Microbial Community Structure of Relict Niter-Beds Previously Used for Saltpeter Production

From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene ( amoA ). The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria , Actinobacteria , Bacteroidetes, Chloroflexi, Firmicutes , Gemmatimonadetes , and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO 3 − , Cl − , K + , and Na + contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira -type ammonia-oxidizing bacteria (AOB) and “ Ca . Nitrososphaera”-type ammonia-oxidizing archaea (AOA), respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.