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

Abstract

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 these soils remain largely uncharacterized. In this study, we manually binned and curated 541 metagenome-assembled genomes (MAGs) from tundra soils in northern Finland. We then searched for MAGs encoding enzymes involved in denitrification, the main biotic process driving N2O emissions. Denitrifying communities were dominated by poorly characterized taxa with truncated denitrification pathways, i.e. lacking one or more denitrification genes. Among these, MAGs with the metabolic potential to produce N2O comprised the most diverse functional group. Re-analysis of a previously published metagenomic dataset from soils in northern Sweden supported these results, suggesting that truncated denitrifiers are dominant throughout the tundra biome.

Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

“…Overall, 4.8% of reads could be mapped to the MAGs. This level is similar to what has been reported recently in genome-resolved metagenomic studies of other soil communities, 2.7−22.4% of the reads from each sample were recruited by the MAGs 27 . As was observed for the total coassembled contigs derived from shotgun data (Fig.…”

The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types

“…The most active microbial phyla were Actinobacteria, Acidobacteria, Alphaproteobacteria, and Planctomycetes, consistent with previous studies from Arctic regions (Hultman et al, 2015;Tas et al, 2018;Tripathi et al, 2019). These phyla, excluding Planctomycetes, were also among the most abundant in the metagenomics dataset from these samples (Pessi et al, 2020). Although the microbial community composition was similar across vegetation types, there were significant differences at the genus level in the active microbes.…”

“…When comparing the 16S rRNA from metatranscriptomes (i.e., RNA; active microbes) to the 16S rRNA genes from metagenomes (i.e., DNA, Pessi et al ., 2020), the most abundant and active microbial groups were the same but notable differences appeared among the datasets (Figures 2 and 4a). Orders with greater relative abundance in metatranscriptomes included Gemmatales (Planctomycetes), Acidothermales (Actinobacteria), Solibacterales (Acidobacteria), and Myxococcales (Deltaproteobacteria), whereas Subgroup 2 (Acidobacteria), Rickettsiales (Alphaproteobacteria), Dormibacterota, Chitinophagales (Verrucomicrobia), and Gemmatimonadales (Gemmatimonadetes) showed higher relative abundance in metagenomes.…”

“…In general, these studies were performed with small sample sizes (Hultman et al, 2015;Schostag et al, 2015;Singleton et al, 2018;Woodcroft et al, 2018), limiting our understanding of the spatial variability in microbial communities. Further, several molecular methods have been used, including phospholipid fatty acid (PLFA), terminal restriction fragment analysis (T-RFLP) (Männistö et al, 2007) and metagenomics (Pessi et al 2020). In metatranscriptomics the target molecule is RNA, allowing analysis of both function and activity of organisms at the time of sampling.…”

Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution

“…Ammonia oxidation is an important process in polar soils despite commonly N limited and cold conditions (Alves et al, 2013;Siljanen et al, 2019;Hayashi et al, 2020). AOA generally outnumber AOB in oligotrophic polar soils and are often represented by a very limited number of species (Alves et al, 2013;Magalhães et al, 2014;Richter et al, 2014;Siljanen et al, 2019;Ortiz et al, 2020;Pessi et al, 2021). Due to their predominance, AOA are important contributors to the N cycle in polar soils and are thus key players in the cycling of the potent greenhouse gas nitrous oxide (N2O).…”