African Journal of
Microbiology Research

  • Abbreviation: Afr. J. Microbiol. Res.
  • Language: English
  • ISSN: 1996-0808
  • DOI: 10.5897/AJMR
  • Start Year: 2007
  • Published Articles: 5238

Full Length Research Paper

16S rRNA gene sequence analysis of the microbial community on microplastic samples from the North Atlantic and Great Pacific Garbage Patches

Dkawlma Tora
  • Dkawlma Tora
  • Institute of Engineering and Marine Sciences, Atlantic Technical University, Cabo Verde, Cape Verde.
  • Google Scholar
Ute Hentschel
  • Ute Hentschel
  • Research Unit Marine Symbioses,GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany.
  • Google Scholar
Stefan Lips
  • Stefan Lips
  • Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany.
  • Google Scholar
Mechthild Schmitt-Jansen
  • Mechthild Schmitt-Jansen
  • Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany.
  • Google Scholar
Erik Borchert
  • Erik Borchert
  • Research Unit Marine Symbioses,GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany.
  • Google Scholar


  •  Received: 30 December 2022
  •  Accepted: 30 March 2023
  •  Published: 31 May 2023

References

Abraham WR, Rohde M (2014). The Family Hyphomonadaceae. The Prokaryotes 8:283-299.
Crossref

 

Ahmed W, Zhang Q, Lobos A, Senkbeil J, Sadowsky MJ, Harwood VJ, Saeidi N, Marinoni O, Ishii S (2018). Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters. Environment International 116:308-318.
Crossref

 

Amaral-Zettler LA, Zettler ER, Slikas B, Boyd GD, Melvin DW, Morrall CE, Proskurowski G, Mincer TJ (2015). The biogeography of the Plastisphere: implications for policy. Frontiers in Ecology and the Environment 13(10):541-546.
Crossref

 

Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecology 26(1):32-46.
Crossref

 

Bodour AA, Wang JM, Brusseau ML, Maier RM (2003). Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system. Environmental Microbiology 5(10):888-895.
Crossref

 

Bogan BW, Sullivan WR, Kayser KJ, Derr K, Aldrich HC, Paterek JR (2003). Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils. International Journal of Systematic and Evolutionary Microbiology 53(5):1389-1395.
Crossref

 

Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG (2013). Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods 10(1):57-59.
Crossref

 

Busch K, Taboada S, Riesgo A, Koutsouveli V, Ríos P, Cristobo J, Franke A, Getzlaff K, Schmidt C, Biastoch A and Hentschel U (2021). Population connectivity of fan-shaped sponge holobionts in the deep Cantabrian Sea. Deep-Sea Research Part I: Oceanographic Research Papers 167:103427.
Crossref

 

Cacciari I, Quatrini P, Zirletta G, Mincione E, Vinciguerra V, Lupattelli P, Giovannozzi Sermanni G (1993). Isotactic polypropylene biodegradation by a microbial community: physicochemical characterization of metabolites produced. Applied and Environmental Microbiology 59(11):3695-3700.
Crossref

 

Callahan BJ, McMurdie PJ, Holmes SP (2017). Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME Journal 11(12):2639-2643.
Crossref

 

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13(7):581-583.
Crossref

 

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences 108(supplement_1):4516-4522.
Crossref

 

Chaineau C, Morel J, Dupont J, Bury E, Oudot J (1999). Comparison of the fuel oil biodegradation potential of hydrocarbon-assimilating microorganisms isolated from a temperate agricultural soil. Science of The Total Environment 227(2-3):237-247.
Crossref

 

Coons AK, Busch K, Lenz M, Hentschel U, Borchert E (2021). Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics. PeerJ 9:e12135.
Crossref

 

Dang H, Lovell CR (2016). Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiology and Molecular Biology Reviews 80(1):91-138.
Crossref

 

Danko AS, Luo M, Bagwell CE, Brigmon RL, Freedman DL (2004). Involvement of linear plasmids in aerobic biodegradation of vinyl chloride. Applied and Environmental Microbiology 70(10):6092-6097.
Crossref

 

Dashti N, Khanafer M, El-Nemr I, Sorkhoh N, Ali N, Radwan S (2009). The potential of oil-utilizing bacterial consortia associated with legume root nodules for cleaning oily soils. Chemosphere 74(10):1354-1359.
Crossref

 

Desjardins P, Conklin D (2010). NanoDrop Microvolume Quantitation of Nucleic Acids. Journal of Visualized Experiments 45:e2565.
Crossref

 

Dris R, Gasperi J, Saad M, Mirande C, Tassin B (2016). Synthetic fibers in atmospheric fallout: A source of microplastics in the environment? Marine Pollution Bulletin 104(1-2):290-293.
Crossref

 

Eriksen M, Lebreton LCM, Carson HS, Thiel M, Moore CJ, Borerro JC, Galgani F, Ryan PG, Reisser J (2014). Plastic Pollution in the World's Oceans: More than 5 Trillion Plastic Pieces Weighing over 250,000 Tons Afloat at Sea. PLoS ONE 9(12):e111913.
Crossref

 

Floodgate GD (1984). The fate of petroleum in marine ecosystems. In Petroleum Microbiology. RM Atlas (ed.). New York: MacMillan, pp. 355-397.

 

Gauthier MJ, Lafay B, Christen R, Fernandez L, Acquaviva M, Bonin P, Bertrand JC (1992). Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a New, Extremely Halotolerant, Hydrocarbon-Degrading Marine Bacterium. International Journal of Systematic Bacteriology 42(4):568-576.
Crossref

 

Golyshin PN, Chernikova TN, Abraham WR, Lünsdorf H, Timmis KN, Yakimov MM (2002). Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. International Journal of Systematic and Evolutionary Microbiology 52(3):901-911.
Crossref

 

González JM, Pinhassi J, Fernández-Gómez B, Coll-Lladó M, González-Velázquez M, Puigbò P, Jaenicke S, Gómez-Consarnau L, Fernàndez-Guerra A, Goesmann A, Pedrós-Alió C (2011). Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134. Applied and Environmental Microbiology 77(24):8676-8686.
Crossref

 

Greenpeace (2021). 34 Plastic Bans in Africa | A Reality Check.

View

 

Griffin GJL (2007). Degradation of polyethylene in compost burial. In Journal of Polymer Science: Polymer Symposia (57(1):281-286). New York: Wiley Subscription Services, Incorporation. A Wiley Company.
Crossref

 

Gupta A, Saha A, Sar P (2021). Thermoplasmata and Nitrososphaeria as dominant archaeal members in acid mine drainage sediment of Malanjkhand Copper Project, India. Archives of Microbiology 203(4):1833-1841.
Crossref

 

Hakkarainen M, Albertsson AC (2004). Environmental degradation of polyethylene. Long Term Properties of Polyolefins 177-200.
Crossref

 

Hamamura N, Arp DJ (2000). Isolation and characterization of alkane-utilizing Nocardioidessp. strain CF8. FEMS Microbiology Letters 186(1):21-26.
Crossref

 

Harrison JP, Sapp M, Schratzberger M, Osborn AM (2011). Interactions Between Microorganisms and Marine Microplastics: A Call for Research. Marine Technology Society Journal 45(2):12-20.
Crossref

 

Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K (2007). Characterization of Diverse Hydrocarbon-Degrading Bacteria Isolated from Indonesian Seawater. Microbes and Environments 22(4):412-415.
Crossref

 

Hedlund BP, Staley JT (2001). Vibrio cyclotrophicus sp. nov., a polycyclic aromatic hydrocarbon (PAH)-degrading marine bacterium. International Journal of Systematic and Evolutionary Microbiology 51(1):61-66.
Crossref

 

Horn DA, Granek EF, Steele CL (2019). Effects of environmentally relevant concentrations of microplastic fibers on Pacific mole crab (Emerita analoga) mortality and reproduction. Limnology and Oceanography Letters 5(1):74-83.
Crossref

 

Ilori MO, Amund D, Robinson GK (2000). Ultrastructure of two oil-degrading bacteria isolated from the tropical soil environment. Folia Microbiologica 45(3):259-262.
Crossref

 

Iwabuchi N, Sunairi M, Urai M, Itoh C, Anzai H, Nakajima M, Harayama S (2002). Extracellular Polysaccharides of Rhodococcus rhodochrous S-2 Stimulate the Degradation of Aromatic Components in Crude Oil by Indigenous Marine Bacteria. Applied and Environmental Microbiology 68(5):2337-2343.
Crossref

 

Jambeck JR, Geyer R, Wilcox C, Siegler TR, Perryman M, Andrady A, Narayan R, Law KL (2015). Plastic waste inputs from land into the ocean. Science 347(6223):768-771.
Crossref

 

Katoh K, Standley DM (2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution 30(4):772-780.
Crossref

 

Kirstein IV, Wichels A, Gullans E, Krohne G, Gerdts G (2019). The Plastisphere - Uncovering tightly attached plastic "specific" microorganisms. PLOS ONE 14(4):e0215859.
Crossref

 

Kodama Y, Stiknowati LI, Ueki A, Ueki K, Watanabe K (2008). Thalassospira tepidiphila sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from seawater. International Journal of Systematic and Evolutionary Microbiology 58(3):711-715.
Crossref

 

Kruskal JB (1964). Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29(1):1-27.
Crossref

 

Le Petit J, Bertrand JC, N'Guyen MH, Tagger S (1975). Etude taxonomique et physiologique de bactéries se développant sur hydrocarbures en milieu marin [On the taxonomy and physiology of bacteria utilizing hydrocarbons in the sea (author's transl)]. Annales de Microbiologie 126(3):367-380.

 

Li G, He Z, An T, Zeng X, Sheng G, Fu J (2008). Comparative study of the elimination of toluene vapours in twin biotrickling filters using two microorganisms Bacillus cereus S1 and S2. Journal of Chemical Technology and Biotechnology 83(7):1019-1026.
Crossref

 

Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71(12):8228-8235.
Crossref

 

Lusher A, McHugh M, Thompson R (2013). Occurrence of microplastics in the gastrointestinal tract of pelagic and demersal fish from the English Channel. Marine Pollution Bulletin 67(1-2):94-99.
Crossref

 

Mato Y, Isobe T, Takada H, Kanehiro H, Ohtake C, Kaminuma T (2001). Plastic Resin Pellets as a Transport Medium for Toxic Chemicals in the Marine Environment. Environmental Science and Technology 35(2):318-324.
Crossref

 

McIlroy SJ, Nielsen PH (2014). The Family Saprospiraceae. The Prokaryotes, pp. 863-889.
Crossref

 

Meyer S, Moser R, Neef A, Stahl U, Kämpfer P (1999). Differential detection of key enzymes of polyaromatic-hydrocarbon-degrading bacteria using PCR and gene probes. Microbiology 145(7):1731-1741.
Crossref

 

Mishamandani S, Gutierrez T, Aitken MD (2014). DNA-based stable isotope probing coupled with cultivation methods implicates Methylophaga in hydrocarbon degradation. Frontiers in Microbiology 5.
Crossref

 

Muyzer G, de Waal EC, Uitterlinden AG (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59(3):695-700.
Crossref

 

Oberbeckmann S, Labrenz M (2020). Marine Microbial Assemblages on Microplastics: Diversity, Adaptation, and Role in Degradation. Annual Review of Marine Science 12(1):209-232.
Crossref

 

Oberbeckmann S, Kreikemeyer B and Labrenz M (2018). Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics. Frontiers in Microbiology, 8.
Crossref

 

Oberbeckmann S, Loeder MG, Gerdts G, Osborn AM (2014). Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters. FEMS Microbiology Ecology 90(2):478-492.
Crossref

 

Okada M (2002). Chemical syntheses of biodegradable polymers. Progress in Polymer Science 27(1):87-133.
Crossref

 

Ozaki S, Kishimoto N, Fujita T (2006). Isolation and Phylogenetic Characterization of Microbial Consortia able to Degrade Aromatic Hydrocarbons at High Rates. Microbes and Environments 21(1):44-52.
Crossref

 

Kershaw PJ, CM Rochman (2014). Sources, fate and effects of microplastics in the marine environment: part 2 of a global assessment. Reports and Studies - IMO/FAO/Unesco-IOC/WMO/IAEA/UN/UNEP Joint Group of Experts on the Scientific Aspects of Marine Environmental Protection (GESAMP) Eng No. 93.

View

 

Peeb A, Dang NP, Truu M, Nõlvak H, Petrich C, Truu J (2022). Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice. Microorganisms 10(2):328.
Crossref

 

Pinnell LJ, Turner JW (2019). Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment. Frontiers in Microbiology 10.
Crossref

 

Pinto M, Langer TM, Hüffer T, Hofmann T, Herndl GJ (2019). The composition of bacterial communities associated with plastic biofilms differs between different polymers and stages of biofilm succession. PLOS ONE 14(6):e0217165.
Crossref

 

Price MN, Dehal PS, Arkin AP (2009). FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. Molecular Biology and Evolution 26(7):1641-1650.
Crossref

 

Price MN, Dehal PS, Arkin AP (2010). FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE 5(3):e9490.
Crossref

 

Purohit J, Chattopadhyay A, Teli B (2020). Metagenomic Exploration of Plastic Degrading Microbes for Biotechnological Application. Current Genomics 21(4):253-270.
Crossref

 

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41(D1):D590-D596.
Crossref

 

Ritchie H, Roser M (2018). Plastic Pollution. Published online at OurWorldInData.org. Retrieved from:

View

 

Saadoun I, Al-Akhras MA, Abu-Ashour J (1999). Bacterial degradation of hydrocarbons as evidenced by respirometric analysis. Microbios 100(395):19-25.

 

Salta M, Wharton JA, Blache Y, Stokes KR, Briand JF (2013). Marine biofilms on artificial surfaces: structure and dynamics. Environmental Microbiology 15(11):2879-2893.
Crossref

 

Sivan A, Szanto M, Pavlov V (2006). Biofilm development of the polyethylene-degrading bacterium Rhodococcus ruber. Applied Microbiology and Biotechnology 72(2):346-352.
Crossref

 

Stucki G, Alexander M (1987). Role of dissolution rate and solubility in biodegradation of aromatic compounds. Applied and Environmental Microbiology 53(2):292-297.
Crossref

 

Szoboszlay S, Atzel B, Kukolya J, Toth EM, Marialigeti K, Schumann P, Kriszt B (2008). Chryseobacterium hungaricum sp. nov., isolated from hydrocarbon-contaminated soil. International Journal of Systematic and Evolutionary Microbiology 58(12):2748-2754.
Crossref

 

Thompson RC, Olsen Y, Mitchell RP, Davis A, Rowland SJ, John AW, McGonigle D and Russell AE (2004). Lost at sea: where is all the plastic? Science (New York, N.Y.) 304(5672):838.
Crossref

 

Tsuchii A (1980). Microbial degradation of polyethylene oligomers. Report of Fermentation Research Institute 55:35-40.

 

Vaksmaa A, Knittel K, Abdala Asbun A, Goudriaan M, Ellrott A, Witte HJ, Vollmer I, Meirer F, Lott C, Weber M, Engelmann JC, Niemann H (2021). Microbial Communities on Plastic Polymers in the Mediterranean Sea. Frontiers in Microbiology 12.
Crossref

 

Wang W, Zhang R, Shan D, Shao Z (2014). Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow sea, China. Applied microbiology and Biotechnology 98(16):7253-7269.
Crossref

 

Wang ZM, Wagner J, Ghosal S, Bedi G, Wall S (2017). SEM/EDS and optical microscopy analyses of microplastics in ocean trawl and fish guts. Science of The Total Environment 603-604, 616-626.
Crossref

 

Willumsen P, Karlson U, Stackebrandt E, Kroppenstedt RM (2001). Mycobacterium frederiksbergense sp. nov., a novel polycyclic aromatic hydrocarbon-degrading Mycobacterium species. International Journal of Systematic and Evolutionary Microbiology 51(Pt 5):1715-1722.
Crossref

 

Wright RJ, Erni-Cassola G, Zadjelovic V, Latva M, Christie-Oleza JA (2020). Marine Plastic Debris: A New Surface for Microbial Colonization. Environmental Science and Technology 54(19):11657-11672.
Crossref

 

Yakimov MM, Denaro R, Genovese M, Cappello S, D'Auria G, Chernikova TN, Timmis KN, Golyshin PN and Giluliano L (2005). Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Environmental Microbiology 7(9):1426-1441.
Crossref

 

Yakimov MM, Giuliano L, Gentile G, Crisafi E, Chernikova TN, Abraham WR, Lünsdorf H, Timmis KN and Golyshin PN (2003). Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water. International Journal of Systematic and Evolutionary Microbiology 53(Pt 3):779-785.
Crossref

 

Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lünsdorf H andTimmis KN (1998). Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. International Journal of Systematic Bacteriology 48(Pt 2):339-348.
Crossref

 

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W and Glöckner FO (2014). The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Research 42(D1):D643-D648.
Crossref

 

Yue W, Yin CF, Sun L, Zhang J, Xu Y, Zhou NY (2021). Biodegradation of bisphenol-A polycarbonate plastic by Pseudoxanthomonas sp. strain NyZ600. Journal of Hazardous Materials 416:125775.
Crossref

 

Zettler ER, Mincer TJ, Amaral-Zettler LA (2013). Life in the "Plastisphere": Microbial Communities on Plastic Marine Debris. Environmental Science and Technology 47(13):7137-7146.
Crossref

 

Zheng Y, Yanful EK, Bassi AS (2005). A review of plastic waste biodegradation. Critical reviews in Biotechnology 25(4):243-250.
Crossref

 

Zobell CE (1946). Action of Microorganisms on Hydrocarbons. Bacteriological Reviews 10(1-2):1-49.
Crossref