Atmospheric n deposition alters co-occurrence, but not functional potential among saprotrophic bacterial communities

Background/Question/Methods

The use of co-occurrence patterns to investigate interactions between microorganisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co-occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. Here, we sought to determine if simulated atmospheric N deposition, a pervasive agent of climate change, has altered biotic interactions within the saprotrophic bacterial community. In a northern hardwood forest ecosystem located in Michigan, USA, twenty years of experimentally increased N deposition has reduced forest floor decay and increased soil C storage. This ecosystem-level response occurred concomitantly with compositional changes in saprophytic fungi and Bacteria, as well as increased the abundance of bacterial assemblages mediating litter decay. It is plausible that chronic N deposition can alter the interactions among the saprotrophic bacterial community, which may elicit a functional response consistent with our biogeochemical observations. To address our objectives, we amplified bacterial 16S rRNA genes to determine if the phylogenetic and co-occurrence network structure were altered by experimental N deposition. Furthermore, we employed predictive functional profiling to assess whether chronic N deposition altered the functional potential of the saprotrophic bacterial community.

Results/Conclusions

Experimental N deposition led to a less rich (-13%) and phylogenetically distinct bacterial community. The saprotrophic bacterial community exhibited a shift in phylogenetic structure from a clustered distribution under the ambient condition (Net Relatedness Index (NRI); +2.25) to an overdispersed distribution under experimental N deposition (NRI; -2.03). OTU co-occurrence patterns differed between bacterial communities in the ambient and experimental deposition treatments. Moreover, the OTU co-occurrence network was more “connected” under experimental N deposition, as indicated by a greater clustering coefficient (+12%), average number of neighbors (+18%), density (+42%), and a slightly lower characteristic path length (-1.5%). Together, these results suggest the presence of increased biotic interactions among saprotrophic bacterial assemblages under future rates of N deposition. However, these changes did not occur concomitantly with discernable differences in abundance or composition of predicted metagenomic functional gene pathways as indicated by PiCRUST. Results presented here support the hypothesis that the nearly two decades of experimental N deposition can modify the organization of soil microbial communities.