Metagenomic insights into the effects of desiccation on functions associated with biogeochemical cycles and resistome of microbial communities

Abstract

Climate change and human activities are altering the hydrological conditions of wetlands, leading to an increasingly severe desiccation phenomenon. Microorganisms play a crucial role in maintaining the ecological health of freshwater ecosystems, and in turn, they are influenced by the state of these ecosystems. However, the changes in composition and diversity of functional gene of microbial communities during wetland desiccation remain poorly understood. To address this knowledge gap, we employed metagenomic techniques to assess the abundance and diversity of methane cycling genes (MCGs), nitrogen cycling genes (NCGs), sulfur cycling genes (SCGs), phosphorus cycling genes (PCGs), antibiotic resistance genes (ARGs), mobile genetic elements (MEGs), and virulence factors (VFs) across various habitats in the Xixi National Wetland Park, including ponds, swamplands, and peatlands. Our results revealed significant differences in gene diversity and abundance, with swampland showing the highest levels of functional gene diversity (mean richness of MCGs: 245, NCGs: 60, SCGs: 165, PCGs: 125, ARGs: 116, MGEs: 39, VFs: 546) among three habitats. Notably, the peatland exhibited a highest abundance of ARGs (mean clean reads >9000), particularly those related to multidrug resistance, and an increase in abundance of virulence factors related to nutritional/metabolic types (from pond and swampland to peatland). Through binning analysis, we identified core functional microbiomes and found that metabolic gene abundance was highest in the peatland. These findings suggest that wetland desiccation may pose risks to ecosystem health by altering the composition and abundance of microbial functional genes.