Abstract:
Soil microorganisms such as Bacteria and Archaea play important roles in the
biogeochemical cycling of soil nutrients, because they act as decomposers or are
mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the
present study, we investigated the vertical distribution of soil metagenomes to a depth
of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock.
We explored the functional genetic potential of soil microorganisms with the aim to
disentangle the effects of tree genus and soil depth on the genetic repertoire, and to
gain insight into the microbial C and N cycling. The relative abundance of reads assigned
to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the
deep soil, while Bacteria showed no change with soil depth. In the deep soil there was
an overrepresentation of genes for carbohydrate-active enzymes, which are involved
in the catalyzation of the transfer of oligosaccharides, as well as in the binding of
carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved
in the degradation and synthesis of N compounds, in nitrification and denitrification,
and in nitrate reduction were overrepresented in the deep soil. Consequently, our results
indicate that N-transformation in the deep soil is affected by soil depth and that N is used
not only for assimilation but also for energy conservation, thus indicating conditions of
low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial
findings on soil microorganisms and their functional genetic potential, and how this may
change depending on soil properties, which shift with increasing soil depth. Thus, our
data provide novel, deeper insight into the “dark matter” of the soil.
