Plastic properties affect the composition of prokaryotic and eukaryotic communities and further regulate the ARGs in their surface biofilms

Temporal dynamics of communities on plastic debris in a polluted marine habitat

This study investigated the succession of prokaryotic and eukaryotic communities on polystyrene panels deployed for 25 weeks in a harbour environment influenced by anthropogenic activities. These activities resulted in an excess of nutrients from sewage and agricultural discharges, as well as the release of hydrocarbons and other pollutants. An eDNA metabarcoding approach targeting the 16S and 18S rRNA genes was used. This innovative methodology allowed a detailed analysis of the community development and succession, providing an in-depth view of biodiversity and ecological dynamics associated with plastic substrates. The microbial biofilm community remained stable throughout the experiment enriched in Rhodobacteraceae (16.97 %) and Flavobacteriaceae (17.99 %). Only minor differences observed between the early and late stages, consistent with their identification as key components of the biofilm. For the eukaryotic community, the early colonization stages were dominated by Alveolata (63.39 %) and Stramenopiles (23.53 %). Later stages showed changes in the community with Chlorophyta (20.14 %) and Opisthokonta (94.32 %) being the most abundant phyla. Richness, as alpha diversity index based on retrieved ASVs, varied from 1875 to 2481 and from 159 to 405 for prokaryotes and eukaryotes, respectively. This indicated an adaptive succession of plastic-associated communities in aquatic ecosystems. Potential plastic-degrading groups found in the prokaryotic community showed a dynamic distribution across colonization stages. Trophic dynamics on plastic debris showed that heterotrophs dominated the eukaryotic community. Our results confirmed the role of plastics as vectors in marine ecosystems, for complex communities composed of bacteria, algae, and invertebrates. This highlighted potential risks to the health of marine ecosystems.

The community dynamic alterations mechanisms of traveling plastics in the Pearl River estuary with the salinity influence

Most ocean plastics originate from terrestrial emissions, and the plastisphere on the plastics would alter during the traveling due to the significant differences in biological communities between freshwater and marine ecosystems. Microorganisms are influenced by the increasing salinity during traveling. To understand the contribution of plastic on the alteration in biological communities of plastisphere during traveling, this study investigated the alterations in microbial communities on plastics during the migration from freshwater to brackish water and saltwater. The results revealed that the migrated plastics can form unique microhabitats with high bacterial and eukaryotic diversity. Compared with the natural carrier (stone), the communities in plastisphere had fewer variations with salinity, indicating that plastisphere can offer stronger protection for freshwater organisms. The hydrophobicity of plastics promoted algal colonization, providing a stable nutrient source for the community during salinity fluctuations. This reduced material exchange between the plastisphere and the surrounding high-salinity environment, facilitating greater community stability. Additionally, the abundant Ochrophyta and Bryozoa of eukaryotes on migrated plastics can facilitate further colonization and promote species diversity. Plastisphere microbial networks revealed that the reduction of salt-intolerant organisms during traveling had fewer effects on the abundance of associated organisms. A more stable community on migrated plastics led to the proliferation of pathogens and carbon cycle-degrading microorganisms. And the increasing relative abundance of carbon cycling functions indicated that the traveling plastics could pose higher environmental risks and exhibit enhanced carbon metabolic capabilities. The study highlighted the biofilms on migrated plastics as a unique ecological niche in estuarine environments, offering a crucial reference for evaluating the ecological risks linked to plastic travel from rivers to the ocean.

Comammox Nitrospira are the dominant ammonia oxidizers in the Yangtze estuarine biofilms

Biofilms are indispensable ecological habitats for microbes that have garnered global attention and play a potential role in influencing the biogeochemical cycling of nitrogen. However, the biogeochemical significance of biofilms and the mechanisms by which they regulate nitrogen cycling remain elusive. In this study, we utilized DNA-stable isotope probing (DNA-SIP) labelling techniques in conjunction with metagenomics to reveal a nitrifying ecological niche in biofilms taken from the Yangtze Estuary, with those from sediment and water samples for comparison. Quantitative analysis showed that the amoA gene abundance of comammox Nitrospira (2.3 × 103 copies ng-1 DNA) was significantly higher than that of ammonia-oxidizing archaea (AOA-amoA, 62.4 copies ng-1 DNA) and ammonia-oxidizing bacteria (AOB-amoA, 218.1 copies ng-1 DNA) in biofilms, and the average abundance of comammox Nitrospira showed the following order: water > biofilm > sediment. Moreover, the NOB nxrB gene was more abundant than the amoA gene of ammonia oxidizers in all three media. DNA-SIP further revealed that the active comammox Nitrospira clade A mediates the nitrification process in biofilms with peak abundance at a buoyant density of 1.715 g mL-1. Active nitrifying bacteria exhibit metabolic diversity in both biofilms and sediments, and occupy unique nitrifying ecological niches. Additionally, the co-occurrence network showed that chlorophyll a, NO3- and salinity emerged as the predominant physicochemical factors affecting the nitrogen transformation genes in biofilms. Taken together, this study indicates that biofilms constitute an emerging nitrifying ecological niche in estuarine environments and deepens our understanding of the mechanisms by which biofilms function in marine biogeochemistry.

Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges

Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.

Viruses in the era of microplastics and plastispheres: Analytical methods, advances and future directions

Research on microplastics and plastispheres now incorporates the study of viruses to evaluate their effects on the environment and human health. Sharing these new discoveries with the scientific community is crucial to fostering further research and collaborations. However, the current research and methodologies used are fragmented. To address this issue, this paper reviews the literature and the use of methodology developments in each study, identifying four emerging research areas: (1) viral interactions with microplastics; (2) viral population, diversity, and function in plastispheres; (3) the effects of viruses and plastic particles in host-associated environments; and (4) the impacts of viruses within plastispheres. To that end, the article is structured to streamline navigation and help readers easily access existing approaches, recent advancements, key findings, challenges, and opportunities in these areas. Our synthesis reveals that research methods include biochemical assays, omics techniques, spectroscopic analysis, and molecular and bioinformatic tools. Various mechanisms enable viruses to attach to microplastics and plastispheres, leading to widespread distribution and contributing to toxic effects and gene transfer. While the growing evidence is intriguing, there is still much to uncover about their ecological interactions, functions, and impacts.

Plastisphere in a low-pollution mountain river: Influence of microplastics on survival of pathogenic bacteria

Microplastics (MPs) are found even in remote and low-pollution freshwater ecosystems. However, the microbial communities associated with MPs in these environments remain poorly understood. We characterized the plastisphere in a low-pollution riverine ecosystem and evaluated the influence of different MPs in the persistence of pathogens in such environments. A mixture of MPs (MPs Mix) composed of polyethylene (PE), polypropylene (PP) and polyethylene terephthalate (PET), was submerged at three locations (L1, L2 and L3) in the river. For comparison purposes, water and sand communities were also analyzed. Our results revealed distinct bacterial communities on MPs compared to those in water or on the natural substrate (sand). However, the resemblance between the plastisphere and communities on natural particles was higher than what has been reported for polluted ecosystems. Although pathogens were predominantly enriched in the water, a few genera (e.g. Acinetobacter, Legionella and Mycobacterium) were enriched in the plastisphere. The abundance of antibiotic resistance genes did not differ significantly between water, sand, and MPs. The influence of different MPs (PE, PP, PET) on the persistence of antibiotic-resistant pathogens (i.e. cefotaxime-resistant Escherichia coli and meropenem-resistant Enterobacter kobei) in unpolluted water was assessed in microcosms. Significant differences were observed between the microcosms with MPs and those with natural particles (sand), after a 36-day exposure. A significantly higher persistence of the pathogens was registered in microcosms with PE and PET. Our results provide new insights into the plastisphere in non-pollution environments and demonstrate that even in these settings, MPs can facilitate the survival and dissemination of pathogens.

Silver nanoparticles regulate antibiotic resistance genes by shifting bacterial community and generating anti-silver genes in estuarine biofilms

Biofilms are thought to be sinks for antibiotic resistance genes (ARGs) and nanoparticles (NPs), however, studies on the interactions between NPs and ARGs in biofilms are limited. This study focused on the occurrence and regulatory mechanisms of ARGs during the formation of biofilms with continuous treatment of zero-valent silver nanoparticles (Ag0-NPs) and Ag ions at an environmental concentration of 10 µg/L in the Yangtze Estuary. The biofilms could enrich large amounts of Ag, with the highest concentration of 97.60 mg/kg and 111.08 mg/kg in the Ag0-NPs and Ag ions group at 28 days. Compared to the blank at 28 days, the abundance of ARGs was reduced 2.2 times in the Ag0-NPs group, whereas it increased 1.3 times in the Ag ion group. Ag0-NPs and Ag ions induced the production of silver resistance genes (SRGs) or selected bacteria with SRGs in biofilms. Based on machine learning, the bacterial community, SRGs, and Ag concentration were the top three dominant regulators of ARGs, with 27.74 %, 25.57 %, and 17.93 % contributions, respectively. Structural equation modeling revealed that Ag could indirectly regulate ARGs by regulating the bacterial community in the Ag0-NPs group. Metagenomic sequencing further showed that most of the decreased ARGs were hosted by Betaproteobacteria in the Ag0-NPs groups. According to the KEGG pathway database, the possible molecular mechanism of Ag0-NPs/Ag ions regulating ARGs may be through the two-component system (arlS/silS-arlR) and beta-lactam resistance system (mexI-mexV-oprM/oprZ/smeF). Overall, this study provides new insights into the effects of Ag0-NPs at environmental concentrations on the ecological environment, especially regarding the mechanism of regulating ARGs in estuarine biofilms.

In situ real-time pathway to study the polyethylene long-term degradation process by a marine fungus through confocal Raman quantitative imaging

Since plastic waste has become a worldwide pollution problem, studying the ability of marine microorganisms to degrade plastic waste is important. However, conventional methods are unable to in situ real-time study the ability of microorganisms to biodegrade plastics. In recent years, Raman spectroscopy has been widely used in the characterization of plastics as well as in the study of biological metabolism due to its low cost, rapidity, label-free, non-destructive, and water-independent features, which provides us with new ideas to address the above limitations. Here, we have established a method to study the degradation ability of microorganisms on plastics using confocal Raman imaging. Alternaria alternata FB1, a recently reported polyethylene (PE) degrading marine fungus, is used as a model to perform a long-term (up to 274 days) in situ real-time nondestructive inspection of its degradation process. We can prove the degradation of PE plastics from the following two aspects, visualization and analysis of the degradation process based on depth imaging and quantification of the degradation rate by crystallinity calculations. The findings also reveal unprecedented degradation details. The method is important for realizing high-throughput screening of microorganisms with potential to degrade plastics and studying the degradation process of plastics in the future.

Polyvinyl chloride microplastics in the aquatic environment enrich potential pathogenic bacteria and spread antibiotic resistance genes in the fish gut

Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.

Potential environmental risks of field bio/non-degradable microplastic from mulching residues in farmland: Evidence from metagenomic analysis of plastisphere

The plastisphere may act as reservoir of antibiotic resistome, accelerating global antimicrobial resistance dissemination. However, the environmental risks in the plastisphere of field microplastics (MPs) in farmland remain largely unknown. Here, antibiotic resistance genes (ARGs) and virulence factors (VFs) on polyethylene microplastics (PE-MPs) and polybutylene adipate terephthalate and polylactic acid microplastics (PBAT/PLA-MPs) from residues were investigated using metagenomic analysis. The results suggested that the profiles of ARG and VF in the plastisphere of PBAT/PLA-MPs had greater number of detected genes with statistically higher values of diversity and abundance than soil and PE-MP. Procrustes analysis indicated a good fitting correlation between ARG/VF profiles and bacterial community composition. Actinobacteria was the major host for tetracycline and glycopeptide resistance genes in the soil and PE-MP plastisphere, whereas the primary host for multidrug resistance genes changed to Proteobacteria in PBAT/PLA-MP plastisphere. Besides, three human pathogens, Sphingomonas paucimobilis, Lactobacillus plantarum and Pseudomonas aeruginosa were identified in the plastisphere. The PE-MP plastisphere exhibited a higher transfer potential of ARGs than PBAT/PLA-MP plastisphere. This work enhances our knowledge of potential environmental risks posed by microplastic in farmland and provides valuable insights for risk assessment and management of agricultural mulching applications.

Metals and microorganisms in a Maar lake sediment core indicating the anthropogenic impact over last 800 years

A closed Maar lake, receiving mostly atmospheric deposition, offers a unique setting for investigating the impact of human activities on the environment. In this study, we aimed to investigate the historical record of metals in core sediments of Maar Lake in Huguangyan (HGY), Southeast China, and elucidate the possible microbial responses to anthropogenic metal stress. Five stages were divided according to the historical record of metals and corresponding distribution of microbial community, among which Pb and Sn showed a peak value around 1760 CE, indicating the ancient mining and smelting activities. Since the 1980s, a substantial enrichment of metals such as Zn, As, Mo, Cd, Sn, Sb, and Pb was observed, due to the rapid industrial growth in China. In terms of microorganisms, Chloroflexi phylum, particularly dominated by Anaerolineales, showed significant correlations with Pb and Sn, and could potentially serve as indicator species for mining and smelting-related contamination. Desulfarculales and Desulfobacterales were found to be more prevalent in recent period and exhibited positive correlations with anthropogenic metals. Moreover, according to the multivariate regression modeling and variance decomposition analysis, Pb and Sn could regulate Anaerolineales and further pose impact on the carbon cycle; while sulfate-reducing bacteria (SRB) could response to anthropogenic metals and influence sulfur cycle. These findings provide new insights into the interaction between metals and microbial communities over human history.

Toxigenic Vibrio cholerae can cycle between environmental plastic waste and floodwater: Implications for environmental management of cholera

Globally, there has been a significant rise in cholera cases and deaths, with an increase in the number of low- and middle-income countries (LMICs) reporting outbreaks. In parallel, plastic pollution in LMICs is increasing, and has become a major constituent of urban dump sites. The surfaces of environmental plastic pollution can provide a habitat for complex microbial biofilm communities; this so-called 'plastisphere' can also include human pathogens. Under conditions simulating a peri-urban environmental waste pile, we determine whether toxigenic Vibrio cholerae (O1 classical; O1 El Tor; O139) can colonise and persist on plastic following a simulated flooding event. Toxigenic V. cholerae colonized and persisted on plastic and organic waste for at least 14 days before subsequent transfer to either fresh or brackish floodwater, where they can further persist at concentrations sufficient to cause human infection. Taken together, this study suggests that plastics in the environment can act as significant reservoirs for V. cholerae, whilst subsequent transfer to floodwaters demonstrates the potential for the wider dissemination of cholera. Further understanding of how diseases interact with plastic waste will be central for combating infection, educating communities, and diminishing the public health risk of plastics in the environment.

Zinc/carbon nanomaterials inhibit antibiotic resistance genes by affecting quorum sensing and microbial community in cattle manure production

This study used metagenomic sequencing to examine the effects of carbon-based zinc oxide nanoparticles (CZnONPs) and graphene-based zinc oxide nanoparticles (GZnONPs) on quorum sensing (QS), antibiotic resistance genes (ARGs) and microbial community changes during cattle manure production. The manure zinc content was significantly reduced in GZnONPs group. In the QS pathway, the autoinducer gene increases significantly in Control group, while the transporter and repressor genes experience a substantial increase in CZnONPs group. These results contributed to the significantly decreased the abundance of ARGs in GZnONPs group. The co-occurrence network analysis revealed a correlation between core ARGs and QS-related KEGG Orthology or ARGs' hosts, indicating that the selective pressure of zinc influences microbial QS, forming a unique ARG pattern in in vivo anaerobic fermentation. These findings suggest that implementing nutritional regulation in farming practices can serve as a preventive measure to mitigate the potential transmission of ARGs resulting from livestock waste.

Microplastics affect soil bacterial community assembly more by their shapes rather than the concentrations

Polyethylene film mulching is a key technology for soil water retention in dryland agriculture, but the aging of the films can generate a large number of microplastics with different shapes. There exists a widespread misunderstanding that the concentrations of microplastics might be the determinant affecting the diversity and assembly of soil bacterial communities, rather than their shapes. Here, we examined the variations of soil bacteria community composition and functioning under two-year field incubation by four shapes (ball, fiber, fragment and powder) of microplastics along the concentration gradients (0.01%, 0.1% and 1%). Data showed that specific surface area of microplastics was significantly positively correlated with the variations of bacterial community abundance and diversity (r=0.505, p<0.05). The fragment- and fiber-shape microplastics displayed more pronounced interfacial continuity with soil particles and induced greater soil bacterial α-diversity, relative to the powder- and ball-shape ones. Strikingly, microplastic concentrations were not significantly correlated with bacterial community indices (r=0.079, p>0.05). Based on the variations of the βNTI, bacterial community assembly actually followed both stochastic and deterministic processes, and microplastic shapes significantly modified soil biogeochemical cycle and ecological functions. Therefore, the shapes of microplastics, rather than the concentration, significantly affected soil bacterial community assembly, in association with microplastic-soil-water interfaces.

Microplastic biofilm, associated pathogen and antimicrobial resistance dynamics through a wastewater treatment process incorporating a constructed wetland

Microplastics in wastewater are colonized by biofilms containing pathogens and antimicrobial resistance (AMR) genes that can be exported into receiving water bodies. This study investigated establishment and changes in microplastic-associated biofilm and AMR during a conventional full-scale 2100 population equivalent wastewater treatment process combined with a free water surface polishing constructed wetland. Sequential microplastic colonization experiments were conducted at different stages of the wastewater treatment process, including in raw sewage, treated effluent and the constructed wetland. Two scenarios were tested in which the constructed wetland served as either (i) a polishing step or (ii) as primary recipient of sewage inoculated microplastics. Bacterial 16S rRNA gene sequencing was carried out for qualitative bacterial community analysis. qPCR was applied for quantitative analysis of AMR genes (sul1, ermB, tetW, intiI1), bacterial biomass (16S rRNA) and a human fecal marker (HF183). Microbial diversity on microplastics increased with incubation time. The initial sewage-derived biofilm composition changed more significantly in the wastewater effluent compared to the constructed wetland. Pathogen and AMR load decreased by up to two orders of magnitude after coupled conventional and constructed wetland treatment, while less impact was observed when sewage-inoculated microplastic material was directly transferred into the constructed wetland. Aeromonas, Klebsiella, and Streptococcus were key pathogenic genera correlated with AMR in microplastic-associated biofilms. Despite decreasing trends on human pathogens and AMR load along the treatment process, microplastic-associated biofilms were a considerable potential hotspot for AMR (intI1 gene) and accommodated Cyanobacteria and fish pathogens.