[en] Plastic debris are accumulating in the marine environment and aggregate microorganisms that form a new ecosystem called the plastisphere. Better understanding the plastisphere is crucial as it has self-sufficient orga- nization and carries pathogens or organisms that may be involved in the pollutant adsorption and/or plastic degradation. To date, the plastisphere is mainly described at the taxonomic level and the functioning of its microbial communities still remains poorly documented. In this work, metagenomic and metaproteomic analyzes were performed on the plastisphere of polypropylene and polyethylene plastic debris sampled on a pebble beach from the Mediterranean Sea. Our results confirmed that the plastisphere was organized as self-sufficient eco- systems containing highly active primary producers, heterotrophs and predators such as nematode. Interestingly, the chemical composition of the polymer did not impact the structure of the microbial communities but rather influenced the functions expressed. Despite the fact that the presence of hydrocarbon-degrading bacteria was observed in the metagenomes, polymer degradation metabolisms were not detected at the protein level. Finally, hydrocarbon degrader (i.e., Alcanivorax) and pathogenic bacteria (i.e., Vibrionaceae) were observed in the plas- tispheres but were not very active as no proteins involved in polymer degradation or pathogeny were detected. This work brings new insights into the functioning of the microbial plastisphere developed on plastic marine debris.
Research Center/Unit :
STARESO FOCUS - Freshwater and OCeanic science Unit of reSearch - ULiège
Amaral-Zettler, L.A., Zettler, E.R., Mincer, T.J., Ecology of the plastisphere. Nat. Rev. Microbiol. 18:3 (2020), 139–151.
Amin, S.A., Parker, M.S., Armbrust, E.V., Interactions between diatoms and bacteria. Microbiol. Mol. Biol. Rev. 76 (2012), 667–684.
Barnes, D.K.A., Invasions by marine life on plastic debris. Nature 416:April (2002), 808–809.
Bolger, A.M., Lohse, M., Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 (2014), 2114–2120.
Bryant, J.A., Clemente, T.M., Viviani, D.A., Fong, A.A., Diversity and activity of communities inhabiting plastic debris in the north pacific gyre. mSystems, 1(3), 2016.
Buchfink, B., Xie, C., Huson, D.H., Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12:1 (2015), 59–60.
Colwell, R.R., Huq, A., Wachsmuth, I.K., Blake, P.A., Olsvik, O., (eds.) Vibrios in the Environment: Viable but Non-culturable Vibrio cholerae. Vibrio cholerae and Cholera: Molecular to Global Perspectives, 1994, ASM Press, Washington, DC), 117–133.
Cózar, A., Sanz-Martín, M., Martí, E., González-Gordillo, J.I., Ubeda, B., Gálvez, J.Á., et al. Plastic accumulation in the Mediterranean sea. PLoS One, 10(4), 2015.
Debroas, D., Mone, A., Halle, A., Plastics in the North Atlantic garbage patch: a boat-microbe for hitchhikers and plastic degraders. Sci. Total Environ. 599–600 (2017), 1222–1232.
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, 2019, 120899.
Delacuvellerie, A., Benali, S., Cyriaque, V., Moins, S., Raquez, J.-M., Gobert, S., Wattiez, R., Microbial biofilm composition and polymer degradation of compostable and non-compostable plastics immersed in the marine environment. J. Hazard Mater., 126526, 2021 0304-3894.
De Tender, C.A., Devriese, L.I., Haegeman, A., Maes, S., Ruttink, T., Dawyndt, P., Bacterial community profiling of plastic litter in the Belgian part of the North Sea. Environ. Sci. Technol. 49 (2015), 9629–9638.
De Tender, C.A., Devriese, L.I., Haegeman, A., Maes, S., vangeyte, J., Cattrijsse, A., Dawyndt, P., Ruttink, T., The temporal dynamics of bacterial and fungal colonization on plastic debris in the North Sea. Environ. Sci. Technol. 49 (2017), 9629–9638.
Galgani, F., Leaute, J.P., Moguedet, P., Souplet, A., Verin, Y., Carpentier, A., Vilar, J., Litter on the sea floor along European coasts. Mar. Pollut. Bull. 40:6 (2000), 516–527.
Garcés, E., Camp, J., Drifting plastic debris as a potential vector for dispersing Harmful Algal Drifting plastic debris as a potential vector for dispersing Harmful Algal Bloom ( HAB ) species. Sci. Mar. 67:1 (2003), 107–111.
Gay, M., Berthe, F.C., Le Roux, F., Screening of Vibrio isolates to develop an experimental infection model in the Pacific oyster Crassostrea gigas. Dis. Aquat. Org. 59 (2004), 49–56.
Géron, A., Werner, J., Wattiez, R., Lebaron, P., Matallana-Surget, S., Deciphering the functioning of microbial communities: shedding light on the critical steps in metaproteomics. Front. Microbiol., 10, 2019.
Geyer, R., Jambeck, J.R., Law, K.L., Production, use, and fate of all plastics ever made. Sci. Adv., 3, 2017, e1700782.
Glass, E.M., Wilkening, J., Wilke, A., Antonopoulos, D., Meyer, F., Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes. 2010, CSH protocols.
Hammer, Ø., Harper, D.A.T., Ryan, P.D., Paleontological statistics software package for education and data analysis. Palaeontol. Electron. 4:1 (2001), 9–18 7.
Huson, D.H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra, S., et al. MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol., 12, 2016, e1004957.
Kirstein, I.V., Kirmizi, S., Wichels, A., Garin-fernandez, A., Erler, R., Martin, L., Dangerous hitchhikers ? Evidence for potentially pathogenic Vibrio spp. on microplastic particles. Mar. Environ. Res. 120 (2016), 1–8.
Kirstein, I.V., Wichels, A., Krohne, G., Gerdts, G., Mature biofilm communities on synthetic polymers in seawater - specific or general. Mar. Environ. Res. 142 (2018), 147–154 2018.
Krueger, M.C., Harms, H., Schlosser, D., Prospects for microbiological solutions to environmental pollution with plastics. Appl. Microbiol. Biotechnol. 99:21 (2015), 8857–8874.
Le Roux, F., Austin, B., Vibrio splendidus. Thompson, F.L., Austin, B., Swings, J., (eds.) The Vibrios., 2006, American Society for Microbiology Press, Washington, DC, USA, 285–296.
Leroy, B., De Meur, Q., Moulin, C., Wegria, G., Wattiez, R., New insight into the photoheterotrophic growth of the isocytrate lyase-lacking purple bacterium Rhodospirillum rubrum on acetate. Microbiology 161 (2015), 1061–1072.
Munari, C., Scoponi, M., Mistri, M., Plastic debris in the Mediterranean sea : types, occurrence and distribution along adriatic shorelines. Waste Manag., 2017, 10.1016/j.wasman.2017.05.020.
Oberbeckmann, S., Loeder, M.G.J., Gerdts, G., Osborn, A.M., Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters. Microb. Ecol. 90 (2014), 478–492.
Oberbeckmann, S., Osborn, A.M., Duhaime, M.B., Carpenter, E., Smith, K., Colton, J., Yamaji, H., Microbes on a bottle: substrate, season and geography influence community composition of microbes colonizing marine plastic debris. PLoS One, 11(8), 2016, e0159289, 10.1371/journal.pone.0159289.
Oberbeckmann, S., Kreikemeyer, B., Labrenz, M., Environmental factors support the formation of specific bacterial assemblages on microplastics. Front. Microbiol., 8, 2018.
Oberbeckmann, S., Bartosik, D., Huang, S., Werner, J., Hirschfeld, C., Wibberg, D., Heiden, S.E., Bunk, B., et al. Genomic and Proteomic Profiles of Biofilms on Microplastics Are Decoupled from Artificial Surface Properties. 2021, Environmental microbiology.
Ogonowski, M., Motiei, A., Ininbergs, K., Hell, E., Gerdes, Z., Udekwu, K.I., et al. Evidence for selective bacterial community structuring on microplastics. Environ. Microbiol. 20 (2018), 2796–2808.
Pinnell, L.J., Turner, J.W., Turner, J.W., Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment, vol. 10, 2019.
Pinto, M., Langer, T.M., Thorsten, H., Hofmann, T., Herndl, G.J., The composition of bacterial communities associated with plastic biofilms differs between different polymers and stages of biofilm succession. PLoS One, 2019.
Pruitt, K.D., Tatusova, T., Maglott, D.R., NCBI reference sequences ( RefSeq ): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35 (2007), 61–65.
Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., Smyth, G.K., Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, 2015, e47.
Rho, M., Tang, H., Ye, Y., FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res., 38, 2010 e191–e191.
Sabirova, J.S., Becker, A., Lünsdorf, H., Nicaud, J.-M., Timmis, K.M., Golyshin, P.N., Transcriptional profiling of the marine oil-degrading bacterium Alcanivorax borkumensis during growth on n-alkanes. FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Lett. 319:2 (2011), 160–168.
Schneiker, S., dos Santos, V., Bartels, D., et al. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat. Biotechnol. 24 (2006), 997–1004.
Virsek, M.K., Lovsin, M.N., Koren, S., Krzan, A., Peterlin, M., Microplastics as a vector for the transport of the bacterial fi sh pathogen species Aeromonas salmonicida. Mar. Pollut. Bull. 125 (2017), 301–309.
Wang, Y., Naumann, U., Wright, S.T., Warton, D.I., Mvabund – an R package for model-based analysis of multivariate abundance data. Methods Ecol. Evol. 3 (2012), 471–474.
Werner, J., Geron, A., Kerssemakers, J., Matallana-Surget, S., mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation. Biorxiv, 2019.
Zettler, E.R., Mincer, T.J., Amaral-Zettler, L.A., Life in the “plastisphere”: microbial communities on plastics marine debris. Environ. Sci. Technol. 47:13 (2013), 7137–7146.