Soil microbes play critical roles in ecosystem function. Although the effects of agriculture management on microbial communities in topsoil have been well studied, few studies have examined such impacts in subsoil.

To determine and compare the effects of long-term fertilizations on the microbial community in topsoil (0–0.2 m) and subsoil (0.2–3 m), the researchers applied high-throughput pyrosequencing to investigate bacterial and archaeal communities in the 0-3m soil profile in a long-term fertilizer experiment started in 1990 in an irrigated farmland in arid zone. The following fertilizer treatments were compared with no fertilizer treatment (CK): inorganic fertilizer alone (CF) and inorganic fertilizer combined with wheat straw (CF/OM).

The results showed that Actinobacteria and Proteobacteria were the predominant phyla (48%–65% of abundance) in topsoil, while Proteobacteria was the overwhelmingly dominant phyla (16%–84%) in subsoil. The most abundant class in topsoil was Alphaproteobacteria (9%–11%) and that in subsoil was Gammaproteobacteria (3%–51%). The results indicated that fertilizer applications changed microbial community structure throughout the profile. In contrast to the similar community structure in the topsoil for the two fertilizer treatments, there was a clear differentiation of the subsoil community. The order Xanthomonadales, order Nitrosomonadales, Gemmatimonadetes and Crenarchaeota were more abundant in the CF compared with CF/OM treatment; whereas the order Methylococcales, order Enterobacteriales, order Pseudomonadales and Nitrospirae were more abundant in CF/OM treatment. Total nitrogen had the greatest impact on microbial community structure in topsoil while organic carbon had the greatest impact on microbial community structure in subsoil.

The results suggested that long-term fertilizer applications altered nitrogen, carbon availability as well as electrical conductivity throughout the profile. However, this resulted in community differentiation only in deep soil. The mechanism underlain should have been that deep soil was altered by substances leached in from above, while the topsoil was altered by direct fertilization and irrigation. The study was available online in Soil Biology and Biochemistry in May 2014.