Differential responses of soil bacterial taxa to long-term P, N, and organic manure application

Soil microorganisms and their interactions with environmental factors govern critical ecosystem processes. However, the changes of soil microbial communities (e.g., relative abundance changes of different phylotypes) and the links between specific environmental factors and microbial communities are not well understood. We applied high-throughput sequencing of 16S rRNA gene amplicons to investigate the effects of mineral fertilizers P (superphosphate), N (urea), and NP and organic manure fertilizer (M) and its combined with mineral fertilizers (NM, PM, NPM) on bacterial and archaeal communities in rain-fed winter wheat soils in a 30-year experiment in the Loess Plateau of northwest China. Dramatic changes of soil respiration and the concentrations of total organic C, total N, and microbial biomass C and N were found in manure application soils (M, NM, PM, NPM) and some of them in NP soil. Soil microbial community structure shifted after fertilization, and a significant difference of prokaryotic community structure was found between mineral fertilizer soils (P, N, and NP) and manure application soils (M, NM, PM, NPM) except the soils between PM and P. The prokaryotic community structure in M soil was different from that in NM and NPM soils and differed between N and P and NP soils. Acidobacteria, Actinobacteria, and Proteobacteria were the predominant phyla (55.5–76.5 % of abundance) and, together with some other phyla, were changed by fertilization at the phylum or lower taxon ranks. No fertilizer soil had the highest relative abundances of phyla WS3 and Gemmatimonadetes. P soil changed the relative abundances of phyla Acidobacteria, Gemmatimonadetes, and Verrucomicrobia, but only enriched the bacteria at the family level (Micrococcaceae) when combined with N or M application (NP, PM, and NPM). Some copiotrophic bacteria showed different responses to nitrogen and manure applications, e.g., Actinobacteria increased in abundance in nitrogen application soils (N, NP, NM, and NPM), whereas Bacteroidetes and Gammaproteobacteria increased in abundance in manure application soils (M, NM, PM, and NPM). The above patterns of the relative abundance vs nitrogen or manure application were correlated to soil C and N contents or C/N ratio. These results supported the hypothesis that different bacterial taxa would be favorable in P, N, and manure application soils and suggested that the changes of bacteria taxa in fertilized soils appeared to be more driven by nitrogen and manure applications than P application.