Abstract
How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1–2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100–530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that Alaska tundra microbial communities are less diverse and more homogenous across spatial scales than previously anticipated, and provided DNA sequences of abundant populations and genes that would be relevant for future studies of the effects of environmental change on tundra ecosystems.
Highlights
Terrestrial soil systems are residence to some of the most functionally and taxonomically diverse microbial communities known (Torsvik et al, 1990; Whitman et al, 1998; Curtis et al, 2002; Handelsman et al, 2007)
Using Nonpareil, a statistical tool that employs read redundancy to estimate the coverage of the microbial community achieved by a metagenomic dataset (Rodriguez-R and Konstantinidis, 2014), a much more diverse community was observed in temperate soils compared to those from Alaskan tundra
A higher level of diversity in the OK soil microbial community is further reflected in the 97% OTU rarefaction curve from 16S PCR amplicon sequences, where the number of OTUs detected at OK is over twofold greater than the number of OTUs observed at AK (Supplementary Figure S1)
Summary
Terrestrial soil systems are residence to some of the most functionally and taxonomically diverse microbial communities known (Torsvik et al, 1990; Whitman et al, 1998; Curtis et al, 2002; Handelsman et al, 2007). Soil systems are estimated to contain more carbon than aboveground plant biomass and atmospheric pools combined in the form of degradable soil organic matter (or SOM) (Grosse et al, 2011). Higher land temperatures are expected to cause the release of considerable amounts of CO2 and CH4 to the atmosphere (Heimann and Reichstein, 2008; Mackelprang et al, 2011; McCalley et al, 2014), primarily through the microbially mediated degradation of SOM. It is projected that permafrost may recede by 30–70% toward the end of the 21st century due to increasing temperatures (Schuur and Abbott, 2011; Lawrence et al, 2012), likely resulting in enormous terrestrial ecosystem C loss
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