Abstract
Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments.
Highlights
Soils are known as hotspots for biodiversity
Whereas no significant differences were found in DNA concentrations comparing rhizosphere samples from the top- and the subsoil, for bulk soil and drilosphere significant lower DNA concentrations were measured in subsoil as compared to topsoil (P = 0.005, P = 0.011)
Higher ratios were found in the rhizosphere of the subsoil (P < 0.001), but no differences were observed between topsoil and subsoil within each soil compartment
Summary
Soils are known as hotspots for biodiversity. soils provide a wide range of ecosystem services including nutrient cycling, carbon sequestration, safeguarding of water resources and plant growth promotion (van der Heijden et al, 2008; Berg, 2009; Bardgett and van der Putten, 2014). The general opinion implies a decrease of abundance, diversity and activity of bacteria, fungi and archaea with soil depth as a result of the more oligotrophic conditions present in deeper soil layers; it is assumed that the contribution of the subsoil microbiome to the overall turnover of nutrients in soil is low (Fuka et al, 2009; Eilers et al, 2012; Stone et al, 2014) These observations are biased by the fact that small-scale spatial heterogeneity of microbes in subsoils has received almost no attention and the presence of hotspots in subsoils, which may change the described low microbial activity in subsoils, has been mostly overlooked (Nunan et al, 2003; Vos et al, 2013). Still data is missing on microbial network structures in the different subsoil compartments and the related ecophysiology of the microbiomes
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