Characterization of microbial assemblages on micro-plastics in a river system

Abstract

Microplastics as pollutants originate from land-based sources and are persistent and ubiquitous in the aquatic environment. The risks posed by microplastics as vectors and habitats for potentially harmful microbial groups and antibiotic resistance genes (ARG) are relatively unexplored in South Africa. The relationship between microplastics and microorganisms’ reels in the threat of creating superbugs that may proliferate resistance profiles of potentially pathogenic bacteria in the environment. This study aimed to characterize the bacterial community composition (BCC) and quantify the ARG on microplastics from freshwater settings. The first objective was to analyze the process of microbial colonization on microplastics and wood substrates through Scanning Electron Microscopy (SEM) using microcosm experiments of river water and wastewater treatment effluent (WWTe). This was followed by next generation sequencing (NGS) targeting the 16S rRNA gene to characterize the BCC on the substrates and surrounding water (river and WWTe) post-incubation. The third objective was to isolate microplastics and collect water samples from across five sites from the Mooi River, followed by the identification of the microbial consortia by 16S rRNA metabarcoding of the environmental DNA samples. The fourth objective was to investigate the prevalence of the intl1 gene and six AmpC β-lactamase gene groups, including ARG copy numbers (AmpC gene groups) on all microplastics, wood, and water samples. The microcosms’ studies showed that substrates can be colonized within 48 hours after incubation. Moreover, the surface properties of the substrates and the nutrient load in water play a role in the process of colonization. SEM images revealed biofilm development in river water is slower than in nutrient-rich water (WWTe) and from environmental microplastic samples, the images revealed a diverse microbial community of bacterial biofilms and eukaryotic organisms inhabiting the surfaces. Two hundred and six (206) microplastics were isolated from 1800 litres of surface running water following in situ filtrations through 300-75 μm pore size metal sieves at each site. Bacterial diversity indices of both microcosm and environmental samples showed that the BCC on microplastics was less rich, diverse, and even than in the surrounding water. Furthermore, the bacterial profiling showed that microbial phyla dominance fluctuated during the incubation period. The BCC dominance on microplastics from the environment differed from that of the surrounding water at each respective site. LEfSe biomarker analysis showed that the families Aeromonadaceae, Enterobacteriaceae, and Legionella were significantly higher (p < 0.05) on microplastics than in water samples, including some of the genera known to contain potentially pathogenic members which show resistance against antibiotics. Conventional PCR revealed that the intl1 gene was present in WWTe samples from the microcosm experiments and in environmental samples that contained more than five AmpC β-lactamase gene groups.