Members of soil bacterial communities sensitive to tillage and crop rotation

Pyrosequencing was used to study the effect of rotation and tillage on total bacterial communities. We designed primers to the bacterial 16s rDNA and amplified DNA from soil samples from a long-term tillage/rotation trial in Kansas for two seasons. The 2 × 2 factorial trial had two rotation treatments (wheat–wheat and wheat–soybean) and two tillage treatments (conventional and no-till). A total of 20,180 16s rDNA sequences were generated and 2337 operational taxonomic units (OTUs) were assembled using a 97% similarity cut-off. The phylum Proteobacteria represented 38% of 299 identified taxa. The second most abundant phylum was Acidobacteria, making up 20% of the sequences, the majority of which were Acidobacteria Group 1. The phyla Actinobacteria and Gemmatimonadetes comprised 12% and 3.5% of the sequences. Other groups detected included TM7, Nitrospira, Verrucomicrobia, and Bacteroidetes. Some clusters of Acidobacteria Group 1 were more frequent in continuous wheat versus wheat–soybean rotation, some Acidobacteria Group 2 were more frequent in no-till, and some Acidobacteria Group 4 were more frequent in wheat–soybean rotation. These results were validated by quantitative real-time PCR. Pyrosequencing provided taxonomic information about the overall bacterial community, and detected community shifts resulting from different cropping practices.

Research highlights► Pyrosequencing can detect shifts in bacterial taxa due to tillage and crop rotation. ► The Phylum Acidobacteria was a predominant component of the soil in a long-term wheat study site in Kansas. ► Groups of Acidobacteria were affected by tillage and crop rotation in a long-term wheat study site in Kansas.