonized by many cold-adapted PGPM able to mobilize soil nutrients and to inhibit growth of plant pathogens. Studies aimed at deeply characterizing the abilities of such PGPM is likely to substantially contribute towards a better crop productivity in mountainous environments. The present review focuses on the importance of this microbial resource to improve crop productivity in IHR and TA. We also present a number of successful examples, which emphasize the effectiveness of some bioinoculants-developed from naturally occurring PGPM-when applied in the field.
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Affiliation(s)
- Anita Pandey
- Centre for Environmental Assessment and Climate Change, G.B. Pant National Institute of Himalayan Environment and Sustainable Development, Kosi-Katarmal, Almora, Uttarakhand, 263643, India.
| | - Luis Andrés Yarzábal
- Unidad de Salud y Bienestar, Universidad Católica de Cuenca, Av. Las Américas y Humboldt, Cuenca, Ecuador.,Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Av. Alberto Carnevalli, Mérida, Venezuela
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43
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Schweizer SA, Hoeschen C, Schlüter S, Kögel-Knabner I, Mueller CW. Rapid soil formation after glacial retreat shaped by spatial patterns of organic matter accrual in microaggregates. Glob Chang Biol 2018; 24:1637-1650. [PMID: 29223134 DOI: 10.1111/gcb.14014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
Global change contributes to the retreat of glaciers at unprecedented rates. The deglaciation facilitates biogeochemical processes on glacial deposits with initiating soil formation as an important driver of evolving ecosystems. The underlying mechanisms of soil formation and the association of soil organic matter (SOM) with mineral particles remain unclear, although further insights are critical to understand carbon sequestration in soils. We investigated the microspatial arrangement of SOM coatings at intact soil microaggregate structures during various stages of ecosystem development from 15 to >700 years after deglaciation in the proglacial environment of the Damma glacier (Switzerland). The functionally important clay-sized fraction (<2 μm) was separated into two density fractions with different amounts of organo-mineral associations: light (1.6-2.2 g/cm3 ) and heavy (>2.2 g/cm3 ). To quantify how SOM extends across the surface of mineral particles (coverage) and whether SOM coatings are distributed in fragmented or connected patterns (connectivity), we developed an image analysis protocol based on nanoscale secondary ion mass spectrometry (NanoSIMS). We classified SOM and mineral areas depending on the 16 O- , 12 C- , and 12 C14 N- distributions. With increasing time after glacial retreat, the microspatial coverage and connectivity of SOM increased rapidly. The rapid soil formation led to a succession of patchy distributed to more connected SOM coatings on soil microaggregates. The maximum coverage of 55% at >700 years suggests direct evidence for SOM sequestration being decoupled from the mineral surface, as it was not completely masked by SOM and retained its functionality as an ion exchange site. The chemical composition of SOM coatings showed a rapid change toward a higher CN:C ratio already at 75 years after glacial retreat, which was associated with microbial succession patterns reflecting high N assimilation. Our results demonstrate that rapid SOM sequestration drives the microspatial succession of SOM coatings in soils, a process that can stabilize SOM for the long term.
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Affiliation(s)
- Steffen A Schweizer
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Carmen Hoeschen
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Steffen Schlüter
- Department of Soil System Sciences, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Ingrid Kögel-Knabner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Carsten W Mueller
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Germany
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44
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Barcytė D, Hodač L, Nedbalová L, Elster J. Chloromonas arctica sp. nov., a psychrotolerant alga from snow in the High Arctic (Chlamydomonadales, Chlorophyta). Int J Syst Evol Microbiol 2018; 68:851-859. [PMID: 29458669 DOI: 10.1099/ijsem.0.002595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
With the advent of molecular phylogenetic methods, it has become possible to assess the bioversity of snow algae more accurately. In this study, we focused on a morphological, ultrastructural and taxonomic description of a new Chloromonas-like alga isolated from snow in the High Arctic (Svalbard). Light and transmission electron microscopy revealed broad ellipsoidal or ellipsoidal-cylindrical, occasionally spherical cells with a chloroplast without a pyrenoid, an inconspicuous eyespot and a papilla. The size difference and the aforementioned morphological traits clearly distinguished the alga from its closest counterparts within the genus Chloromonas. Moreover, we were able to cultivate the alga at both 5 and 20 °C, revealing the psychrotolerant nature of the strain. Phylogenetic analyses of the plastid rbcL and nuclear 18S rRNA gene showed that the alga is nested within a clade containing a number of psychrotolerant strains within the Chloromonadinia phylogroup (Chlorophyceae). In the rbcL phylogeny, the alga formed an independent lineage, sister to the freshwater species Chloromonas paraserbinowii. Comparisons of secondary structure models of a highly variable ITS2 rDNA marker showed support for a distinct species identity for the new strain. The ITS2 secondary structure of the new isolate differed from the closest matches 'Chlamydomonas' gerloffii and Choloromonas reticulata by three and five compensatory base changes, respectively. Considering the morphological and molecular differences from its closest relatives, a new psychrotolerant species from the Arctic, Choromonas arctica sp. nov., is proposed.
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Affiliation(s)
- Dovilė Barcytė
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 44, Czech Republic
| | - Ladislav Hodač
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-University of Göttingen, Untere Karspüle 2, Göttingen, 37073, Germany
| | - Linda Nedbalová
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 44, Czech Republic.,The Czech Academy of Sciences, Institute of Botany, Dukelská 135, Třeboň, 379 82, Czech Republic
| | - Josef Elster
- The Czech Academy of Sciences, Institute of Botany, Dukelská 135, Třeboň, 379 82, Czech Republic.,Centre for Polar Ecology, University of South Bohemia, Na Zlaté stoce 3, České Budějovice, 370 05, Czech Republic
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45
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Darcy JL, King AJ, Gendron EMS, Schmidt SK. Spatial autocorrelation of microbial communities atop a debris-covered glacier is evidence of a supraglacial chronosequence. FEMS Microbiol Ecol 2017; 93:4002671. [PMID: 28830070 DOI: 10.1093/femsec/fix095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/14/2017] [Indexed: 12/17/2022] Open
Abstract
Although microbial communities from many glacial environments have been analyzed, microbes living in the debris atop debris-covered glaciers represent an understudied frontier in the cryosphere. The few previous molecular studies of microbes in supraglacial debris have either had limited phylogenetic resolution, limited spatial resolution (e.g. only one sample site on the glacier) or both. Here, we present the microbiome of a debris-covered glacier across all three domains of life, using a spatially-explicit sampling scheme to characterize the Middle Fork Toklat Glacier's microbiome from its terminus to sites high on the glacier. Our results show that microbial communities differ across the supraglacial transect, but surprisingly these communities are strongly spatially autocorrelated, suggesting the presence of a supraglacial chronosequence. This pattern is dominated by phototrophic microbes (both bacteria and eukaryotes) which are less abundant near the terminus and more abundant higher on the glacier. We use these data to refute the hypothesis that the inhabitants of the glacier are randomly deposited atmospheric microbes, and to provide evidence that succession from a predominantly photosynthetic to a more heterotrophic community is occurring on the glacier.
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Affiliation(s)
- John L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Andrew J King
- King Ecological Consulting, 2504 Scarlett Oak Ct, Knoxville, TN 37909, USA
| | - Eli M S Gendron
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.,Molecular, Cellular, and Developmental Biology Department, University of Colorado, Boulder, CO 80309, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
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46
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Yan W, Ma H, Shi G, Li Y, Sun B, Xiao X, Zhang Y. Independent Shifts of Abundant and Rare Bacterial Populations across East Antarctica Glacial Foreland. Front Microbiol 2017; 8:1534. [PMID: 28848537 PMCID: PMC5554324 DOI: 10.3389/fmicb.2017.01534] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 07/28/2017] [Indexed: 11/13/2022] Open
Abstract
Glacial forelands are extremely sensitive to temperature changes and are therefore appropriate places to explore the development of microbial communities in response to climate-driven deglaciation. In this study, we investigated the bacterial communities that developed at the initial stage of deglaciation using space-for-time substitution in the foreland of an ice sheet in Larsemann Hills. A series of soil samples across the glacial foreland were deeply sequenced with 16S rRNA gene amplicon sequencing to determine the bacterial community, including both abundant bacteria, which contribute more to geobiochemistry, and rare bacteria, which serve as a seed bank for diversity. Our results show that abundant bacterial communities were more sensitive to changing conditions in the early stages of deglaciation than rare community members. Moreover, among the environmental parameters tested, which included total organic carbon, pH, and moisture of the soils, ice thickness was the most influential factor affecting the community structure of abundant bacteria. These results show the different effects of abundant and rare bacteria on community shifts and highlight ice thickness as the primary factor affecting the bacterial community in the early stages of deglaciation. The response of microbial community to climate change can be predicted with more certainty in this polar region.
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Affiliation(s)
- Wenkai Yan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Hongmei Ma
- SOA Key Laboratory for Polar Science, Polar Research Institute of ChinaShanghai, China
| | - Guitao Shi
- SOA Key Laboratory for Polar Science, Polar Research Institute of ChinaShanghai, China
| | - Yuansheng Li
- SOA Key Laboratory for Polar Science, Polar Research Institute of ChinaShanghai, China
| | - Bo Sun
- SOA Key Laboratory for Polar Science, Polar Research Institute of ChinaShanghai, China
| | - Xiang Xiao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Yu Zhang
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China.,Institute of Oceanography, Shanghai Jiao Tong UniversityShanghai, China
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47
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Sun S, Li S, Avera BN, Strahm BD, Badgley BD. Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration. Appl Environ Microbiol 2017; 83:e00966-17. [PMID: 28476769 DOI: 10.1128/AEM.00966-17] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 01/06/2023] Open
Abstract
Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities.IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages.
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48
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Weiland-Bräuer N, Fischer MA, Schramm KW, Schmitz RA. Polychlorinated Biphenyl (PCB)-Degrading Potential of Microbes Present in a Cryoconite of Jamtalferner Glacier. Front Microbiol 2017; 8:1105. [PMID: 28663747 PMCID: PMC5471330 DOI: 10.3389/fmicb.2017.01105] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022] Open
Abstract
Aiming to comprehensively survey the potential pollution of an alpine cryoconite (Jamtalferner glacier, Austria), and its bacterial community structure along with its biodegrading potential, first chemical analyses of persistent organic pollutants, explicitly polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) as well as polycyclic aromatic hydrocarbons (PAHs), revealed a significant contamination. In total, 18 PCB congeners were detected by high resolution gas chromatography/mass spectrometry with a mean concentration of 0.8 ng/g dry weight; 16 PAHs with an average concentration of 1,400 ng/g; and 26 out of 29 OCPs with a mean concentration of 2.4 ng/g. Second, the microbial composition was studied using 16S amplicon sequencing. The analysis revealed high abundances of Proteobacteria (66%), the majority representing α-Proteobacteria (87%); as well as Cyanobacteria (32%), however high diversity was due to 11 low abundant phyla comprising 75 genera. Biodegrading potential of cryoconite bacteria was further analyzed using enrichment cultures (microcosms) with PCB mixture Aroclor 1242. 16S rDNA analysis taxonomically classified 37 different biofilm-forming and PCB-degrading bacteria, represented by Pseudomonas, Shigella, Subtercola, Chitinophaga, and Janthinobacterium species. Overall, the combination of culture-dependent and culture-independent methods identified degrading bacteria that can be potential candidates to develop novel bioremediation strategies.
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Affiliation(s)
- Nancy Weiland-Bräuer
- Institute for General Microbiology, Christian-Albrechts-Universität zu KielKiel, Germany
| | - Martin A. Fischer
- Institute for General Microbiology, Christian-Albrechts-Universität zu KielKiel, Germany
| | - Karl-Werner Schramm
- Molecular EXposomics, German Research Center for Environmental Health, Helmholtz Zentrum München GmbHNeuherberg, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität zu KielKiel, Germany
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49
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Tian J, Qiao Y, Wu B, Chen H, Li W, Jiang N, Zhang X, Liu X. Ecological Succession Pattern of Fungal Community in Soil along a Retreating Glacier. Front Microbiol 2017; 8:1028. [PMID: 28649234 PMCID: PMC5465267 DOI: 10.3389/fmicb.2017.01028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 01/12/2023] Open
Abstract
Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2-188 years of deglaciation. Shannon diversity and evenness peaked at a distance of 370 m and declined afterwards. The response of fungal diversity to distance varied in different phyla. Basidiomycota Shannon diversity significantly decreased with distance, while the pattern of Rozellomycota Shannon diversity was unimodal. Abundance of most frequencies OTU2 (Cryptococcus terricola) increased with successional distance, whereas that of OTU65 (Tolypocladium tundrense) decreased. Based on null deviation analyses, composition of the fungal community was initially governed by deterministic processes strongly but later less deterministic processes. Our results revealed that distance, altitude, soil microbial biomass carbon, soil microbial biomass nitrogen and [Formula: see text]-N significantly correlated with fungal community composition along the chronosequence. These results suggest that the drivers of fungal community are dynamics in a glacier chronosequence, that may relate to fungal ecophysiological traits and adaptation in an evolving ecosystem. The information will provide understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession under different scales and scenario.
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Affiliation(s)
- Jianqing Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Yuchen Qiao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
- Beijing Radiation Centre, Beijing Academy of Science and TechnologyBeijing, China
| | - Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of SciencesChengdu, China
- Zoige Peatland and Global Change Research Station, Chengdu Institute of Biology, Chinese Academy of SciencesHongyuan, China
| | - Wei Li
- School of Ecology and Environmental Science, Yunnan UniversityKunming, China
| | - Na Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
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50
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Nascimbene J, Mayrhofer H, Dainese M, Bilovitz PO. Assembly patterns of soil-dwelling lichens after glacier retreat in the European Alps. J Biogeogr 2017; 44:1393-1404. [PMID: 28701808 PMCID: PMC5484317 DOI: 10.1111/jbi.12970] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
AIM To assess the spatial-temporal dynamics of primary succession following deglaciation in soil-dwelling lichen communities. LOCATION European Alps (Austria, Switzerland and Italy). METHODS Five glacier forelands subjected to relevant glacier retreat during the last century were investigated. In each glacier foreland, three successional stages were selected at increasing distance from the glacier, corresponding to a gradient of time since deglaciation between 25 and 160 years. In each successional stage, soil-dwelling lichens were surveyed within five 1 × 1 m plots. In addition to a classical ecological framework, based on species richness and composition, we applied a functional approach to better elucidate community assembly mechanisms. RESULTS A positive relationship was found between species richness and time since deglaciation indicating that richer lichen communities can be found at increasing terrain ageing. This pattern was associated with compositional shifts, suggesting that different community assemblages can be found along the successional stages. The analysis of β-diversity revealed a significant nested pattern of species assemblages along the gradient (i.e. earlier successional stages hosted a subset of the species already established in older successional stages), while the turnover component was less relevant. Considering functional groups, we found contrasting patterns in relation to time since deglaciation: the incidence of species with a cyanobacterial photobiont and those reproducing by spores decreased, while that of species reproducing by vegetative propagules increased. MAIN CONCLUSIONS This study reveals that community assembly patterns of soil-dwelling lichens in alpine glacier forelands are ruled by mechanisms of directional species accumulation and trait selection that involve a trade-off between different functional strategies. Functional traits that reflect the dispersal and adaptation capability of the species underpin the colonization success of soil-dwelling lichens in glacier forelands.
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Affiliation(s)
- Juri Nascimbene
- Department of BiologicalGeological and Environmental SciencesUniversity of BolognaI‐40126BolognaItaly
| | - Helmut Mayrhofer
- Institute of Plant SciencesNAWI GrazUniversity of Graz8010GrazAustria
| | - Matteo Dainese
- Department of Animal Ecology and Tropical Biology, BiocenterUniversity of Würzburg97074WürzburgGermany
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