Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria

Abstract

The nitrogen (N) cycle represents one of the most well-studied systems, yet the taxonomic diversity of the organisms that contribute to it is mostly unknown, or linked to poorly characterized microbial groups. While new information has allowed functional groups to be refined, they still rely on a priori knowledge of enzymes involved and the assumption of functional conservation, with little connection to the role the transformations, plays for specific organisms. Here, we use soil microcosms to test the impact of N deposition on prokaryotic communities. By combining chemical, genomic and transcriptomic analysis, we are able to identify and link changes in community structure to specific organisms catalysing given chemical reactions. Urea deposition led to a decrease in prokaryotic richness, and a shift in community composition. This was driven by replacement of stable native populations, which utilize energy from N-linked redox reactions for physiological maintenance, with fast responding populations that use this energy for growth. This model can be used to predict response to N disturbances and allows us to identify putative life strategies of different functional and taxonomic groups, thus providing insights into how they persist in ecosystems by niche differentiation.

Soil‐Gas Diffusivity and Soil‐Moisture effects on N2O Emissions from Intact Pasture Soils

“…6). Besides soil physical conditions, the magnitude of an N 2 O flux is a function of both substrate availability and the microbial community structure and its functional response to the soil physical and chemical conditions (Samad et al, 2017). The size of the microbial community may also vary with management intensity and soil depth (Dignam et al, 2018).…”

Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil

“…On the other hand, based on the abundance, latitude and soil pH had significant effects on the community structure (Tables 3 and 4 ), and therefore the effects of environmental selection seemed to be prevalent in the bacterial communities in spite of their low β-diversity. In agricultural lands, soil bacterial communities show a large divergence between conventional and organic farms [ 43 , 44 ], between different tillage regimes [ 45 , 46 ], and between nitrogen treatments [ 47 , 48 ]. Therefore, the low β-diversity of bacterial communities seems to be related to similar management conditions at the farms examined in this study, which could cause directional selection and resulting convergence of the communities.…”

Critical transition of soil bacterial diversity and composition triggered by nitrogen enrichment

“…S4). The rRNA operon copy number correlates with bacterial reproduction rate and response rate to resource availability (Roller et al 2016, Wu et al 2017, thus reflects the ecological strategies of bacteria, as higher rRNA operon copy number is associated with the fastergrowing copiotrophic bacteria (Roller et al 2016, Samad et al 2017. The increased abundance-weighted average rRNA operon copy number under N addition thus provided another line of evidence that elevated N input favored copiotrophic taxa.…”