Dataset Information

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.

ABSTRACT:

Background

In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N₂O). However, the microorganisms involved in the cycling of N₂O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N₂O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra.

Results

We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N₂O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N₂O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N₂O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23.

Conclusions

By coupling an in-depth characterization of microbial communities with in situ measurements of N₂O fluxes, our results suggest that the observed spatial patterns of N₂O fluxes in the tundra are related to differences in the composition of denitrifier communities.

SUBMITTER: Pessi IS

PROVIDER: S-EPMC9188126 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Publications

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.

Pessi Igor S IS Viitamäki Sirja S Virkkala Anna-Maria AM Eronen-Rasimus Eeva E Delmont Tom O TO Marushchak Maija E ME Luoto Miska M Hultman Jenni J

Environmental microbiome 20220611 1

<h4>Background</h4>In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N<sub>2</sub>O). However, the microorganisms involved in the cycling of N<sub>2</sub>O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N<sub>2</sub>O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra.<h4>Results</h4> ...[more]

PMID: 35690846

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Project description:In maritime Antarctica, sea animals, such as penguins or seals, provide a large amount of external nitrogen input into tundra soils, which greatly impact nitrogen cycle in tundra ecosystems. Denitrification, which is closely related with the denitrifiers, is a key step in nitrogen cycle. However, effects of sea animal activities on tundra soil denitrification and denitrifier community structures still have received little attention. Here, the abundance, activity, and diversity of nirS- and nirK-encoding denitrifiers were investigated in penguin and seal colonies, and animal-lacking tundra in maritime Antarctica. Sea animal activities increased the abundances of nirS and nirK genes, and the abundances of nirS genes were significantly higher than those of nirK genes (p < 0.05) in all tundra soils. Soil denitrification rates were significantly higher (p < 0.05) in animal colonies than in animal-lacking tundra, and they were significantly positively correlated (p < 0.05) with nirS gene abundances instead of nirK gene abundances, indicating that nirS-encoding denitrifiers dominated the denitrification in tundra soils. The diversity of nirS-encoding denitrifiers was higher in animal colonies than in animal-lacking tundra, but the diversity of nirK-encoding denitrifiers was lower. Both the compositions of nirS- and nirK-encoding denitrifiers were similar in penguin or seal colony soils. Canonical correspondence analysis indicated that the community structures of nirS- and nirK-encoding denitrifiers were closely related to tundra soil biogeochemical processes associated with penguin or seal activities: the supply of nitrate and ammonium from penguin guano or seal excreta, and low C:N ratios. In addition, the animal activity-induced vegetation presence or absence had an important effect on tundra soil denitrifier activities and nirK-encoding denitrifier diversities. This study significantly enhanced our understanding of the compositions and dynamics of denitrifier community in tundra ecosystems of maritime Antarctica.

Project description:The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.

Dataset Information

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.

Background

Results

Conclusions

Publications

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.

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