Abstract
The persistence of plastics and its effects in different environments where they accumulate, particularly in coastal areas, is of serious concern. These plastics exhibit signs of degradation, possibly mediated by microorganisms. In this study, we investigated the potential of sediment microbial communities from Manila Bay, Philippines, which has a severe plastics problem, to degrade low-density polyethylene (LDPE). Plastics in selected sites were quantified and sediment samples from sites with the lowest and highest plastic accumulation were collected. These sediments were then introduced and incubated with LDPE in vitro for a period of 91 days. Fourier transform infrared spectroscopy detected the appearance of carbonyl and vinyl products on the plastic surface, indicating structural surface modifications attributed to polymer degradation. Communities attached to the plastics were profiled using high-throughput sequencing of the V4-V5 region of the 16S rRNA gene. Members of the phylum Proteobacteria dominated the plastic surface throughout the experiment. Several bacterial taxa associated with hydrocarbon degradation were also enriched, with some taxa positively correlating with the biodegradation indices, suggesting potential active roles in the partial biodegradation of plastics. Other taxa were also present, which might be consuming by-products or providing nourishment for other groups, indicating synergy in utilizing the plastic as the main carbon source and creation of a microenvironment within the plastics biofilm. This study showed that sediment microbes from Manila Bay may have naturally occurring microbial groups potentially capable of partially degrading plastics, supporting previous studies that the biodegradation potential for plastics is ubiquitously present in marine microbial assemblages.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
All data from this study were included in this article.
References
Abed RMM, Al-Kharusi S, Prigent S, Headley T (2014) Diversity, distribution and hydrocarbon biodegradation capabilities of microbial communities in oil-contaminated cyanobacterial mats from a constructed wetland. PLoS One 9:e114570. https://doi.org/10.1371/journal.pone.0114570
Albertsson A, Karlsson S (1990) The influence of biotic and abiotic environments on the degradation of polyethylene. Prog Polym Sci 15:177–192. https://doi.org/10.1016/0079-6700(90)90027-X
Albertsson A-C, Andersson SO, Karlsson S (1987) The mechanism of biodegradation of polyethylene. Polym Degrad Stab 18:73–87. https://doi.org/10.1016/0141-3910(87)90084-X
Al-Mailem DM, Kansour MK, Radwan SS (2017) Capabilities and limitations of DGGE for the analysis of hydrocarbonoclastic prokaryotic communities directly in environmental samples. MicrobiologyOpen 6:e00495. https://doi.org/10.1002/mbo3.495
Artham T, Sudhakar M, Venkatesan R et al (2009) Biofouling and stability of synthetic polymers in sea water. Int Biodeterior Biodegradation 63:884–890. https://doi.org/10.1016/j.ibiod.2009.03.003
Bacosa HP, Suto K, Inoue C (2012) Bacterial community dynamics during the preferential degradation of aromatic hydrocarbons by a microbial consortium. Int Biodeterior Biodegradation 74:109–115. https://doi.org/10.1016/j.ibiod.2012.04.022
Bacosa HP, Kamalanathan M, Chiu M-H et al (2018) Extracellular polymeric substances (EPS) producing and oil degrading bacteria isolated from the northern Gulf of Mexico. PLoS One 13:e0208406. https://doi.org/10.1371/journal.pone.0208406
Baird FJ, Wadsworth MP, Hill JE (2012) Evaluation and optimization of multiple fluorophore analysis of a Pseudomonas aeruginosa biofilm. J Microbiol Methods 90:192–196. https://doi.org/10.1016/j.mimet.2012.05.004
Balasubramanian V, Natarajan K, Hemambika B et al (2010) High-density polyethylene (HDPE)-degrading potential bacteria from marine ecosystem of Gulf of Mannar, India: high-density polyethylene (HDPE)-degrading potential bacteria from marine ecosystem. Lett Appl Microbiol. https://doi.org/10.1111/j.1472-765X.2010.02883.x
Barnes DKA, Galgani F, Thompson RC, Barlaz M (2009) Accumulation and fragmentation of plastic debris in global environments. Phil Trans R Soc B 364:1985–1998. https://doi.org/10.1098/rstb.2008.0205
Berry D, Gutierrez T (2017) Evaluating the detection of hydrocarbon-degrading bacteria in 16S rRNA gene sequencing surveys. Front Microbiol 8:896. https://doi.org/10.3389/fmicb.2017.00896
Besseling E, Foekema EM, Van Franeker JA et al (2015) Microplastic in a macro filter feeder: humpback whale Megaptera novaeangliae. Mar Pollut Bull 95:248–252
Blanco-Enríquez E, Zavala-Díaz de la Serna F, Peralta-Pérez M et al (2018) Characterization of a microbial consortium for the bioremoval of polycyclic aromatic hydrocarbons (PAHs) in water. IJERPH 15:975. https://doi.org/10.3390/ijerph15050975
Bryant JA, Clemente TM, Viviani DA et al (2016) Diversity and activity of communities inhabiting plastic debris in the north Pacific Gyre. mSystems. https://doi.org/10.1128/mSystems.00024-16
Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303
Cappello S, Yakimov MM (2010) Mesocosms for Oil Spill Simulation. In: Timmis KN (ed) Handbook of Hydrocarbon and Lipid Microbiology. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 3513–3521
Caron DA, Countway PD, Savai P et al (2009) Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol 75:5797–5808. https://doi.org/10.1128/AEM.00298-09
Caruso G (2015) Plastic degrading microorganisms as a tool for bioremediation of plastic contamination in aquatic environments. J Pollut Eff Cont. https://doi.org/10.4172/2375-4397.1000e112
Caruso G (2020) Microbial colonization in marine environments: overview of current knowledge and emerging research Topics. JMSE 8:78. https://doi.org/10.3390/jmse8020078
Chen Y, Mi T, Liu Y et al (2020) Microbial community composition and function in sediments from the Pearl river mouth basin. J Ocean Univ China 19:941–953. https://doi.org/10.1007/s11802-020-4225-7
Cruz LLB, Shimozono T (2021) Transport of floating litter within Manila Bay Philippines. Mar Pollut Bull 163:111944. https://doi.org/10.1016/j.marpolbul.2020.111944
Cyvin JB, Ervik H, Kveberg AA, Hellevik C (2021) Macroplastic in soil and peat. A case study from the remote islands of Mausund and Froan landscape conservation area, Norway; implications for coastal cleanups and biodiversity. Sci Total Environ 787:147547. https://doi.org/10.1016/j.scitotenv.2021.147547
Dashti N, Ali N, Eliyas M et al (2015) Most Hydrocarbonoclastic bacteria in the total environment are diazotrophic, which highlights their value in the bioremediation of hydrocarbon contaminants. Microbes Environ 30:70–75. https://doi.org/10.1264/jsme2.ME14090
Davidov Y, Jurkevitch E (2004) Diversity and evolution of Bdellovibrio-and-like organisms (BALOs), reclassification of Bacteriovorax starrii as Peredibacter starrii gen. nov., comb. nov., and description of the Bacteriovorax-Peredibacter clade as Bacteriovoracaceae fam. nov. Int J Syst Evol Microbiol 54:1439–1452. https://doi.org/10.1099/ijs.0.02978-0
De Tender CA, Devriese LI, Haegeman A et al (2015) Bacterial community profiling of plastic litter in the belgian part of the north sea. Environ Sci Technol 49:9629–9638. https://doi.org/10.1021/acs.est.5b01093
Dela Torre DYZ, Delos Santos LA, Reyes MLC, Baculi RQ (2018) Biodegradation of low-density polyethylene by bacteria isolated from serpentinization-driven alkaline spring. Philipp Sci Lett 11:12
Delacuvellerie A, Cyriaque V, Gobert S et al (2019) 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. https://doi.org/10.1016/j.jhazmat.2019.120899
Denaro R, Aulenta F, Crisafi F et al (2020) Marine hydrocarbon-degrading bacteria breakdown poly(ethylene terephthalate) (PET). Sci Total Environ 749:141608. https://doi.org/10.1016/j.scitotenv.2020.141608
Dixon P (2003) VEGAN, a package of R functions for community ecology. J Veg Sci 14:927–930. https://doi.org/10.1111/j.1654-1103.2003.tb02228.x
Dussud C, Hudec C, George M et al (2018a) Colonization of non-biodegradable and biodegradable plastics by marine microorganisms. Front Microbiol 9:1571. https://doi.org/10.3389/fmicb.2018.01571
Dussud C, Meistertzheim AL, Conan P et al (2018b) Evidence of niche partitioning among bacteria living on plastics, organic particles and surrounding seawaters. Environ Pollut 236:807–816. https://doi.org/10.1016/j.envpol.2017.12.027
Dussud C, Ghiglione J-F (2014) Bacterial degradation of synthetic plastics. In: Fondation Tara Océan. https://oceans.taraexpeditions.org/en/m/science/news/bacterial-degradation-of-synthetic-plastics/. Accessed 14 Jun 2021
Erni-Cassola G, Zadjelovic V, Gibson MI, Christie-Oleza JA (2019) Distribution of plastic polymer types in the marine environment; a meta-analysis. J Hazard Mater 369:691–698. https://doi.org/10.1016/j.jhazmat.2019.02.067
Feinstein LM, Sul WJ, Blackwood CB (2009) Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl Environ Microbiol 75:5428–5433. https://doi.org/10.1128/AEM.00120-09
Franco FM (2018) Simpson’s Reciprocal Diversity Index. http://www.fmfranco.com/Text/ib_biology/simpsons_reciprocal_diversity_index_2018.pdf. Accessed 14 Jun 2021
Friedrich MW (2011) Microbial communities, structure, and function. In: Reitner J, Thiel V (eds) Encyclopedia of geobiology. Springer Netherlands, Dordrecht, pp 592–595
Geyer R, Jambeck JR, Law KL (2017) Production, use, and fate of all plastics ever made. Sci Adv 3:e1700782. https://doi.org/10.1126/sciadv.1700782
Ghatge S, Yang Y, Ahn J-H, Hur H-G (2020) Biodegradation of polyethylene: a brief review. Appl Biol Chem 63:27. https://doi.org/10.1186/s13765-020-00511-3
Gulmine JV, Janissek PR, Heise HM, Akcelrud L (2002) Polyethylene characterization by FTIR. Polym Testing 21:557–563. https://doi.org/10.1016/S0142-9418(01)00124-6
Gutierrez T (2017) Aerobic hydrocarbon-degrading gammaproteobacteria: Xanthomonadales. In: McGenity TJ (ed) Taxonomy, genomics and ecophysiology of hydrocarbon-degrading microbes. Springer International Publishing, Cham, pp 1–15
Hammer Ø, Harper DAT, Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9
Hamzah M, Khenfouch M, Rjeb A et al (2018) Surface chemistry changes and microstructure evaluation of low density nanocluster polyethylene under natural weathering: a spectroscopic investigation. J Phys Conf Ser 984:012010. https://doi.org/10.1088/1742-6596/984/1/012010
Harrison JP, Schratzberger M, Sapp M, Osborn AM (2014) Rapid bacterial colonization of low-density polyethylene microplastics in coastal sediment microcosms. BMC Microbiol 14:232. https://doi.org/10.1186/s12866-014-0232-4
Harshvardhan K, Jha B (2013) Biodegradation of low-density polyethylene by marine bacteria from pelagic waters, Arabian Sea, India. Mar Pollut Bull 77:100–106. https://doi.org/10.1016/j.marpolbul.2013.10.025
Huang W, Chen X, Jiang X, Zheng B (2017) Characterization of sediment bacterial communities in plain lakes with different trophic statuses. MicrobiologyOpen 6:e00503. https://doi.org/10.1002/mbo3.503
Iebba V, Totino V, Santangelo F et al (2014) Bdellovibrio bacteriovorus directly attacks Pseudomonas aeruginosa and Staphylococcus aureus cystic fibrosis isolates. Front Microbiol. https://doi.org/10.3389/fmicb.2014.00280
Jacinto GS, Velasquez IB, San Diego-McGlone ML et al (2006) Biophysical environment of Manila Bay—then and now. In: Wolanski E (ed) The environment in Asia Pacific harbours. Springer-Verlag, Berlin/Heidelberg, pp 293–307
Jacquin J, Cheng J, Odobel C et al (2019) Microbial ecotoxicology of marine plastic debris: a review on colonization and biodegradation by the “plastisphere.” Front Microbiol 10:865. https://doi.org/10.3389/fmicb.2019.00865
Jambeck JR, Geyer R, Wilcox C et al (2015) Plastic waste inputs from land into the ocean. Science 347:768–771. https://doi.org/10.1126/science.1260352
Jiang P, Zhao S, Zhu L, Li D (2018) Microplastic-associated bacterial assemblages in the intertidal zone of the Yangtze Estuary. Sci Total Environ 624:48–54. https://doi.org/10.1016/j.scitotenv.2017.12.105
Jin HM, Kim JM, Lee HJ et al (2012) Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil-contaminated coastal sediment. Environ Sci Technol 46:7731–7740. https://doi.org/10.1021/es3018545
Jung MR, Horgen FD, Orski SV et al (2018) Validation of ATR FT-IR to identify polymers of plastic marine debris, including those ingested by marine organisms. Mar Pollut Bull 127:704–716. https://doi.org/10.1016/j.marpolbul.2017.12.061
Kalyuzhnaya MG, Bowerman S, Lara JC et al (2006) Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae. Int J Syst Evol Microbiol 56:2819–2823. https://doi.org/10.1099/ijs.0.64191-0
Kanaly RA, Harayama S, Watanabe K (2002) Rhodanobacter sp. Strain BPC1 in a Benzo[a ]pyrene-mineralizing bacterial consortium. Appl Environ Microbiol 68:5826–5833. https://doi.org/10.1128/AEM.68.12.5826-5833.2002
Kolde R (2019) pheatmap: Pretty Heatmaps. R package version 1.0.12. Version R package version 1.0.12.URL https://CRAN.R-project.org/package=pheatmap. Accessed 01 Nov 2021
Konduri MKR, Anupam KS, Vivek JS et al (2010) Synergistic effect of chemical and photo treatment on the rate of biodegradation of high density polyethylene by indigenous fungal isolates. Int J Biotechnol Biochem 6:157–175
Kopeček J, Rejmanova P (2019) Enzymatically degradable bonds in synthetic polymers. In: Bruck SD (ed) Controlled drug delivery: volume 2 clinical applications. CRC Press, Boca Raton
Lebreton LCM, van der Zwet J, Damsteeg J-W et al (2017) River plastic emissions to the world’s oceans. Nat Commun 8:15611. https://doi.org/10.1038/ncomms15611
Lebreton L, Egger M, Slat B (2019) A global mass budget for positively buoyant macroplastic debris in the ocean. Sci Rep 9:12922. https://doi.org/10.1038/s41598-019-49413-5
Liesack W, Bak F, Kreft J-U, Stackebrandt E (1994) Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Arch Microbiol 162:85–90. https://doi.org/10.1007/BF00264378
Lippiatt S, Opfer S, Arthur C (2013) Marine debris monitoring and assessment : recommendations for Monitoring Debris Trends in the Marine Environment
Liu C, Wang W, Wu Y et al (2011) Multiple alkane hydroxylase systems in a marine alkane degrader, Alcanivorax dieselolei B-5: A. dieselolei alkane hydroxylases. Environ Microbiol 13:1168–1178. https://doi.org/10.1111/j.1462-2920.2010.02416.x
Lucas N, Bienaime C, Belloy C et al (2008) Polymer biodegradation: mechanisms and estimation techniques – a review. Chemosphere 73:429–442. https://doi.org/10.1016/j.chemosphere.2008.06.064
Manzur A, Limón-González M, Favela-Torres E (2004) Biodegradation of physicochemically treated LDPE by a consortium of filamentous fungi: biodegradation of LDPE by filamentous fungi. J Appl Polym Sci 92:265–271. https://doi.org/10.1002/app.13644
Mayor-Gordove D, Aguinaldo RMT (2013) Information Sheet on Ramsar Wetlands Ramsar Site no. 2124.
Meijer LJJ, van Emmerik T, van der Ent R et al (2021) More than 1000 rivers account for 80% of global riverine plastic emissions into the ocean. Sci Adv 7:eaaz5803. https://doi.org/10.1126/sciadv.aaz5803
Miri M, Bambai B, Tabandeh F et al (2010) Production of a recombinant alkane hydroxylase (AlkB2) from Alcanivorax borkumensis. Biotechnol Lett 32:497–502. https://doi.org/10.1007/s10529-009-0177-0
Mishamandani S, Gutierrez T, Aitken MD (2014) DNA-based stable isotope probing coupled with cultivation methods implicates Methylophaga in hydrocarbon degradation. Front Microbiol. https://doi.org/10.3389/fmicb.2014.00076
Mishamandani S, Gutierrez T, Berry D, Aitken MD (2016) Response of the bacterial community associated with a cosmopolitan marine diatom to crude oil shows a preference for the biodegradation of aromatic hydrocarbons: alga-bacterial dynamics to crude oil exposure. Environ Microbiol 18:1817–1833. https://doi.org/10.1111/1462-2920.12988
Montazer Z, Habibi-Najafi MB, Mohebbi M, Oromiehei A (2018) Microbial degradation of UV-pretreated low-density polyethylene films by novel polyethylene-degrading bacteria isolated from plastic-dump soil. J Polym Environ 26:3613–3625. https://doi.org/10.1007/s10924-018-1245-0
Montazer Z, Habibi Najafi MB, Levin DB (2020) Challenges with verifying microbial degradation of polyethylene. Polymers 12:123. https://doi.org/10.3390/polym12010123
Mu D-S, Wang S, Liang Q-Y et al (2020) Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. Microbiome 8:126. https://doi.org/10.1186/s40168-020-00902-0
Mueller R-J (2006) Biological degradation of synthetic polyesters—enzymes as potential catalysts for polyester recycling. Process Biochem 41:2124–2128. https://doi.org/10.1016/j.procbio.2006.05.018
Neethu CS, Saravanakumar C, Purvaja R et al (2019) Oil-spill triggered shift in indigenous microbial structure and functional dynamics in different marine environmental matrices. Sci Rep 9:1354. https://doi.org/10.1038/s41598-018-37903-x
Neuwirth E (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1–2. https://CRAN.R-project.org/package=RColorBrewer. Accessed 01 Nov 2021
Nowak B, Pająk J, Drozd-Bratkowicz M, Rymarz G (2011) Microorganisms participating in the biodegradation of modified polyethylene films in different soils under laboratory conditions. Int Biodeterior Biodegrad 65:757–767. https://doi.org/10.1016/j.ibiod.2011.04.007
Oberbeckmann S, Osborn AM, Duhaime MB (2016) Microbes on a bottle: substrate, season and geography influence community composition of microbes colonizing marine plastic debris. PLoS One 11:e0159289. https://doi.org/10.1371/journal.pone.0159289
Ogonowski M, Motiei A, Ininbergs K et al (2018) Evidence for selective bacterial community structuring on microplastics: Selective bacterial community structuring. Environ Microbiol 20:2796–2808. https://doi.org/10.1111/1462-2920.14120
Oh H-M, Giovannoni SJ, Lee K et al (2009) Complete genome sequence of Robiginitalea biformata HTCC2501. J Bacteriol 191:7144–7145. https://doi.org/10.1128/JB.01191-09
Onda DFL, Benico G, Sulit AF et al (2013) Morphological and molecular characterization of some HAB- forming dinoflagellates from Philippine waters. Philipp Sci Lett 1:97–106
Onda DFL, Lluisma AO, Azanza RV (2014) Development, morphological characteristics and viability of temporary cysts of Pyrodinium bahamense var. compressum (Dinophyceae) in vitro. Eur J Phycol 49:265–275. https://doi.org/10.1080/09670262.2014.915062
Onda DFL, Azanza RV, Lluisma AO (2015) Potential DMSP-degrading Roseobacter clade dominates endosymbiotic microflora of Pyrodinium bahamense var. compressum (Dinophyceae) in vitro. Arch Microbiol 197:965–971. https://doi.org/10.1007/s00203-015-1133-0
Ormerod KL, Wood DLA, Lachner N et al (2016) Genomic characterization of the uncultured Bacteroidales family S24–7 inhabiting the guts of homeothermic animals. Microbiome 4:36. https://doi.org/10.1186/s40168-016-0181-2
Orr IG, Hadar Y, Sivan A (2004) Colonization, biofilm formation and biodegradation of polyethylene by a strain of Rhodococcus ruber. Appl Microbiol Biotechnol. https://doi.org/10.1007/s00253-004-1584-8
Pankratov TA, Dedysh SN (2010) Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs. Int J Syst Evol Microbiol 60:2951–2959. https://doi.org/10.1099/ijs.0.021824-0
Parada AE, Needham DM, Fuhrman JA (2016) Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: primers for marine microbiome studies. Environ Microbiol 18:1403–1414. https://doi.org/10.1111/1462-2920.13023
Park W, Jeon CO, Cadillo H et al (2004) Survival of naphthalene-degrading Pseudomonas putida NCIB 9816–4 in naphthalene-amended soils: toxicity of naphthalene and its metabolites. Appl Microbiol Biotechnol 64:429–435. https://doi.org/10.1007/s00253-003-1420-6
Pasumarthi R, Chandrasekaran S, Mutnuri S (2013) Biodegradation of crude oil by Pseudomonas aeruginosa and Escherichia fergusonii isolated from the Goan coast. Mar Pollut Bull 76:276–282. https://doi.org/10.1016/j.marpolbul.2013.08.026
Philippine Statistics Authority (2015) Philippine Population Surpassed the 100 Million Mark (Results from the 2015 Census of Population) | Philippine Statistics Authority. https://psa.gov.ph/content/philippine-population-surpassed-100-million-mark-results-2015-census-population. Accessed 14 Jun 2021
Pinnell LJ, Turner JW (2019) Shotgun Metagenomics reveals the benthic microbial community response to plastic and bioplastic in a coastal marine environment. Front Microbiol 10:1252. https://doi.org/10.3389/fmicb.2019.01252
Pinto M, Langer TM, Hüffer T et al (2019) The composition of bacterial communities associated with plastic biofilms differs between different polymers and stages of biofilm succession. PLoS One 14:e0217165. https://doi.org/10.1371/journal.pone.0217165
Pinto M, Polania Zenner P, Langer TM et al (2020) Putative degraders of low-density polyethylene-derived compounds are ubiquitous members of plastic-associated bacterial communities in the marine environment. Environ Microbiol 22:4779–4793. https://doi.org/10.1111/1462-2920.15232
Prince RC, Amande TJ, McGenity TJ (2018) Prokaryotic hydrocarbon degraders. In: McGenity TJ (ed) Taxonomy, genomics and ecophysiology of hydrocarbon-degrading microbes. Springer International Publishing, Cham, pp 1–41
Pujalte MJ, Lucena T, Ruvira MA et al (2014) The Family Rhodobacteraceae. In: Rosenberg E, DeLong EF, Lory S et al (eds) The Prokaryotes. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 439–512
Quero GM, Luna GM (2017) Surfing and dining on the “plastisphere”: microbial life on plastic marine debris. Adv Ocean Limnol. https://doi.org/10.4081/aiol.2017.7211
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinform 12:38. https://doi.org/10.1186/1471-2105-12-38
R Core Team (2021) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria
Radwan SS, Khanafer MM, Al-Awadhi HA (2019) Ability of the so-called obligate hydrocarbonoclastic bacteria to utilize nonhydrocarbon substrates thus enhancing their activities despite their misleading name. BMC Microbiol 19:41. https://doi.org/10.1186/s12866-019-1406-x
Ranada P (2014) Plastic bags most common trash in Manila Bay – groups. https://www.rappler.com/environment/plastic-bags-garbage-manila-bay. Accessed 14 Jun 2021
Restrepo-Flórez J-M, Bassi A, Thompson MR (2014) Microbial degradation and deterioration of polyethylene – a review. Int Biodeterior Biodegradation 88:83–90. https://doi.org/10.1016/j.ibiod.2013.12.014
Ritchie H, Roser M (2018) Plastic Pollution. Our World in Data. https://ourworldindata.org/plastic-pollution. Accessed 14 Jun 2021
Ritchie H (2021) Where does the plastic in our oceans come from? In: Our World in Data. https://ourworldindata.org/ocean-plastics. Accessed 14 Jun 2021
Rong J-C, Ji B-W, Zheng N et al (2021) Genomic insights into antioxidant activities of Pyruvatibacter mobilis CGMCC 1.15125T, a pyruvate-requiring bacterium isolated from the marine microalgae culture. Mar Genom 55:100791. https://doi.org/10.1016/j.margen.2020.100791
Rummel CD, Jahnke A, Gorokhova E et al (2017) Impacts of biofilm formation on the fate and potential effects of microplastic in the aquatic environment. Environ Sci Technol Lett 4:258–267. https://doi.org/10.1021/acs.estlett.7b00164
Sánchez-Fortún A, Fajardo C, Martín C et al (2021) Effects of polyethylene-type microplastics on the growth and primary production of the freshwater phytoplankton species Scenedesmus armatus and Microcystis aeruginosa. Environ Exp Bot 188:104510. https://doi.org/10.1016/j.envexpbot.2021.104510
Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. https://doi.org/10.1128/AEM.01541-09
Schneiker S, dos Santos VAM, Bartels D et al (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24:997–1004. https://doi.org/10.1038/nbt1232
Sivan A (2011) New perspectives in plastic biodegradation. Curr Opin Biotechnol 22:422–426. https://doi.org/10.1016/j.copbio.2011.01.013
Suarez C, Ratering S, Kramer I, Schnell S (2014) Cellvibrio diazotrophicus sp. nov., a nitrogen-fixing bacteria isolated from the rhizosphere of salt meadow plants and emended description of the genus Cellvibrio. Int J Syst Evol Microbiol 64:481–486. https://doi.org/10.1099/ijs.0.054817-0
Syranidou E, Karkanorachaki K, Amorotti F et al (2019) Biodegradation of mixture of plastic films by tailored marine consortia. J Hazard Mater 375:33–42. https://doi.org/10.1016/j.jhazmat.2019.04.078
Teramoto M, Queck SY, Ohnishi K (2013) Specialized Hydrocarbonoclastic bacteria prevailing in seawater around a port in the strait of Malacca. PLoS One 8:e66594. https://doi.org/10.1371/journal.pone.0066594
Tetu SG, Sarker I, Schrameyer V et al (2019) Plastic leachates impair growth and oxygen production in Prochlorococcus, the ocean’s most abundant photosynthetic bacteria. Commun Biol 2:184. https://doi.org/10.1038/s42003-019-0410-x
Thompson RC, Swan SH, Moore CJ, vom Saal FS (2009) Our plastic age. Phil Trans R Soc B 364:1973–1976. https://doi.org/10.1098/rstb.2009.0054
Thompson H, Angelova A, Bowler B et al (2017) Enhanced crude oil biodegradative potential of natural phytoplankton-associated hydrocarbonoclastic bacteria: phytoplankton-bacterial biodegradation of crude oil PAHs. Environ Microbiol 19:2843–2861. https://doi.org/10.1111/1462-2920.13811
Vacca M, Celano G, Calabrese FM et al (2020) The Controversial role of human gut Lachnospiraceae. Microorganisms 8:573. https://doi.org/10.3390/microorganisms8040573
Vaksmaa A, Knittel K, Abdala Asbun A et al (2021) Microbial communities on plastic polymers in the mediterranean sea. Front Microbiol 12:673553. https://doi.org/10.3389/fmicb.2021.673553
van Dorst JM, Hince G, Snape I, Ferrari BC (2016) Novel culturing techniques select for heterotrophs and hydrocarbon degraders in a subantarctic soil. Sci Rep 6:36724. https://doi.org/10.1038/srep36724
van Emmerik T, van Klaveren J, Meijer LJJ et al (2020) Manila river mouths act as temporary sinks for macroplastic pollution. Front Mar Sci 7:545812. https://doi.org/10.3389/fmars.2020.545812
Vimala PP, Mathew L (2016) Biodegradation of polyethylene using Bacillus subtilis. Procedia Technol 24:232–239. https://doi.org/10.1016/j.protcy.2016.05.031
Walters W, Hyde ER, Berg-Lyons D et al (2016) Improved bacterial 16S rRNA gene (V4 and V4–5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems. https://doi.org/10.1128/mSystems.00009-15
Wang W, Zhong R, Shan D, Shao Z (2014) Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow Sea, China. Appl Microbiol Biotechnol 98:7253–7269. https://doi.org/10.1007/s00253-014-5817-1
Wei T, Simko V (2017) R package “corrplot”: Visualization of a Correlation Matrix. Version 0.84URL https://github.com/taiyun/corrplot. Accessed 01 Nov 2021
Whitmire SL, Van Bloem SJ (2017) Quantification of Microplastics on National Park Beaches. National Oceanic and Atmospheric Administration
Wickham H (2016) ggplot2: elegant graphics for data analysis. Springer-Verlag, New York
Wilkes RA, Aristilde L (2017) Degradation and metabolism of synthetic plastics and associated products by Pseudomonas sp.: capabilities and challenges. J Appl Microbiol 123:582–593. https://doi.org/10.1111/jam.13472
Yakimov MM, Golyshin PN, Crisafi F et al (2019) Marine, Aerobic Hydrocarbon-Degrading Gammaproteobacteria: the Family Alcanivoracaceae. In: McGenity TJ (ed) Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Springer International Publishing, Cham, pp 167–179
Yoon MG, Jeong Jeon H, Nam Kim M (2012) Biodegradation of polyethylene by a soil bacterium and alkb cloned recombinant cell. J Bioremed Biodegrad. https://doi.org/10.4172/2155-6199.1000145
Zbyszewski M, Corcoran PL (2011) Distribution and degradation of fresh water plastic particles along the beaches of lake Huron, Canada. Water Air Soil Pollut 220:365–372. https://doi.org/10.1007/s11270-011-0760-6
Zerbi G, Gallino G, Del Fanti N, Baini L (1989) Structural depth profiling in polyethylene films by multiple internal reflection infra-red spectroscopy. Polymer 30:2324–2327. https://doi.org/10.1016/0032-3861(89)90269-3
Zettler ER, Mincer TJ, Amaral-Zettler LA (2013) Life in the “Plastisphere”: microbial communities on plastic Marine Debris. Environ Sci Technol 47:7137–7146. https://doi.org/10.1021/es401288x
Zheng R, Cai R, Liu R et al (2020) Bacteroidetes contribute to the carbon and nutrient cycling of deep sea through breaking down diverse glycans. BioRxiv. https://doi.org/10.1101/2020.11.07.372516
Zhukov A (2017) The distribution, abundance and characteristics of plastic debris along the Coast of Grândola, Portugal. Portugal Degree Programme in Sustainable Coastal Management.“, Novia University of applied sciences.
Acknowledgements
We would like to acknowledge the Protected Area Management and Biodiversity Section of the Conservation and Development Division of the Department of Environment and Natural Resources—National Capital region for allowing us to conduct field work in LPPCHEA. As well as local government units of Brgy. Bucana in Ternate, Brgy. Bucana Malaki in Naic, Brgy. San Rafael III in Noveleta, and Brgy. Baseco in Manila for allowing us to conduct field work and sample collection. We would also like to acknowledge the Marine Research Center under the Marine Environmental Protection Command of the Philippine Coast Guard for providing assistance during one of our fieldworks. Members of the Microbial Oceanography Laboratory for helping during field works. And to Daniel John E. Purganan and Justine Marey S. Bitalac for helping us obtain CLS micrographs.
Funding
This study was funded by the PhD Incentive Award (Project No. 191906 PhDIA) from the Office of the Vice Chancellor for Research and Development of the University of the Philippines (UP), and the Department of Science and Technology and National Research Council of the Philippines (DOST-NRCP) through the project entitled "Plastics in the marine environment, trophic system and aquaculture in the Philippines (PlasMics)".
Author information
Authors and Affiliations
Contributions
NCFG: conducted field surveys and sample collection, performed laboratory experiments, did data analysis, wrote the manuscript, and prepared the figures and tables. DFLO: reviewed and edited the manuscript, figures, and tables, as well as provided advice and guidance throughout the study. All authors conceptualized the project idea, designed the experiment and data analyses, and finalized the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Ethical approval
Not applicable.
Consent to participate
Not applicable.
Consent for publication
Not applicable.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Gomez, N.C.F., Onda, D.F.L. Potential of sediment bacterial communities from Manila Bay (Philippines) to degrade low-density polyethylene (LDPE). Arch Microbiol 205, 38 (2023). https://doi.org/10.1007/s00203-022-03366-y
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-022-03366-y