Windsor, F. M. et al. A catchment-scale perspective of plastic pollution. Glob. Change Biol. 25, 1207–1221 (2019).
Boucher, J. & Billard, G. The challenges of measuring plastic pollution. Field Actions Sci. Rep. J. Field Actions 19, 68–75 (2019).
Jambeck, J. R. et al. Plastic waste inputs from land into the ocean. Science 347, 768–771 (2015).
Worm, B., Lotze, H. K., Jubinville, I., Wilcox, C. & Jambeck, J. Plastic as a persistent marine pollutant. Annu. Rev. Environ. Resour. 42, 1–26 (2017).
Amaral-Zettler, L. A., Zettler, E. R. & Mincer, T. J. Ecology of the plastisphere. Nat. Rev. Microbiol. 18, 139–151 (2020).
Zettler, E. R., Mincer, T. J. & Amaral-Zettler, L. A. Life in the “plastisphere”: microbial communities on plastic marine debris. Environ. Sci. Technol. 47, 7137–7146 (2013).
Dussud, C. et al. Evidence of niche partitioning among bacteria living on plastics, organic particles and surrounding seawaters. Environ. Pollut. 236, 807–816 (2018).
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. & Willerslev, E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 21, 2045–2050 (2012).
De Tender, C. A. et al. Bacterial community profiling of plastic litter in the Belgian part of the North Sea. Environ. Sci. Technol. 49, 9629–9638 (2015).
Santos, A., van Aerle, R., Barrientos, L. & Martinez-Urtaza, J. Computational methods for 16S metabarcoding studies using Nanopore sequencing data. Comput. Struct. Biotechnol. J. 18, 296–305 (2020).
Jacquin, J. et al. Microbial ecotoxicology of marine plastic debris: a review on colonization and biodegradation by the ‘plastisphere’. Front. Microbiol. 10, 865 (2019).
Bleidorn, C. Third generation sequencing: technology and its potential impact on evolutionary biodiversity research. Syst. Biodivers. 14, 1–8 (2016).
Krehenwinkel, H. et al. Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale. GigaScience 8, giz006 (2019).
Pawlowski, J. et al. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 10, e1001419 (2012).
Leray, M. & Knowlton, N. Censusing marine eukaryotic diversity in the twenty-first century. Philos. Trans. R. Soc. B Biol. Sci. 371, 20150331 (2016).
Piganeau, G., Eyre-Walker, A., Grimsley, N. & Moreau, H. How and why DNA barcodes underestimate the diversity of microbial eukaryotes. PLoS ONE 6, e16342 (2011).
Saunders, G. W. & Kucera, H. An evaluation of rbcL, tufA, UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae. Cryptogamie Algologie 31, 487 (2010).
Schoch, C. L. et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. 109, 6241–6246 (2012).
Hebert, P. D., Cywinska, A., Ball, S. L. & Dewaard, J. R. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. Ser. B Biol. Sci. 270, 313–321 (2003).
Bahram, M., Anslan, S., Hildebrand, F., Bork, P. & Tedersoo, L. Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment. Environ. Microbiol. Rep. 11, 487–494 (2019).
Debeljak, P. et al. Extracting DNA from ocean microplastics: a method comparison study. Anal. Methods 9, 1521–1526 (2017).
Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697–703 (1991).
Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).
Hadziavdic, K. et al. Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS ONE 9, e87624 (2014).
Vieira, H. H. et al. tufA gene as molecular marker for freshwater Chlorophyceae. Algae 31, 155–165 (2016).
De Beeck, M. O. et al. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. PLoS ONE 9, e97629 (2014).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34, 2666–2669 (2018).
Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864 (2011).
Baloğlu, B. et al. A workflow for accurate metabarcoding using nanopore MinION sequencing. BioRxiv. https://doi.org/10.1101/2020.05.21.108852 (2020).
Srivathsan, A. et al. A Min IONTM-based pipeline for fast and cost-effective DNA barcoding. Mol. Ecol. Resour. 18, 1035–1049 (2018).
Maestri, S. et al. A rapid and accurate MinION-based workflow for tracking species biodiversity in the field. Genes 10, 468 (2019).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Voorhuijzen-Harink, M. M. et al. Toward on-site food authentication using nanopore sequencing. Food Chem. X2 (2019).
Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, 259–264 (2019).
Sauvage, T., Schmidt, W. E., Suda, S. & Fredericq, S. A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA. BMC Ecol. 16, 8 (2016).
Heller, P., Casaletto, J., Ruiz, G. & Geller, J. A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator. Sci. Data 5, 180156 (2018).
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Andersen, K. S., Kirkegaard, R. H., Karst, S. M. & Albertsen, M. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. BioRxiv, 299537 (2018).
R Core Team. R: a language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, 2014).
Mafune, K. K., Godfrey, B. J., Vogt, D. J. & Vogt, K. A. A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer. BioTechniques 68, 72–78 (2019).
Herbst, F. A. et al. Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP). Proteomics 13, 2910–2920 (2013).
Jin, H. M., Kim, J. M., Lee, H. J., Madsen, E. L. & Jeon, C. O. Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil-contaminated coastal sediment. Environ. Sci. Technol. 46, 7731–7740 (2012).
Lin, X., Yang, B., Shen, J. & Du, N. Biodegradation of crude oil by an Arctic psychrotrophic bacterium Pseudoalteromomas sp. P29. Curr. Microbiol. 59, 341–345 (2009).
Hedlund, B. P. & Staley, J. T. Isolation and characterization of Pseudoalteromonas strains with divergent polycyclic aromatic hydrocarbon catabolic properties. Environ. Microbiol. 8, 178–182 (2006).
Schneiker, S. et al. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat. Biotechnol. 24, 997–1004 (2006).
Yakimov, M. M. et al. Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int. J. Syst. Evolut. Microbiol. 48, 339–348 (1998).
Delacuvellerie, A., Cyriaque, V., Gobert, S., Benali, S. & Wattiez, R. The plastisphere in marine ecosystem hosts potential specific microbial degraders including Alcanivorax borkumensis as a key player for the low-density polyethylene degradation. J. Hazard. Mater. 380, 120899 (2019).
Wangensteen, O. S. & Turon, X. Metabarcoding techniques for assessing biodiversity of marine animal forests. Mar. Anim. For. Ecol. Benthic Biodivers. Hotspots 1, 445–503 (2017).
Truelove, N. K., Andruszkiewicz, E. A. & Block, B. A. A rapid environmental DNA method for detecting white sharks in the open ocean. Methods Ecol. Evol. 10, 1128–1135 (2019).
Gillespie, R. et al. Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale. GigaScience 8, giz006 (2019).
Kono, N. & Arakawa, K. Nanopore sequencing: review of potential applications in functional genomics. Dev. Growth Differ. 61, 316–326 (2019).
Nair, S. A., Devassy, V., Dwivedi, S. & Selvakumar, R. Preliminary observations on tar-like material observed on some beaches. Curr. Sci. India 41, 766–767 (1972).
Kasai, Y. et al. Predominant growth of Alcanivorax strains in oil-contaminated and nutrient-supplemented sea water. Environ. Microbiol. 4, 141–147 (2002).
Reisser, J. et al. Millimeter-sized marine plastics: a new pelagic habitat for microorganisms and invertebrates. PLoS ONE 9, e100289 (2014).
Masó, M., Fortuño, J. M., de Juan, S. & Demestre, M. Microfouling communities from pelagic and benthic marine plastic debris sampled across Mediterranean coastal waters. Sci. Mar. 80, 117–127 (2016).
Wang, S. et al. The interactions between microplastic polyvinyl chloride and marine diatoms: physiological, morphological, and growth effects. Ecotoxicol. Environ. Saf. 203, 111000 (2020).
De Tender, C. et al. A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities. Anal. Methods 9, 2132–2143 (2017).
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