PDF(Sci-hub)
Abstract：
Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput FluidigmTM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.
摘要：
尽管居住在地下水和相连的生态系统中的微生物具有明显的生态意义，我们目前对它们栖息地的了解，功能，控制其组装的生态过程受到限制。在这项研究中,一个有效的管道结合了地球化学，开发了高通量FluidigmTM功能基因扩增和测序，以分析居住在伊利诺伊州盆地五个地下水监测井中的悬浮和附着的微生物群落，美国。悬浮和附着的微生物群落中的优势类群在α-和β-多样性方面表现出明显不同的时空变化。与N2固定（nifH）相关的代表性功能基因的进一步分析，甲烷氧化（pmoA），和硫酸盐还原(dsrB，和aprA)，建议浅层含水层微生物群内的功能冗余。虽然除了pmoA外，悬浮微生物群落比附着的微生物群落观察到更多样化的功能基因分类群，在这些功能基因之间观察到不同水平的随时间和空间的变化。值得注意的是,确定性和随机性的生态过程对微生物群落和功能基因库的组装形成了不同的影响。虽然同质选择是控制微生物群落组装的主要过程，中性过程(例如，扩散限制，漂移和其他)对功能基因更重要。结果表明浅层含水层微生物群复杂多变，其功能和组装甚至在空间上接近的栖息地和部分之间也有所不同。这项研究强调了包括所有界面组件以更全面地了解含水层生态系统中的生物地球化学过程的重要性，这对实际应用也有指导意义。
