Metagenomic exploration of microbial and enzymatic traits involved in microplastic biodegradation

Agricultural mulch films are frequently applied to achieve high yield, resulting in large quantities of microplastic (MP) pollution in agroecosystem. However, studies focusing specifically on the diversity of MP-degrading enzymes and related microbial communities have yet to be conducted. Here, we established a soil microcosmic incubation with addition of 5% (w/w) conventional (low-density polyethylene (LDPE)) and biodegradable (blend of polylactic acid (PLA) and polybutylene adipate terephthalate (PBAT)) MPs for incubation 90 days. The DNA samples extracted from soils and plastisphere of MPs were examined by metagenomics and genome binning methods, specifically targeting carbohydrate-active enzymes (CAZymes) and plastic-degrading enzymes (PDZymes). The results revealed that plastisphere of MPs exhibited significantly distinct patterns of CAZymes and PDZymes from soils, and abundances of all examined exoenzymes were higher in plastisphere than those in soils. Plastisphere of LDPE-MPs selectively enriched proteases and alkane monooxygenase (alkB), and required families of carbohydrate-binding module (CBM) to increase the binding of CAZymes with MPs. Dissimilarly, diverse CAZymes with high abundances were observed in the plastisphere of PBAT-PLA MPs and esterases were important indicative PDZymes for PBAT-PLA degradation. The enriched exoenzymes in plastisphere of LDPE-MPs were mainly assigned to Actinobacteria while Proteobacteria with higher abundance in plastisphere of PBAT-PLA MPs containing most indicative exoenzymes. Moreover, a high-quality genome classified as Amycolatopsis japonica was reconstructed and found to contain one or more gene copies of indicative exoenzymes for polyethylene. Two novel genomes classified as Sphingomonas were selectively enriched in plastisphere of PBAT-PLA MPs and contained diverse genes encoding degrading exoenzymes. Taken together, our study highlighted the CAZymes and PDZymes can be exploited as potent microbial strategies for solving MPs pollution in croplands.

Microplastics in the insular marine environment of the Southwest Indian Ocean carry a microbiome including antimicrobial resistant (AMR) bacteria: A case study from Reunion Island

The increasing threats to ecosystems and humans from marine plastic pollution require a comprehensive assessment. We present a plastisphere case study from Reunion Island, a remote oceanic island located in the Southwest Indian Ocean, polluted by plastics. We characterized the plastic pollution on the island's coastal waters, described the associated microbiome, explored viable bacterial flora and the presence of antimicrobial resistant (AMR) bacteria. Reunion Island faces plastic pollution with up to 10,000 items/km2 in coastal water. These plastics host microbiomes dominated by Proteobacteria (80 %), including dominant genera such as Psychrobacter, Photobacterium, Pseudoalteromonas and Vibrio. Culturable microbiomes reach 107 CFU/g of microplastics, with dominance of Exiguobacterium and Pseudomonas. Plastics also carry AMR bacteria including β-lactam resistance. Thus, Southwest Indian Ocean islands are facing serious plastic pollution. This pollution requires vigilant monitoring as it harbors a plastisphere including AMR, that threatens pristine ecosystems and potentially human health through the marine food chain.

Accessing the intrinsic factors of carbonyl index of microplastics: Physical and spectral properties, baseline correction, calculation methods, and their interdependence

Carbonyl index (CI) is a measure of the degradation status of microplastics. While many studies address environmental factors of microplastic degradation, intrinsic factors like physical properties, spectral properties, baseline correction, and CI calculation methods are less explored. This research focused on these aspects using surface seawater samples. We found that color and shape have limited dependence on particle size or signal-to-noise ratio (SNR). Baseline correction can significantly alter CI values, with the direction of the shift depending on the methods used. Additionally, most CI values before and after baseline correction and those calculated using different methods tend to be strongly correlated. Using the selected CI calculation methods, we found that CI values varied significantly by shape and color. CI's relation to the similarity between the sample and its pristine form suggests an alternative degradation measure. Our findings emphasize the need for standardized CI calculation methods.

"Omics" Techniques Used in Marine Biofouling Studies

Biofouling is the growth of organisms on wet surfaces. Biofouling includes micro- (bacteria and unicellular algae) and macrofouling (mussels, barnacles, tube worms, bryozoans, etc.) and is a major problem for industries. However, the settlement and growth of some biofouling species, like oysters and corals, can be desirable. Thus, it is important to understand the process of biofouling in detail. Modern "omic" techniques, such as metabolomics, metagenomics, transcriptomics, and proteomics, provide unique opportunities to study biofouling organisms and communities and investigate their metabolites and environmental interactions. In this review, we analyze the recent publications that employ metagenomic, metabolomic, and proteomic techniques for the investigation of biofouling and biofouling organisms. Specific emphasis is given to metagenomics, proteomics and publications using combinations of different "omics" techniques. Finally, this review presents the future outlook for the use of "omics" techniques in marine biofouling studies. Like all trans-disciplinary research, environmental "omics" is in its infancy and will advance rapidly as researchers develop the necessary expertise, theory, and technology.

Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere"

Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment.

Ecotoxicological and health implications of microplastic-associated biofilms: a recent review and prospect for turning the hazards into benefits

Microplastics (MPs), over the years, have been regarded as a severe environmental nuisance with adverse effects on our ecosystem as well as human health globally. In recent times, microplastics have been reported to support biofouling by genetically diverse organisms resulting in the formation of biofilms. Biofilms, however, could result in changes in the physicochemical properties of microplastics, such as their buoyancy and roughness. Many scholars perceived the microplastic-biofilm association as having more severe consequences, providing evidence of its effects on the environment, aquatic life, and nutrient cycles. Furthermore, other researchers have shown that microplastic-associated biofilms have severe consequences on human health as they serve as vectors of heavy metals, toxic chemicals, and antibiotic resistance genes. Despite what is already known about their adverse effects, other interesting avenues are yet to be fully explored or developed to turn the perceived negative microplastic-biofilm association to our advantage. The major inclusion criteria for relevant literature were that it must focus on microplastic association biofilms, while we excluded papers solely on biofilms or microplastics. A total of 242 scientific records were obtained. More than 90% focused on explaining the environmental and health impacts of microplastic-biofilm association, whereas only very few studies have reported the possibilities and opportunities in turning the microplastic biofilms association into benefits. In summary, this paper concisely reviews the current knowledge of microplastic-associated biofilms and their adverse consequences and further proposes some approaches that can be developed to turn the negative association into positive.