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Microorganisms
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Arctic Microbiome
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Arctic Microbiome

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 10248

Special Issue Editor

Dr. Jiří Bárta

E-Mail Website
Guest Editor
Department of Ecosystem Biology, University of South Bohemia, Budweis, Czech Republic
Interests: soil microbiology; Arctic; permafrost; sequencing; bioinformatics

Special Issue Information

Dear Colleagues,

Microorganisms play crucial roles in biogeochemical cycles in soils. Their activity and distinct metabolic capabilities influence the rates of soil organic transformations, the release of metabolites, and waste products such as CO2, CH4, and N2O. By the activity of microorganisms, the concentrations of these gases increase in the atmosphere and largely contribute to global climate change. One of the most vulnerable ecosystems on our planet is permafrost-affected soils, cryosols, in the Arctic. Cryosols store a tremendous amount of soil organic carbon (approximately half of the global soil carbon pool), which has recently become vulnerable to decomposition by the higher activity of complex soil microbial communities due to the higher soil temperatures. To predict the rates of soil organic matter transformations and the release of metabolites and gases, there is an urge for microbial studies, including bacteria, archaea, and fungi. Recent sequencing technologies allow us to study microbial communities in very high taxonomic resolution. Based on these datasets, we can predict functional potential and reconstruct important relationships among the microbial community by network construction. Understanding carbon and nitrogen cycles in cryosol and the role of specific microbial taxa, interactions between bacterial, archaeal, and fungal communities are crucial for predicting future climate changes in the Arctic.

This Special Issue wishes to encourage the submission of original research papers and review manuscripts dealing with the composition, activities, functioning of soil microbial communities in arctic cryosols.

I look forward to receiving your contributions.

Dr. Jiří Bárta
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cryosols
  • Arctic
  • bacteria
  • fungi
  • archaea
  • climate change
  • sequencing

Published Papers (5 papers)

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Research

14 pages, 1892 KiB  
Article
Biodiversity and Structure of Microbial Community in Glacial Melts and Soil in the High Arctic Ny-Ålesund, Svalbard
by Fang Zhang, Fenglin Lv and Mianrun Chen
Microorganisms 2022, 10(10), 1941; https://doi.org/10.3390/microorganisms10101941 - 29 Sep 2022
Cited by 1 | Viewed by 1385
Abstract
Ny-Ålesund in Svalbard is a complex area with both continental and tidal glaciers. There are a lot of studies on prokaryotic and eukaryotic communities in coastal water and soil, but without studies in glacial-related waters. We make a distinctive and consolidated study on [...] Read more.
Ny-Ålesund in Svalbard is a complex area with both continental and tidal glaciers. There are a lot of studies on prokaryotic and eukaryotic communities in coastal water and soil, but without studies in glacial-related waters. We make a distinctive and consolidated study on the structure of the prokaryotic and eukaryotic communities of pure glacial meltwater, glacial melting lake, glacial meltwater flowing via different types of soil at various elevations, estuarine glacial water and marine water. Moreover, we analyze the environmental–microbial relationships of the prokaryotic and eukaryotic communities via a canonical correspondence analysis and redundant analysis compared by a Pearson analysis. We found that there were distinct microbes in different environments. Altitude had significant correlations with prokaryotic and eukaryotic species in the 12 water samples (ppro = 0.001, npro = 1010, and peuk = 0.012, npro = 1651) (Pearson analysis). Altitude, temperature and salinity, respectively, accounted for 28.27%, 10.86% and 8.24% in the prokaryotic community structure and 25.77%, 17.72% and 3.46% in the eukaryotic, respectively, in water. Nitrogen, silicate and pH accounted for 38.15%, 6.15% and 2.48% in the prokaryotic community structure in soil and 26.65%, 12.78% and 8.66% in the eukaryotic. Eukaryotes were more stable than prokaryotes in changing environments. Cyanobacteria and dinoflagellates better adapt to a warming environment. Gammaproteobacteria and Chrysophysceae were most abundant in soil. Alphaproteobacteria, Bacteroidia, Mamiellophyceae and Prasinophytae were most abundant in water. Within these microbes, Bacilli and Chlorophyceae were only found in glaciers; Actinobacteria, KD94-96, Thermleophilia, Embryophyta, Trebouxiophyceae and Sordariomycetes were unique to soil. Full article
(This article belongs to the Special Issue Arctic Microbiome)
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12 pages, 2125 KiB  
Article
The Study of Soil Bacterial Diversity and the Influence of Soil Physicochemical Factors in Meltwater Region of Ny-Ålesund, Arctic
by Long Wang, Jie Liu, Jialin Yuan and Nengfei Wang
Microorganisms 2022, 10(10), 1913; https://doi.org/10.3390/microorganisms10101913 - 27 Sep 2022
Cited by 4 | Viewed by 1331
Abstract
Global climate change has caused the changes of the ecological environment in the Arctic region, including sea ice melting, runoff increase, glacial lake expansion, and a typical meltwater area has formed in the Arctic coastal area. In this study, the meltwater areas near [...] Read more.
Global climate change has caused the changes of the ecological environment in the Arctic region, including sea ice melting, runoff increase, glacial lake expansion, and a typical meltwater area has formed in the Arctic coastal area. In this study, the meltwater areas near six different characteristic areas of Ny-Ålesund in 2018 were taken as the research objects, and high-throughput sequencing of V3–V4 regions of all samples were performed using 16S rDNA. Among the soil samples of six glacial meltwater areas in Ny-Ålesund, Arctic, the meltwater area near the reservoir bay had the highest bacterial abundance, and the meltwater area near the sand had the lowest one. The dominant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria. The NH4+-N content in intertidal soil was higher than that in subtidal soil. Through WGCNA analysis and LEFSE analysis, it was found that the core bacteria significantly related to NH4+-N were basically distributed in the intertidal area. For example, Nitrosomonadaceae, Nitrospira and Sphingomonas were the core bacteria showed significant different abundance in the intertidal area, which have the ability to metabolize NH4+-N. Our findings suggest that NH4+-N plays an important role in soil bacterial community structure in the Arctic meltwater areas. Full article
(This article belongs to the Special Issue Arctic Microbiome)
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19 pages, 2270 KiB  
Article
A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice
by Stefan Thiele, Julia E. Storesund, Mar Fernández-Méndez, Philipp Assmy and Lise Øvreås
Microorganisms 2022, 10(8), 1618; https://doi.org/10.3390/microorganisms10081618 - 10 Aug 2022
Cited by 7 | Viewed by 1922
Abstract
The Arctic is warming 2–3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide [...] Read more.
The Arctic is warming 2–3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community. Full article
(This article belongs to the Special Issue Arctic Microbiome)
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16 pages, 22856 KiB  
Article
Qualitative and Quantitative Characteristics of Soil Microbiome of Barents Sea Coast, Kola Peninsula
by Maria Korneykova, Dmitry Nikitin and Vladimir Myazin
Microorganisms 2021, 9(10), 2126; https://doi.org/10.3390/microorganisms9102126 - 10 Oct 2021
Cited by 5 | Viewed by 1925
Abstract
The soil microbiome of the Barents Sea coast of the Kola Peninsula is here characterized for the first time. The content of copies of ribosomal genes of archaea, bacteria, and fungi was determined by real-time PCR. Reserves and structure of biomass of soil [...] Read more.
The soil microbiome of the Barents Sea coast of the Kola Peninsula is here characterized for the first time. The content of copies of ribosomal genes of archaea, bacteria, and fungi was determined by real-time PCR. Reserves and structure of biomass of soil microorganisms such as total biomass of fungi and prokaryotes, length and diameter of mycelium of fungi and actinomycetes, proportion of mycelium in biomass, number of spores and prokaryotic cells, proportion of small and large fungal propagules, and morphology of mycobiota spores were determined. The largest number of ribosomal gene copies was found for bacteria (from 6.47 × 109 to 3.02 × 1011 per g soil). The number of copies of ribosomal genes of fungi and archaea varied within 107–109 copies of genes/g soil. The biomass of microorganisms (prokaryotes and fungi in total) varied from 0.023 to 0.840 mg/g soil. The share of mycobiota in the microbial biomass ranged from 90% to 97%. The number of prokaryotes was not large and varied from 1.87 × 108 to 1.40 × 109 cells/g of soil, while the biomass of fungi was very significant and varied from 0.021 to 0.715 mg/g of soil. The length of actinomycete mycelium was small—from 0.77 to 88.18 m/g of soil, as was the length of fungal hyphae—an order of magnitude higher (up to 504.22 m/g of soil). The proportion of fungal mycelium, an active component of fungal biomass, varied from 25% to 89%. Most (from 65% to 100%) of mycobiota propagules were represented by specimens of small sizes, 2–3 microns. Thus, it is shown that, despite the extreme position on the mainland land of Fennoscandia, local soils had a significant number of microorganisms, on which the productivity of ecosystems largely depends. Full article
(This article belongs to the Special Issue Arctic Microbiome)
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23 pages, 4409 KiB  
Article
Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network
by Milan Varsadiya, Tim Urich, Gustaf Hugelius and Jiří Bárta
Microorganisms 2021, 9(9), 1943; https://doi.org/10.3390/microorganisms9091943 - 13 Sep 2021
Cited by 10 | Viewed by 2805
Abstract
Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in [...] Read more.
Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil. Full article
(This article belongs to the Special Issue Arctic Microbiome)
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