Multi-scale variability analysis reveals the importance of spatial distance in shaping Arctic soil microbial functional communities

• This is the first pan-Arctic study of microbial functional gene biogeography.
• Spatial distance strongly influenced soil functional gene distribution patterns.
• Functional gene distributions varied most at large spatial scales.
• Functional gene richness was not correlated with bacterial community richness.

Understanding biological diversity and distribution patterns at multiple spatial scales is a central issue in ecology. Here, we investigated the biogeographical patterns of microbial functional genes in 24 heath soils from across the Arctic using GeoChip-based metagenomics and principal coordinates of neighbour matrices (PCNM)-based analysis. Functional gene richness varied considerably among sites, while the proportions of each major functional gene category were evenly distributed. Functional gene composition varied significantly at most medium to large spatial scales, and the PCNM analyses indicated that 14–20% of the variation in total and major functional gene categories could be attributed primarily to relatively large-scale spatial effects that were consistent with broad-scale variation in soil pH and total nitrogen. The combination of variance partitioning and multi-scales analysis indicated that spatial distance effects accounted for 12% of the total variation in functional gene composition, whereas environmental factors accounted for only 3%. This small but significant influence of spatial variation in determining functional gene distributions contrasts sharply with typical microbial phylotype/species-based biogeographical patterns (including these same Arctic soil samples), which are primarily determined by contemporary environmental heterogeneities. Therefore, our results suggest that historical contingencies such as disturbance events, physical heterogeneities, community interactions or dispersal barriers that occurred in the past, have some significant influence on soil functional gene distribution patterns.