A Metagenomic and Metaproteomic Analysis of River-Associated Communities

Rivers are vulnerable to human influences and climate change, therefore studying them is increasingly important if they are to be preserved. Here, the effect of a prolonged period of inundation on biological communities at a specific sampling site in Lane Cove River was investigated. The composition, structure, and functionality of the communities was examined through metagenomic and metaproteomic analyses. Metagenomic analyses revealed marked differences in the composition and structure of the communities sampled in 2021 and 2022. The observed decrease from 5,278 to 3,024 validly designated sequence variants, suggested a community-wide loss in biodiversity. The eukaryotic families of Neoptera, Bdelloidea, and Bacillariophyceae, were abundant in the 2022 communities. However, unique sequences, corresponding to bacteria, protists, algae, diatoms, fungi, animals, and plants, were identified in both the 2021 and 2022 sequencing data, suggesting the communities remain taxonomically diverse and ecologically productive. The metaproteomic analysis of the 2022 communities identified 134,427 peptides which mapped to 1,666 reproducibly identified proteins, with notable biological functions including photosynthesis and methane oxidation. Metaproteomic analyses provided evidence supporting the identification of specific organisms in the communities such as methylotrophs, cyanobacteria, insects and bdelloid rotifers, while indicating the main substrate constituent of the communities is an uncharacterized moss.