Effects of fertilization and straw incorporation on bacterial communities in lime concretion black soil

Soil bacteria are important drivers of nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformation processes in the soil. Thus knowledge about the shift of microbial community structure and diversity following different agricultural management practices could improve our understanding of soil processes and help us to develop agricultural management strategies. Because most soil bacteria are nonculturable, and traditional molecular biology methods, such as DGGE, are partial, the researches on soil bacterial are limited. High-throughput sequencing technology provides an effective tool for microbial molecular biology research. In this study, the technology of high-throughput sequencing on Illumina MiSeq platform was adopted to investigate the effects of fertilization and straw residue incorporation on bacterial communities in lime concretion black soils. The 16S rRNA genes of topsoil bacteria in lime concretion black soil were sequenced by high-throughput sequencing on Illumina MiSeq platform and related biological analysis conducted to investigate the changes in soil bacterial composition, diversity and structure under 4 different fertilization practices at wheat tillering stage. Soil samples were collected in lime concretion black soils in Mengcheng, Anhui Province, China with 3 treatments (CK: no fertilization, no straw return; F: chemical fertilization without straw return; W: straw return without chemical fertilization). The results showed that 173 323 reads of 14 873 OTUs (operational taxonomic unit) were generated at 3% cutoff level under all treatments with an average length of 439 bp. Bacterial OTUs were classified into 19 different known phyla and 41 classes. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla (with relative abundance > 10%) in lime concretion black soils. Then Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, Acidobacteria and Gammaproteobacteria were the dominant classes (with relative abundance > 10%). The total number of dominant genera (with relative abundance > 1%) in all 3 treatments was 47, of which 21 genera were found in all treatments, and the largest number (39) of dominant genera occurred under F treatment. The dominant phylum, class and genus with the highest relative abundances were Proteobacteria (38.7%?43.1%), Alphaproteobacteria (14.5%?18.1%) and Sphingomonas (4.6%?7.7%) in all 3 treatments. The richness indexes (Chao1 and ACE indexes) were significantly lower for F treatment than for CK and W treatments. ACE index decreased by 22.8% under F treatment compared with CK. The richness indexes (Chao1 and ACE indexes) of CK and W treatments were not significantly different from each other. The Shannon index of W treatment was significantly higher than that of CK and F treatments, it increased by 4.1% compared with CK. Then the Shannon indexes of CK and F treatments were also not significantly different from each other. The Simpson index of F treatment was significantly higher than that of CK and W treatments. The Simpson index of F treatment increased by 38.1% compared with CK treatment. The Simpson index of W treatment was lowest among 3 treatments, decreasing by 23.8% compared with CK treatment. Hierarchical cluster analysis showed that CK and W treatments were in the same cluster group, while F was in a different cluster group. All the above findings suggested that chemical fertilization had a stronger effect on the composition, relative abundance of the dominant bacterial group and bacterial structure in soils than incorporation of straw residue. While chemical fertilization decreased soil bacterial richness, it increased bacterial predominance. On the contrary, straw residue incorporation increased soil bacterial diversity, but decreased bacterial predominance.