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 NO3−, 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.

16至18世纪的日本，采用生物硝床工艺生产硝石，其生产位点位于被联合国教育、科学及文化组织（UNESCO）列入世界遗产名录的白川乡与五箇山历史村落内的合掌造（gassho-style）房屋地板下方。现存的硝床遗迹如今被保护于合掌造房屋的地板空间中，免受不稳定环境因素的干扰，且仍具备生成硝酸盐的能力。然而，目前学界对这类硝床遗迹生态系统中的硝化微生物仍了解甚少。本研究针对16S rRNA基因以及细菌、古菌氨单加氧酶基因（amoA），采用454焦磷酸标签测序技术分析了9处硝床遗迹土壤的微生物群落结构。16S rRNA基因焦磷酸标签测序结果显示，变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、拟杆菌门（Bacteroidetes）、绿弯菌门（Chloroflexi）、厚壁菌门（Firmicutes）、芽单胞菌门（Gemmatimonadetes）以及浮霉菌门（Planctomycetes）为该类土壤中的主要微生物类群；主坐标分析表明，硝床遗迹土壤中的硝酸根离子（NO₃⁻）、氯离子（Cl⁻）、钾离子（K⁺）及钠离子（Na⁺）含量是调控整体微生物群落结构的潜在关键因素。细菌与古菌amoA基因文库分析结果显示，亚硝化螺菌属（Nitrosospira）型氨氧化细菌（AOB）以及“候选亚硝化球囊菌属”（"Ca. Nitrososphaera"）型氨氧化古菌（AOA）分别为硝床遗迹土壤中的优势类群。此外，土壤pH值与有机碳含量是影响硝床遗迹土壤生态系统中氨氧化细菌与氨氧化古菌生态位的重要环境因子。