Location-dependent impacts of liming and crop rotation on bacterial communities in acid soils of the Pacific Northwest

The cropping systems of northern Idaho and eastern Washington are dominated by a cereal-based (winter wheat) rotation that is exclusively rainfed. Following the green revolution, the productivity of wheat increased dramatically with semi-dwarf varieties and inexpensive synthetic fertilizers. However, long-term and frequent use of ammonium-based nitrogen fertilizers has resulted in the gradual acidification of fields in the region, with reduced productivity and symptoms of aluminum toxicity in some locations. A micronized liquid formulation of lime (calcium carbonate) was evaluated at three locations to mitigate soil acidification in comparison to a no-lime control. To examine how liming affects bacterial community structure, soil samples were taken in the spring in wheat and pea rotations 7 and 19 months after lime application, DNA was extracted and the V1-V3 portion of the 16S rRNA gene was amplified and sequenced with Illumina MiSeq. pH was only increased ∼0.2–0.3 units in most locations, and liming only had a significant effect on bacterial community composition at one location (Pullman). Liming had no consistent or significant effect on community richness or diversity. Location had a stronger effect on communities than liming or crop rotation, but some specific taxa increased in relative abundance in response to liming, including the families Cytophagaceae and Flavobacteriaceae (Phylum Bacteroidetes), A4b (Phylum Chloroflexi), and Opitutaceae (Phylum Verrucomicrobia). A number of operational taxonomic units (OTU) in Chitinophagaceae and Xanthomonadaceae were increased by liming at the Pullman location, which had 3–4 X more OTUs affected by liming than the other locations. Streptomycetaceae and Oxalobacteraceae were more abundant in root zone soil of wheat than pea. In conclusion, there was a strong interaction between liming and location in determining soil bacterial composition, but specific components of the bacterial community responded to even minimal increases in soil pH.