Microbiome of permeable sandy substrate in headwater river is shaped by water chemistry rather than grain size and heterogeneity

Abstract

The reservoir of microbial communities within the soil and the sediment performs many ecological functions and offers many ecosystem services. It has been suggested that its diversity and community structure could be explained by different grain size and heterogeneity. However, most of these conclusions come from studies conducted in terrestrial soil, impermeable marine and freshwater sediment (substrate). It remains to be seen whether these conclusions hold true in permeable substrate, especially in headwater river ecosystems. To address this, a field experiment was aimed to evaluate the link between grain median size and distribution heterogeneity and microbial diversity and community structure. Permeable substrate with gradient grain sizes and heterogeneities was inoculated in a headwater river in central China, while the diversity and community composition of the total microbial community and three denitrifier communities were investigated by high throughput sequencing three months later. The total microbial community was sequenced by 16S rRNA, a marker for taxonomic diversity. Three denitrifier communities were sequenced using three functional gene markers: nirK, nirS, and nosZ. The result showed that both the diversity and community structure of the total microbial community and three denitrifier communities were determined by water chemistry rather than grain size and size distribution heterogeneity, although grain size and heterogeneity positively influenced the nutrient concentrations of the substrate. Compared to the total microbial community, denitrification functional groups had more unique species proportions, indicating that functional genes were more sensitive to environmental change than the 16S rRNA gene. Our study fills a gap in understanding microbial communities in permeable sediment in a headwater river and highlights the less importance of grain size and heterogeneity on mm-scale in shaping the diversity and structure of microbiome.

Keywords: Denitrifier communities; Grain size and heterogeneity; Headwater river; Microbial communities; Permeable sandy substrate.