Plastic pollution is a serious global problem, with more than 12 million tonnes of plastic waste entering the oceans every year. Plastic debris can have considerable impacts on microbial community structure and functions in marine environments, and has been associated with an enrichment in pathogenic bacteria and antimicrobial resistance (AMR) genes. However, our understanding of these impacts is largely restricted to microbial assemblages on plastic surfaces. It is therefore unclear whether these effects are driven by the surface properties of plastics, providing an additional niche for certain microbes residing in biofilms, and/or chemicals leached from plastics, the effects of which could extend to surrounding planktonic bacteria. Here, we examine the effects of polyvinyl chloride (PVC) plastic leachate exposure on the relative abundance of genes associated with bacterial pathogenicity and AMR within a seawater microcosm community. We show that PVC leachate, in the absence of plastic surfaces, drives an enrichment in AMR and virulence genes. In particular, leachate exposure significantly enriches AMR genes that confer multidrug, aminoglycoside and peptide antibiotic resistance. Additionally, enrichment of genes involved in the extracellular secretion of virulence proteins was observed among pathogens of marine organisms. This study provides the first evidence that chemicals leached from plastic particles alone can enrich genes related to microbial pathogenesis within a bacterial community, expanding our knowledge of the environmental impacts of plastic pollution with potential consequences for human and ecosystem health.
Abstract With ongoing climate change, research into the biological changes occurring in particularly vulnerable ecosystems, such as Antarctica, is critical. The Totten Glacier region, Sabrina Coast, is currently experiencing some of the highest rates of thinning across all East Antarctica. An assessment of the microscopic organisms supporting the ecosystem of the marginal sea‐ice zone over the continental rise is important, yet there is a lack of knowledge about the diversity and distribution of these organisms throughout the water column, and their occurrence and/or preservation in the underlying sediments. Here, we provide a taxonomic overview of the modern and ancient marine bacterial and eukaryotic communities of the Totten Glacier region, using a combination of 16S and 18S rRNA amplicon sequencing (modern DNA) and shotgun metagenomics (sedimentary ancient DNA, sed aDNA). Our data show considerable differences between eukaryote and bacterial signals in the water column versus the sediments. Proteobacteria and diatoms dominate the bacterial and eukaryote composition in the upper water column, while diatoms, dinoflagellates, and haptophytes notably decrease in relative abundance with increasing water depth. Little diatom sed aDNA is preserved in the sediments, which are instead dominated by Proteobacteria and Retaria. We compare the diatom microfossil and sed aDNA record and link the weak preservation of diatom sed aDNA to DNA degradation while sinking through the water column to the seafloor. This study provides the first assessment of DNA transfer from ocean waters to sediments and an overview of the microscopic communities occurring in the climatically important Totten Glacier region.
Abstract Background Anchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood. Results Here, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling. Conclusion These findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments.
Additional file 2: Table S1. Flow cytometric counts (cells mL-1) and forward scatter (FSC) of Synechococcus and two photosynthetic eukaryotic populations along with the ratio of the Synechococcus to total photosynthetic eukaryote populations. Table S2. Flow cytometric counts (cells mL-1) of bacterial and viral subpopulations and total populations along with the ratio of total virus populations to total bacterial populations. Table S3. Statistics for changes in flow cytometrically-quantified population abundances (count) of various populations at experimental day 6 for different treatments. Table S4. Measurements of photosynthetic efficiency for each treatment during the 6 days of the experiment. Table S5. (a) Concentrations of all of the metal tested with ICP-MS. Metal concentration is espressed in mg/L. Highlighted in green are the metal for which the concentration was above the limit of the detection for at least one of the treatment or for the seawater control. ICP-MS analysis was performed at the Elemental Analysis Facility at the Southern Cross University in Lismore,NSW (Australia) an accredited NATA facility for the analysis of seawater samples. Methods reference has the code for the NATA standard methodology followed. T0 indicates samples that were collected at the beginning of the experiment, day 6 samples that were collected at the end of the experiment . *PQL= Minimum dectection limit. (b) Concentrations of all of the metal tested with ICP-MS for the preliminary batch of PVC. Metal concentration is espressed in ug/L. Highlighted in green are the metal for which the concentration was above the limit of the detection for at least one of the replicate. ICP-MS analysis was performed at the Elemental Analysis Facility at the Southern Cross University in Lismore,NSW (Australia) an accredited NATA facility for the analysis of seawater samples. Table S6. Statistical test results for community profile groupings based on amplicon analyses. Table S7. Alpha diversity calculations for the bacterial and eukaryotic communities based on amplicon analyses. Table S8. DESeq2 results for the bacterial community. Only results with an alpha < 0.01 were chosen. Table S9. Anova followed by pairwise t-test FDR corrected calculated for the photosynthetic groups identified based on cyanobacteria and plastid sequences from 16S rRNA. Table S10. DESeq2 results for the eukaryotic community. Only results with an alpha < 0.01 were chosen. Table S11. Taxonomic assignment of reads for genes in the bacterial metagenomes and the statistical analyses of the taxonomic groups in each treatment. Table S12. DESeq2 results for PVC10 vs SW on day 6. Only KEGG orthologs with log2Fold change >2 and < -2 are displayed. Table S13. DESeq2 results for PVC1 vs SW on day 6. Only KEGG orthologs with log2Fold change >2 and < -2 are displayed. Table S14. DESeq2 results for ZnH vs SW on day 6. Only KEGG orthologs with log2Fold change >2 and < -2 are displayed. Table S15. DESeq2 results for ZnL vs SW on day 6. Only KEGG orthologs with log2Fold change >2 and < -2 are displayed. Table S16. Pairwise comparison of the abundance of integrase genes in the different treatments. Only significant comparisons (p.adj < 0.05) are reported here. Significance was calculated with an ANOVA followed by a pairwise t-test and the p value FDR adjusted. n1 and n2 represents the number of replicates for treatment group 1 and group 2 respectively. Table S17. (a) Summary information on the assembled metagenome-assembled genomes (bins) and MAGs coverage in the different samples. (b) Pairwise test on the MAGs distribution between the different treatments, p-value was calculate in R with the r-statix package and FDR corrected. Table S18. Pairwise comparison of the coverage of almost complete metabolic pathway modules of the identified MAGs (completion >49%) across the different treatments. Significance was calculated with an ANOVA followed by a pairwise t-test and the pvalue FDR adjusted. n1 and n2 represents the number of replicates for group 1 and group 2 respectively.
Abstract Plastic pollution is a serious global problem, with more than 12 million tonnes of plastic waste entering the oceans every year. Plastic debris can have considerable impacts on microbial community structure and functions in marine environments, and has been associated with an enrichment in pathogenic bacteria and antimicrobial resistance (AMR) genes. However, our understanding of these impacts is largely restricted to microbial assemblages on plastic surfaces. It is therefore unclear whether these effects are driven by the surface properties of plastics, providing an additional niche for certain microbes residing in biofilms, and/or chemicals leached from plastics, the effects of which could extend to surrounding planktonic bacteria. Here, we examine the effects of polyvinyl chloride (PVC) plastic leachate exposure on the relative abundance of genes associated with bacterial pathogenicity and AMR within a seawater microcosm community. We show that PVC leachate, in the absence of plastic surfaces, drives an enrichment in AMR and virulence genes. In particular, leachate exposure significantly enriches AMR genes that confer multidrug, aminoglycoside and peptide antibiotic resistance. Additionally, enrichment of genes involved in the extracellular secretion of virulence proteins was observed among pathogens of marine organisms. This study provides the first evidence that chemicals leached from plastic particles alone can enrich genes related to microbial pathogenesis within a bacterial community, expanding our knowledge of the environmental impacts of plastic pollution with potential consequences for human and ecosystem health.
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