Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska

Abstract

Permafrost-underlain tundra soils in Northern Hemisphere are one of the largest reservoirs of terrestrial carbon, which are highly sensitive to microbial decomposition due to climate warming. However, knowledge about the taxonomy and functions of microbiome residing in different horizons of permafrost-underlain tundra soils is still limited. Here we compared the taxonomic and functional composition of microbiome between different horizons of soil cores from a moist tussock tundra ecosystem in Council, Alaska, using 16S rRNA gene and shotgun metagenomic sequencing. The composition, diversity, and functions of microbiome varied significantly between soil horizons, with top soil horizon harboring more diverse communities than sub-soil horizons. The vertical gradient in soil physico-chemical parameters were strongly associated with composition of microbial communities across permafrost soil horizons; however, a large fraction of the variation in microbial communities remained unexplained. The genes associated with carbon mineralization were more abundant in top soil horizon, while genes involved in acetogenesis, fermentation, methane metabolism (methanogenesis and methanotrophy), and N cycling were dominant in sub-soil horizons. The results of phylogenetic null modeling analysis showed that stochastic processes strongly influenced the composition of the microbiome in different soil horizons, except the bacterial community composition in top soil horizon, which was largely governed by homogeneous selection. Our study expands the knowledge on the structure and functional potential of microbiome associated with different horizons of permafrost soil, which could be useful in understanding the effects of environmental change on microbial responses in tundra ecosystems.

The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession

“…These results are consistent with findings from Monteux et al (2018) where the authors also observed more variation in community composition of the deeper soils at the same field site. Increases in stochastic assembly have been observed with increased depth in permafrost systems, particularly the influence of drift (Tripathi et al, 2018(Tripathi et al, , 2019. Tripathi et al (2019) also found dispersal limitation was highest in the deepest soil horizon in their study.…”

“…Increases in stochastic assembly have been observed with increased depth in permafrost systems, particularly the influence of drift (Tripathi et al, 2018(Tripathi et al, , 2019. Tripathi et al (2019) also found dispersal limitation was highest in the deepest soil horizon in their study.…”

“…Upper active layer bacterial communities were completely dominated by homogenous selection indicating that there was less turnover between active layer communities than expected by chance. Tripathi et al (2019) also found homogeneous selection was the dominant process structuring upper active layer bacterial communities which they attributed to minimal variation in physiochemical properties within this layer. We also observed little variation in pH and % carbon.…”

“…Bottos et al (2018) also found dispersal limitation as the dominant process structuring permafrost bacterial communities across a permafrost transect in Central Alaska and found contributions of homogenizing dispersal and homogenous selection. Homogenizing dispersal describes high dispersal rates that outweigh selection pressures and is often seen in combination with dispersal limitation, but generally one is much more dominant than the other (Bottos et al, 2018;Tripathi et al, 2019). Homogenous selection occurs when a homogenous environment selects for ecologically similar taxa, which demonstrates that the permafrost environment is spatially homogenous and imposes limitations on the phylogenetic and functional diversity of the system.…”

“…Increases in soil temperature due to either experimental warming or long-term permafrost thaw have resulted in an increase of deterministic processes structuring active layer microbial communities (Mondav et al, 2017;Feng et al, 2020). Furthermore, Tripathi et al (2018Tripathi et al ( , 2019 found stochastic processes dominate community assembly in deeper soils compared to surface soils in permafrost systems. However, these studies lack a direct comparison of assembly processes in permafrost soils pre-and post-thaw.…”