DNA barcode survey of aquatic bacterial and eukaryotic microorganism communities in the Mooi River system

Abstract

Freshwater aquatic ecosystems are critical to both environmental sustainability and human well-being. However, the long-term sustainability of these ecosystems is under threat from a variety of anthropogenic influences, such as agricultural activities, industrial and mining operations, urban runoff, and land use changes. These activities lead to declining water quality and biodiversity in aquatic ecosystems, necessitating innovative and comprehensive ecosystem assessment and management strategies. The present study surveyed the aquatic bacterial and eukaryotic microorganism communities of the Mooi River system and its tributaries using DNA metabarcoding alongside physico-chemical parameters and metal concentrations.

13 sampling sites along the Mooi River catchment, Loop Spruit and Wonderfontein Spruit, were strategically chosen to represent varying degrees of anthropogenic influence, including wastewater treatment plant discharges, agricultural runoff, and mining operations. Water samples were collected in triplicate at each site from 2021 to 2022. A calibrated Oakton PCS Testr™ 35 waterproof field multi-parameter probe was used to conduct on-site measurements of physical and chemical parameters such as pH, temperature, total dissolved solids (TDS), salinity, and turbidity. Furthermore, inductively coupled plasma mass spectrometry (ICP-MS) analysed trace and heavy metal concentrations. Environmental DNA (eDNA) was extracted from filtered membranes using the Macherey-Nagel NucleoSpin® Soil DNA Isolation Kit. Furthermore, metabarcoding of 16S rRNA and COI genes was conducted, facilitating the identification of bacterial and eukaryotic microorganisms. Several diversity indices were used to assess and compare species richness, diversity, dominance, and similarity between the sites. Multivariate analyses were further conducted to assess the impact of anthropogenic influences on the microbial communities.

The findings of this study indicate significant regional and temporal variation in the physico-chemical parameters which assessed water quality. Specifically, total dissolved solids (TDS), turbidity, and trace and heavy metals, such as aluminium, zinc, and copper, consistently surpassed the prescribed threshold, signifying the negative effect of mining and urban effluents on the Mooi River system and its tributaries.

Furthermore, microbial communities exhibited varied responses to environmental influences. Bacterial phyla such as Proteobacteria, Bacteroidota, and Actinobacteriota thrived in nutrient-rich and metal-contaminated sites. Whereas eukaryotic communities, dominated by Arthropoda and Chromista, displayed site-specific and seasonal adaptations, with taxa such as Cyanobacteria and Pythium indicating eutrophication risks in phosphorus enriched waters.

The findings of this study emphasise the value of adopting a comprehensive and integrative approach that combines physico-chemical analyses with metabarcoding techniques to improve biomonitoring frameworks used to assess aquatic ecosystems. Furthermore, this study contributes to both research and practice by demonstrating the use of DNA metabarcoding techniques to survey aquatic bacterial and eukaryotic microorganism communities in aquatic ecosystems, thereby informing sustainable water resource management in South Africa.