In comparison to inorganic N cycling, only little is known regarding the assimilation of organic N in soil. Therefore, we used 16S and 18S rDNA gene profiling and functional metaproteomics to characterize the composition of a soil microbial community assimilating (15)N-labeled plant-derived organic matter (OM).

Genomic results showed an increase of the abundance of fungi and Proteobacteria related to the utilization of plant-derived OM within the first days of exposure. Similarly, metaproteomic analysis revealed Proteobacteria as the most abundant phylum followed by Actinobacteria and Ascomycota. Finally, protein stable isotope probing (protein-SIP) demonstrated copiotrophic behavior for Rhizobiales belonging to Proteobacteria, Actinomycetales belonging to Actinobacteria and Chroococcales belonging to Cyanobacteria as these phylotypes immediately incorporated (15)N from the added plant tissue. Conversely, the fungal Saccharomycetales and the bacterial Enterobacteriales, Pseudomonadales, Sphingomonadales and Xanthomonadales displayed slower (15)N-assimilation.

We showed that, in contrast to the dominance of fungi in the degradation of complex carbon compounds, mostly bacteria were involved in the short-term assimilation of plant-derived N. The combined use of genomic and proteomic approaches allowed to track the flow of N within the soil microbial community.