Microplastics in rivers harbor unique microbial communities, spreading antibiotic resistance

In a recent study published in the journal Nature Water, researchers investigated the viral distribution, host interactions, and antibiotic resistance gene (ARG) transfer on microplastics using metagenomic and viromic sequencing.

Study: Viral metagenome reveals microbial hosts and the associated antibiotic resistome on microplastics. Image Credit: Kletr / ShutterstockStudy: Viral metagenome reveals microbial hosts and the associated antibiotic resistome on microplastics. Image Credit: Kletr / Shutterstock


Persistent microplastic pollution is a hallmark of the Anthropocene, posing environmental and health risks through toxic leachates and direct entry into biological tissues. Microplastics create unique niches for microbial colonization and biofilm growth, forming the 'plastisphere,' which includes diverse microbial communities. These surfaces can selectively enrich pathogens, potentially impacting disease transmission. Despite their ubiquity, viruses have been largely overlooked in plastisphere studies, although recent evidence shows they persist on microplastics and interact with bacterial hosts. Further research is needed to fully understand the ecological impact of viral communities and ARG transfer on microplastics and their implications for environmental and human health.

About the study 

In March 2021, the present study was conducted on two types of microplastics, polyethylene (PE) and polypropylene (PP), in the Beilun River, Guangxi Province, China. Five sites along the river were selected based on urbanization and physicochemical properties, ranging from rural to urban regions. At each site, 2.0 g of microplastics (PE and PP) and natural particles (stone, wood, sand) were cultured in river water. The microplastics were disinfected with 70% ethanol and rinsed with sterile water, while natural particles were sterilized to eliminate original bacterial and viral communities. The incubation duration was based on prior studies showing successful biofilm formation on plastics within 30 days.

Following incubation, microplastics, natural particles, and water samples were collected and stored at -20°C for analysis. Large particles and herbivores were filtered out, and metal concentrations were determined using inductively coupled plasma optical-emission spectrometry. Additional physicochemical properties and urbanization levels were measured.

Deoxyribonucleic Acid (DNA) was extracted using a FastDNA Spin kit and sequenced on the HiSeq X platform. High-quality reads were processed to predict open reading frames and remove redundant genes. Bacterial genomes were assembled and annotated using various bioinformatics tools. Viral DNA was extracted, enriched, and sequenced to identify viral contigs and potential virus clusters on microplastics.

Statistical analyses were performed using R, including alpha and beta diversity analyses, Adonis analysis, and Linear Discriminant Analysis Effect Size (LEfSe) analysis to classify shared taxa or genes across samples.

Study results 

Using metagenomic sequencing, 28,732 bacterial species were identified in microplastic samples from the Beilun River watershed. Dominant phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, constituting 52.6% of the bacterial community. Species richness and evenness showed no significant differences by site or microplastic type. The core bacterial community, comprising 25,883 species, represented 78.4% of the total detected species, with 12,284 species shared across all samples except one PE sample. Most species (28,599) were shared between PE and PP microplastics, with 49 and 84 species unique to PE and PP, respectively.

Approximately 0.32% of bacterial species were potential pathogens, with 91 species detected across 11 phyla. Dominant pathogens included Burkholderia cepacia (13.29%), Klebsiella pneumoniae (10.21%), and Pseudomonas aeruginosa (7.59%). A significant distance–day effect was observed in microbial community similarity between sites (R2 = 0.842, P < 0.001). Non-metric multi-dimensional scaling (NMDS) analysis showed distinct bacterial community structures between PE and PP microplastics.

For viral communities, 226,853 contig fragments were obtained, mostly under 1,000 kb. Myoviridae and Siphoviridae dominated, accounting for 58.8% of viral abundance. Viral richness and evenness did not differ significantly between microplastic types. Viral contigs were classified into 501 genera, with 364 shared between PE and PP. A significant distance–day effect was observed in viral communities between sites. NMDS analysis revealed distinct viral communities between PE and PP microplastics.

Functional gene annotation of bacterial and viral sequences on microplastics was used in various databases. Most viral genes were unclassified or poorly characterized, with some linked to genetic information processing and cellular processes. Bacterial functional genes were similarly unclassified, with some associated with metabolic pathways and biosynthesis. Metal resistance genes (MRGs) and ARGs were detected in both viral and bacterial sequences, with resistance to Cu, Zn, As, and Fe being the most common.

Bacterial ARGs primarily encoded resistance to multidrug, Macrolide-Lincosamide-Streptogramin (MLS), and tetracycline, while viral ARGs included trimethoprim, tetracycline, and MLS resistance genes. Horizontal gene transfer (HGT) of ARGs and MRGs was observed between viruses and their bacterial hosts, indicating potential genetic exchange facilitated by microplastics.

Microplastics offer a unique niche for microbial colonization and genetic exchange. This study enhances understanding of bacterial and viral community dynamics, resistance gene distribution, and host-virus interactions on microplastics compared to natural particles, highlighting their role in spreading antimicrobial resistance through HGT.


To summarize, the study revealed distinct bacterial and viral communities colonizing microplastics compared to natural particles in the Beilun River. While diversity remained similar across sites, microplastic type influenced community composition. Notably, the researchers identified potential pathogens and ARGs associated with both bacteria and viruses on microplastics. They observed evidence of HGT between viruses and bacteria, suggesting microplastics may facilitate the spread of antimicrobial resistance in aquatic environments. These findings highlight the potential ecological and human health risks associated with microplastic pollution.

Journal reference:
Vijay Kumar Malesu

Written by

Vijay Kumar Malesu

Vijay holds a Ph.D. in Biotechnology and possesses a deep passion for microbiology. His academic journey has allowed him to delve deeper into understanding the intricate world of microorganisms. Through his research and studies, he has gained expertise in various aspects of microbiology, which includes microbial genetics, microbial physiology, and microbial ecology. Vijay has six years of scientific research experience at renowned research institutes such as the Indian Council for Agricultural Research and KIIT University. He has worked on diverse projects in microbiology, biopolymers, and drug delivery. His contributions to these areas have provided him with a comprehensive understanding of the subject matter and the ability to tackle complex research challenges.    


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