Abstract
Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them.
Key points
• Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions.
• Marine environments are an important source of new bacterial plastic-degrading enzymes.
• Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.
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References
Alam I, Aalismail N, Martin C, Kamau A, Guzmán-Vega FJ, Jamil T, Momin AA, Acinas SG, Gasol JM, Arold ST, Gojobori T, Agusti S, Duarte CM (2020) Rapid Evolution of Plastic-degrading enzymes prevalent in the global ocean. bioRxiv:2020.09.07.285692. https://doi.org/10.1101/2020.09.07.285692
Almeida EL, Carrillo Rincón AF, Jackson SA, Dobson ADW (2019) In silico screening and heterologous expression of a polyethylene terephthalate hydrolase (PETase)-like enzyme (SM14est) with polycaprolactone (PCL)-degrading activity, from the marine sponge-derived strain Streptomyces sp. SM14. Front Microbiol 10(2187). https://doi.org/10.3389/fmicb.2019.02187
Alvarez-Yela AC, Mosquera-Rendón J, Noreña-P A, Cristancho M, López-Alvarez D (2019) Microbial diversity exploration of marine hosts at Serrana Bank, a coral atoll of the seaflower biosphere reserve. Front Mar Sci 6(338). https://doi.org/10.3389/fmars.2019.00338
Amani H (2015) Study of enhanced oil recovery by rhamnolipids in a homogeneous 2D micromodel. J Pet Sci Eng 128:212–219. https://doi.org/10.1016/j.petrol.2015.02.030
Antoniou E, Fodelianakis S, Korkakaki E, Kalogerakis N (2015) Biosurfactant production from marine hydrocarbon-degrading consortia and pure bacterial strains using crude oil as carbon source. Front Microbiol 6(274). https://doi.org/10.3389/fmicb.2015.00274
Austin HP, Allen MD, Donohoe BS, Rorrer NA, Kearns FL, Silveira RL, Pollard BC, Dominick G, Duman R, El Omari K, Mykhaylyk V, Wagner A, Michener WE, Amore A, Skaf MS, Crowley MF, Thorne AW, Johnson CW, Woodcock HL, McGeehan JE, Beckham GT (2018) Characterization and engineering of a plastic-degrading aromatic polyesterase. PNAS 115(19):E4350–E4357. https://doi.org/10.1073/pnas.1718804115
Auta HS, Emenike CU, Jayanthi B, Fauziah SH (2018) Growth kinetics and biodeterioration of polypropylene microplastics by Bacillus sp. and Rhodococcus sp. isolated from mangrove sediment. Mar Pollut Bull 127:15–21. https://doi.org/10.1016/j.marpolbul.2017.11.036
Azam F, Malfatti F (2007) Microbial structuring of marine ecosystems. Nat Rev Microbiol 5(10):782–791. https://doi.org/10.1038/nrmicro1747
Balasubramanian V, Natarajan K, Hemambika B, Ramesh N, Sumathi CS, Kottaimuthu R, Rajesh Kannan V (2010) High-density polyethylene (HDPE)-degrading potential bacteria from marine ecosystem of Gulf of Mannar. India Lett Appl Microbiol 51(2):205–211. https://doi.org/10.1111/j.1472-765X.2010.02883.x
Baker BJ, Appler KE, Gong X (2021) New microbial biodiversity in marine sediments. Ann Rev Mar Sci 13:161–175. https://doi.org/10.1146/annurev-marine-032020-014552
Bertrand B, Martínez-Morales F, Rosas-Galván NS, Morales-Guzmán D, Trejo-Hernández MR (2018) Statistical design, a powerful tool for optimizing biosurfactant production: a review. Colloids Interfaces 2(3):36. https://doi.org/10.3390/colloids2030036
Bollinger A, Thies S, Knieps-Grünhagen E, Gertzen C, Kobus S, Höppner A, Ferrer M, Gohlke H, Smits SHJ, Jaeger K-E (2020) A novel polyester hydrolase from the marine bacterium Pseudomonas aestusnigri – Structural and functional insights. Front Microbiol 11(114). https://doi.org/10.3389/fmicb.2020.00114
Bollmann M, Bosch T, Colijn F, Ebinghaus R, Froese R, Güssow K, Khalilian S, Krastel S, Körtzinger A, Langenbuch M, Latif M, Matthiessen B, Melzner F, Oschlies A, Petersen S, Proelß A, Quaas M, Reichenbach J, Requate T, Reusch T, Rosenstiel P, Schmidt JO, Schrottke K, Sichelschmidt H, Siebert U, Soltwedel R, Sommer U, Stattegger K, Sterr H, Sturm R, Treude T, Vafeidis A, Bernem C, Beusekom JV, Voss R, Visbeck M, Wahl M, Wallmann K, Weinberger F (2010) World Ocean Review 1 (WOR1). Living with the oceans: a report on the state of the world’s oceans. Tech. rep., World Ocean Review. http://worldoceanreview.com/en/wor-1/. Accessed 04 Aug 2020
Bosch R, García-Valdés E, Moore ER (2000) Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10. Gene 245(1):65–74. https://doi.org/10.1016/S0378-1119(00)00038-X
Cao J, Lai Q, Yuan J, Shao Z (2015) Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T. Sci Rep 5(1):7741. https://doi.org/10.1038/srep07741
Chakraborty J, Das S (2016) Characterization of the metabolic pathway and catabolic gene expression in biphenyl degrading marine bacterium Pseudomonas aeruginosa JP-11. Chemosphere 144:1706–1714. https://doi.org/10.1016/j.chemosphere.2015.10.059
Charette MA, Smith WHF (2010) The volume of Earth’s ocean. Oceanography 23(2):112–114. https://doi.org/10.5670/oceanog.2010.51
Cheffi M, Hentati D, Chebbi A, Mhiri N, Sayadi S, Marqués AM, Chamkha M (2020) Isolation and characterization of a newly naphthalene-degrading Halomonas pacifica, strain Cnaph3: biodegradation and biosurfactant production studies. 3 Biotech 10(3):89. https://doi.org/10.1007/s13205-020-2085-x
Chen Q, Li J, Liu M, Sun H, Bao M (2017) Study on the biodegradation of crude oil by free and immobilized bacterial consortium in marine environment. PLoS ONE 12(3):e0174445. https://doi.org/10.1371/journal.pone.0174445
Cram JA, Chow C-ET, Sachdeva R, Needham DM, Parada AE, Steele JA, Fuhrman JA (2015) Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME J 9(3):563–580. https://doi.org/10.1038/ismej.2014.153
Danso D, Schmeisser C, Chow J, Zimmermann W, Wei R, Leggewie C, Li X, Hazen T, Streit WR (2018) New insights into the function and global distribution of polyethylene terephthalate (PET)-degrading bacteria and enzymes in marine and terrestrial metagenomes. Appl Environ Microbiol 84(8):e02773-e2817. https://doi.org/10.1128/aem.02773-17
Dash HR, Mangwani N, Chakraborty J, Kumari S, Das S (2013) Marine bacteria: potential candidates for enhanced bioremediation. Appl Microbiol Biotechnol 97(2):561–571. https://doi.org/10.1007/s00253-012-4584-0
de la Calle F (2017) Marine microbiome as source of natural products. Microb Biotechnol 10(6):1293–1296. https://doi.org/10.1111/1751-7915.12882
Deines P, Hammerschmidt K, Bosch TCG (2020) Microbial species coexistence depends on the host environment. mBio 11(4):e00807-20. https://doi.org/10.1128/mBio.00807-20
Delacuvellerie A, Cyriaque V, Gobert S, Benali S, Wattiez R (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, Di Pippo F, Cruz Viggi C, Matturro B, Tomei P, Smedile F, Martinelli A, Di Lisio V, Venezia C, Rossetti S (2020) Marine hydrocarbon-degrading bacteria breakdown poly(ethylene terephthalate) (PET). Sci Total Environ 749:141608. https://doi.org/10.1016/j.scitotenv.2020.141608
Deng M-C, Li J, Liang F-R, Yi M, Xu X-M, Yuan J-P, Peng J, Wu C-F, Wang J-H (2014) Isolation and characterization of a novel hydrocarbon-degrading bacterium Achromobacter sp. HZ01 from the crude oil-contaminated seawater at the Daya Bay, southern China. Mar Pollut Bull 83(1):79–86. https://doi.org/10.1016/j.marpolbul.2014.04.018
Dharamshi JE, Tamarit D, Eme L, Stairs CW, Martijn J, Homa F, Jørgensen SL, Spang A, Ettema TJG (2020) Marine sediments illuminate Chlamydiae diversity and evolution. Curr Biol 30(6):1032-1048.e7. https://doi.org/10.1016/j.cub.2020.02.016
Dubinsky EA, Conrad ME, Chakraborty R, Bill M, Borglin SE, Hollibaugh JT, Mason OU, Piceno Y, Reid FC, Stringfellow WT, Tom LM, Hazen TC, Andersen GL (2013) Succession of hydrocarbon-degrading bacteria in the aftermath of the Deepwater Horizon oil spill in the gulf of Mexico. Environ Sci Technol 47(19):10860–10867. https://doi.org/10.1021/es401676y
Dussud C, Hudec C, George M, Fabre P, Higgs P, Bruzaud S, Delort A-M, Eyheraguibel B, Meistertzheim A-L, Jacquin J, Cheng J, Callac N, Odobel C, Rabouille S, Ghiglione J-F (2018) Colonization of non-biodegradable and biodegradable plastics by marine microorganisms. Front Microbiol 9(1571). https://doi.org/10.3389/fmicb.2018.01571
Flemming H-C, Wuertz S (2019) Bacteria and archaea on Earth and their abundance in biofilms. Nat Rev Microbiol 17(4):247–260. https://doi.org/10.1038/s41579-019-0158-9
Fu Y, Rivkin RB, Lang AS (2019) Effects of vertical water mass segregation on bacterial community structure in the Beaufort Sea. Microorganims 7(10):385. https://doi.org/10.3390/microorganisms7100385
Ganesh Kumar A, Mathew NC, Sujitha K, Kirubagaran R, Dharani G (2019) Genome analysis of deep sea piezotolerant Nesiotobacter exalbescens COD22 and toluene degradation studies under high pressure condition. Sci Rep 9(1):18724. https://doi.org/10.1038/s41598-019-55115-9
Gauthier MJ, Lafay B, Christen R, Fernandez L, Acquaviva M, Bonin P, Bertrand J-C (1992) Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int J Syst Evol Microbiol 42(4):568–576. https://doi.org/10.1099/00207713-42-4-568
Gawin A, Valla S, Brautaset T (2017) The XylS/Pm regulator/promoter system and its use in fundamental studies of bacterial gene expression, recombinant protein production and metabolic engineering. Microb Biotechnol 10(4):702–718. https://doi.org/10.1111/1751-7915.12701
Gentile G, Bonsignore M, Santisi S, Catalfamo M, Giuliano L, Genovese L, Yakimov MM, Denaro R, Genovese M, Cappello S (2016) Biodegradation potentiality of psychrophilic bacterial strain Oleispira antarctica RB-8T. Mar Pollut Bull 105(1):125–130. https://doi.org/10.1016/j.marpolbul.2016.02.041
George KW, Hay AG (2011) Bacterial strategies for growth on aromatic compounds. Adv Appl Microbiol 74:1–33. https://doi.org/10.1016/B978-0-12-387022-3.00005-7
Ghosal D, Ghosh S, Dutta TK, Ahn Y (2016) Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): a review. Front Microbiol 7(1369). https://doi.org/10.3389/fmicb.2016.01369
Giovannoni SJ (2017) SAR11 Bacteria: The most abundant plankton in the oceans. Annu Rev Mar Sci 9(1):231–255. https://doi.org/10.1146/annurev-marine-010814-015934
Godoy-Lozano EE, Escobar-Zepeda A, Raggi L, Merino E, Gutierrez-Rios RM, Juarez K, Segovia L, Licea-Navarro AF, Gracia A, Sanchez-Flores A, Pardo-Lopez L (2018) Bacterial diversity and the geochemical landscape in the southwestern gulf of Mexico. Front Microbiol 9(2528). https://doi.org/10.3389/fmicb.2018.02528
Guzik U, Hupert-Kocurek K, Wojcieszyñska D (2013) Intradiol Dioxygenases — The key enzymes in xenobiotics degradation. In: Chamy F, Rosenkranz R (eds) Biodegradation of hazardous and special products. InTech Open, Vienna, pp 129–153. https://doi.org/10.5772/56205
Harshvardhan K, Jha B (2013) Biodegradation of low-density polyethylene by marine bacteria from pelagic waters, Arabian Sea, India. Mar Pollut Bull 77(1):100–106. https://doi.org/10.1016/j.marpolbul.2013.10.025
Hentati D, Cheffi M, Hadrich F, Makhloufi N, Rabanal F, Manresa A, Sayadi S, Chamkha M (2021) Investigation of halotolerant marine Staphylococcus sp. CO100, as a promising hydrocarbon-degrading and biosurfactant-producing bacterium, under saline conditions. J Environ Manage 277:111480. https://doi.org/10.1016/j.jenvman.2020.111480
Higuchi-Takeuchi M, Morisaki K, Toyooka K, Numata K (2016) Synthesis of high-molecular-weight polyhydroxyalkanoates by marine photosynthetic purple bacteria. PLoS ONE 11(8):e0160981. https://doi.org/10.1371/journal.pone.0160981
Hoshino T, Doi H, Uramoto G-I, Wörmer L, Adhikari RR, Xiao N, Morono Y, D’Hondt S, Hinrichs K-U, Inagaki F (2020) Global diversity of microbial communities in marine sediment. PNAS 201919139. https://doi.org/10.1073/pnas.1919139117
Hou D, Shen X, Luo Q, He Y, Wang Q, Liu Q (2013) Enhancement of the diesel oil degradation ability of a marine bacterial strain by immobilization on a novel compound carrier material. Mar Pollut Bull 67(1):146–151. https://doi.org/10.1016/j.marpolbul.2012.11.021
Hu P, Dubinsky EA, Probst AJ, Wang J, Sieber CMK, Tom LM, Gardinali PR, Banfield JF, Atlas RM, Andersen GL (2017) Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. PNAS 114(28):7432–7437. https://doi.org/10.1073/pnas.1703424114
Jacquin J, Cheng J, Odobel C, Pandin C, Conan P, Pujo-Pay M, Barbe V, Meistertzheim A-L, Ghiglione J-F (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
Jaiswal S, Shukla P (2020) Alternative strategies for microbial remediation of pollutants via synthetic biology. Front Microbiol 11(808). https://doi.org/10.3389/fmicb.2020.00808
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. https://doi.org/10.1126/science.1260352
Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie J-M, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P, the Tara Oceans Consortium (2011) A holistic approach to marine eco-systems biology. PloS Biol 9(10):e1001177. https://doi.org/10.1371/journal.pbio.1001177
Khandare SD, Chaudhary DR, Jha B (2021) Marine bacterial biodegradation of low-density polyethylene (LDPE) plastic. Biodegradation. https://doi.org/10.1007/s10532-021-09927-0
Knott BC, Erickson E, Allen MD, Gado JE, Graham R, Kearns FL, Pardo I, Topuzlu E, Anderson JJ, Austin HP, Dominick G, Johnson CW, Rorrer NA, Szostkiewicz CJ, Copié V, Payne CM, Woodcock HL, Donohoe BS, Beckham GT, McGeehan JE (2020) Characterization and engineering of a two-enzyme system for plastics depolymerization. PNAS 117(41):25476–25485. https://doi.org/10.1073/pnas.2006753117
Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O’Dwyer J, Koeppel AF, Green JL, Pollard KS (2013) Global marine bacterial diversity peaks at high latitudes in winter. ISME J 7(9):1669–1677. https://doi.org/10.1038/ismej.2013.37
Lai Q, Cao J, Yuan J, Li F, Shao Z (2014) Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int J Syst Evol Microbiol 64(Pt_12):4160–4167. https://doi.org/10.1099/ijs.0.069039-0
Lin M, Liu Y, Chen W, Wang H, Hu X (2014) Use of bacteria-immobilized cotton fibers to absorb and degrade crude oil. Int Biodeterior Biodegrad 88:8–12. https://doi.org/10.1016/j.ibiod.2013.11.015
Liu Y-C, Li L-Z, Wu Y, Tian W, Zhang L-P, Xu L, Shen Q-R, Shen B (2010) Isolation of an alkane-degrading Alcanivorax sp. strain 2B5 and cloning of the alkB gene. Bioresour Technol 101(1):310–316. https://doi.org/10.1016/j.biortech.2009.08.028
Liu H, Xu J, Liang R, Liu J (2014) Characterization of the medium- and long-chain n-alkanes degrading Pseudomonas aeruginosa strain SJTD-1 and its alkane hydroxylase genes. PLoS ONE 9(8):e105506. https://doi.org/10.1371/journal.pone.0105506
Liu G, Zhong H, Yang X, Liu Y, Shao B, Liu Z (2018) Advances in applications of rhamnolipids biosurfactant in environmental remediation: a review. Biotechnol Bioeng 115(4):796–814. https://doi.org/10.1002/bit.26517
Mahapatra GP, Raman S, Nayak S, Gouda S, Das G, Patra JK (2020) Metagenomics approaches in discovery and development of new bioactive compounds from marine Actinomycetes. Curr Microbiol 77(4):645–656. https://doi.org/10.1007/s00284-019-01698-5
Mapelli F, Scoma A, Michoud G, Aulenta F, Boon N, Borin S, Kalogerakis N, Daffonchio D (2017) Biotechnologies for marine oil spill cleanup: indissoluble ties with microorganisms. Trends Biotechnol 35(9):860–870. https://doi.org/10.1016/j.tibtech.2017.04.003
McGenity TJ (2010) Halophilic hydrocarbon degraders. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer: Berlin, pp 1939–1951. https://doi.org/10.1007/978-3-540-77587-4_142
Millán-López S (2021) Isolation and molecular characterization of a strain with 2,3-extradiol dioxigenase activity and heterologous expression of the enzyme responsible for the activity. Dissertation. National Autonomous University of Mexico
Mnif S, Chamkha M, Sayadi S (2009) Isolation and characterization of Halomonas sp. strain C2SS100, a hydrocarbon-degrading bacterium under hypersaline conditions. J Appl Microbiol 107(3):785–794. https://doi.org/10.1111/j.1365-2672.2009.04251.x
Mujumdar S, Joshi P, Karve N (2019) Production, characterization, and applications of bioemulsifiers (BE) and biosurfactants (BS) produced by Acinetobacter spp.: a review. J Basic Microbiol 59(3):277–287. https://doi.org/10.1002/jobm.201800364
Muriel-Millán LF, Rodríguez-Mejía JL, Godoy-Lozano EE, Rivera-Gómez N, Gutierrez-Rios R-M, Morales-Guzmán D, Trejo-Hernández MR, Estradas-Romero A, Pardo-López L (2019) Functional and genomic characterization of a Pseudomonas aeruginosa strain isolated from the southwestern Gulf of Mexico reveals an enhanced adaptation for long-chain alkane degradation. Front Mar Sci 6(572). https://doi.org/10.3389/fmars.2019.00572
Nhi-Cong LT, Lien DT, Gupta BS, Mai CTN, Ha HP, Nguyet NTM, Duan TH, Van Quyen D, Zaid HFM, Sankaran R, Show PL (2020) Enhanced degradation of diesel oil by using biofilms formed by indigenous purple photosynthetic bacteria from oil-contaminated coasts of Vietnam on different carriers. Appl Biochem Biotechnol 191(1):313–330. https://doi.org/10.1007/s12010-019-03203-x
Nie Y, Chi C-Q, Fang H, Liang J-L, Lu S-L, Lai G-L, Tang Y-Q, Wu X-L (2014) Diverse alkane hydroxylase genes in microorganisms and environments. Sci Rep 4:4968. https://doi.org/10.1038/srep04968
Nikolova C, Gutierrez T (2020) Use of microorganisms in the recovery of oil from recalcitrant oil reservoirs: current state of knowledge, technological advances and future perspectives. Front Microbiol 10(2996). https://doi.org/10.3389/fmicb.2019.02996
Oberbeckmann S, Labrenz M (2020) Marine microbial assemblages on microplastics: diversity, adaptation, and role in degradation. Annu Rev Mar Sci 12(1):209–232. https://doi.org/10.1146/annurev-marine-010419-010633
Pardo-López L (2019) Marine bioprospecting. In: Muller MR, Oyanedel R, Monteferri B (eds) Marine and fisheries policies in Latin America: a comparison of selected countries, Routledge, London, pp 33–34. https://doi.org/10.4324/9780429426520
Park H-J, Jeon JH, Kang SG, Lee J-H, Lee S-A, Kim H-K (2007) Functional expression and refolding of new alkaline esterase, EM2L8 from deep-sea sediment metagenome. Protein Expr Purif 52(2):340–347. https://doi.org/10.1016/j.pep.2006.10.010
Qiao N, Shao Z (2010) Isolation and characterization of a novel biosurfactant produced by hydrocarbon-degrading bacterium Alcanivorax dieselolei B-5. J Appl Microbiol 108(4):1207–1216. https://doi.org/10.1111/j.1365-2672.2009.04513.x
Raggi L, García-Guevara F, Godoy-Lozano EE, Martínez-Santana A, Escobar-Zepeda A, Gutierrez-Rios RM, Loza A, Merino E, Sanchez-Flores A, Licea-Navarro A, Pardo-Lopez L, Segovia L, Juarez K (2020) Metagenomic profiling and microbial metabolic potential of Perdido Fold Belt (NW) and Campeche knolls (SE) in the Gulf of Mexico. Front Microbiol 11(1825). https://doi.org/10.3389/fmicb.2020.01825
Raghul SS, Bhat SG, Chandrasekaran M, Francis V, Thachil ET (2014) Biodegradation of polyvinyl alcohol-low linear density polyethylene-blended plastic film by consortium of marine benthic vibrios. Int J Environ Sci Technol 11(7):1827–1834. https://doi.org/10.1007/s13762-013-0335-8
Reisfeld A, Rosenberg E, Gutnick D (1972) Microbial degradation of crude oil: factors affecting the dispersion in sea water by mixed and pure cultures. Appl Microbiol 24(3):363–368
Roager L, Sonnenschein EC (2019) Bacterial candidates for colonization and degradation of marine plastic debris. Environ Sci Technol 53(20):11636–11643. https://doi.org/10.1021/acs.est.9b02212
Rodríguez-Salazar J, Almeida-Juarez AG, Ornelas-Ocampo K, Millán-López S, Raga-Carbajal E, Rodríguez-Mejía JL, Muriel-Millán LF, Godoy-Lozano EE, Rivera-Gómez N, Rudiño-Piñera E, Pardo-López L (2020) Characterization of a novel functional trimeric catechol 1,2-dioxygenase from a Pseudomonas stutzeri isolated from the gulf of Mexico. Front Microbiol 11(1100). https://doi.org/10.3389/fmicb.2020.01100
Rodríguez-Salazar J, Loza A, Ornelas-Ocampo K, Gutierrez-Rios RM, Pardo-López L (2021) Bacteria from the southern gulf of Mexico: baseline, diversity, hydrocarbon-degrading potential and future applications. Front Mar Sci 8(232). https://doi.org/10.3389/fmars.2021.625477
Rojo F (2009) Degradation of alkanes by bacteria. Environ Microbiol 11:2477–2490. https://doi.org/10.1111/j.1462-2920.2009.01948.x
Rosas-Díaz J, Escobar-Zepeda A, Adaya L, Rojas-Vargas J, Cuervo-Amaya DH, Sánchez-Reyes A, Pardo-López L (2021) Paenarthrobacter sp. GOM3 is a novel marine species with monoaromatic degradation relevance. Front Microbiol 12(2191). https://doi.org/10.3389/fmicb.2021.713702
Salazar G, Sunagawa S (2017) Marine microbial diversity. Curr Biol 27(11):R489–R494. https://doi.org/10.1016/j.cub.2017.01.017
Santisi S, Catalfamo M, Bonsignore M, Gentile G, Di Salvo E, Genovese M, Mahjoubi M, Cherif A, Mancini G, Hassanshahian M, Pioggia G, Cappello S (2019) Biodegradation ability of two selected microbial autochthonous consortia from a chronically polluted marine coastal area (Priolo Gargallo, Italy). J Appl Microbiol 127(3):618–629. https://doi.org/10.1111/jam.14246
Satpute SK, Banat IM, Dhakephalkar PK, Banpurkar AG, Chopade BA (2010) Biosurfactants, bioemulsifiers and exopolysaccharides from marine microorganisms. Biotechnol Adv 28(4):436–450. https://doi.org/10.1016/j.biotechadv.2010.02.006
Schneiker S, dos Santos VAPM, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter F-J, Weidner S, Kaiser O, Golyshin PN (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 24(8):997–1004. https://doi.org/10.1038/nbt1232
Scoma A, Boon N (2016) Osmotic stress confers enhanced cell integrity to hydrostatic pressure but impairs growth in Alcanivorax borkumensis SK2. Front Microbiol 7(729). https://doi.org/10.3389/fmicb.2016.00729
Seeley ME, Song B, Passie R, Hale RC (2020) Microplastics affect sedimentary microbial communities and nitrogen cycling. Nat Commun 11(1):2372. https://doi.org/10.1038/s41467-020-16235-3
Seghal Kiran G, Nishanth Lipton A, Kennedy J, Dobson ADW, Selvin J (2014) A halotolerant thermostable lipase from the marine bacterium Oceanobacillus sp. PUMB02 with an ability to disrupt bacterial biofilms. Bioengineered 5(5):305–318. https://doi.org/10.4161/bioe.29898
Smith D, Buddie AG, Goss RJM, Overmann J, Lepleux C, Brönstrup M, Kloareg B, Meiners T, Brennecke P, Ianora A, Bouget FY, Gribbon P, Pina M (2019) Discovery pipelines for marine resources: an ocean of opportunity for biotechnology? World J Microbiol Biotechnol 35(7):107. https://doi.org/10.1007/s11274-019-2685-y
Soberón-Chávez G, González-Valdez A, Soto-Aceves MP, Cocotl-Yañez M (2021) Rhamnolipids produced by Pseudomonas: from molecular genetics to the market. Microb Biotechnol 4(1):136–146. https://doi.org/10.1111/1751-7915.13700
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d’Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P (2015) Structure and function of the global ocean microbiome. Science 348(6237):1261359. https://doi.org/10.1126/science.1261359
Syranidou E, Karkanorachaki K, Amorotti F, Repouskou E, Kroll K, Kolvenbach B, Corvini PFX, Fava F, Kalogerakis N (2017) Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films. PloS One 12(8):e0183984. https://doi.org/10.1371/journal.pone.0183984
Tetu SG, Sarker I, Schrameyer V, Pickford R, Elbourne LDH, Moore LR, Paulsen IT (2019) Plastic leachates impair growth and oxygen production in Prochlorococcus, the ocean’s most abundant photosynthetic bacteria. Commun Biol 2(1):184. https://doi.org/10.1038/s42003-019-0410-x
Thessen AE, North EW (2017) Calculating in situ degradation rates of hydrocarbon compounds in deep waters of the Gulf of Mexico. Mar Poll Bull 122(1):77–84. https://doi.org/10.1016/j.marpolbul.2017.06.004
Thiele S, Fuchs BM, Amann R, Iversen MH (2015) Colonization in the photic zone and subsequent changes during sinking determine bacterial community composition in marine snow. Appl Environ Microbiol 81(4):1463–1471. https://doi.org/10.1128/aem.02570-14
Thomas JC, Wafula D, Chauhan A, Green SJ, Gragg R, Jagoe C (2014) A survey of deepwater horizon (DWH) oil-degrading bacteria from the Eastern oyster biome and its surrounding environment. Front Microbiol 5(149). https://doi.org/10.3389/fmicb.2014.00149
Tripathi L, Irorere VU, Marchant R, Banat IM (2018) Marine derived biosurfactants: a vast potential future resource. Biotechnol Lett 40(11):1441–1457. https://doi.org/10.1007/s10529-018-2602-8
Tripathi L, Twigg MS, Zompra A, Salek K, Irorere VU, Gutierrez T, Spyroulias GA, Marchant R, Banat IM (2019) Biosynthesis of rhamnolipid by a Marinobacter species expands the paradigm of biosurfactant synthesis to a new genus of the marine microflora. Microb Cell Fact 18(1):164. https://doi.org/10.1186/s12934-019-1216-8
Twigg MS, Tripathi L, Zompra A, Salek K, Irorere VU, Gutierrez T, Spyroulias GA, Marchant R, Banat IM (2018) Identification and characterisation of short chain rhamnolipid production in a previously uninvestigated, non-pathogenic marine pseudomonad. Appl Microbiol Biotechnol 102(19):8537–8549. https://doi.org/10.1007/s00253-018-9202-3
Uzoigwe C, Burgess JG, Ennis CJ, Rahman PKSM (2015) Bioemulsifiers are not biosurfactants and require different screening approaches. Front Microbiol 6(245). https://doi.org/10.3389/fmicb.2015.00245
van Beilen JB, Smits THM, Roos FF, Brunner T, Balada SB, Röthlisberger M, Witholt B (2005) Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases. J Bacteriol 187(1):85–91. https://doi.org/10.1128/JB.187.1.85-91.2005
Van Landuyt J, Cimmino L, Dumolin C, Chatzigiannidou I, Taveirne F, Mattelin V, Zhang Y, Vandamme P, Scoma A, Williamson A, Boon N (2020) Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders. FEMS Microbiol Ecol 96(9). https://doi.org/10.1093/femsec/fiaa097
Vásquez-Ponce F, Higuera-Llantén S, Pavlov MS, Ramírez-Orellana R, Marshall SH, Olivares-Pacheco J (2017) Alginate overproduction and biofilm formation by psychrotolerant Pseudomonas mandelii depend on temperature in Antarctic marine sediments. Electron J Biotechnol 28:27–34. https://doi.org/10.1016/j.ejbt.2017.05.001
Walsh EA, Kirkpatrick JB, Rutherford SD, Smith DC, Sogin M, D’Hondt S (2016) Bacterial diversity and community composition from seasurface to subseafloor. ISME J 10(4):979–989. https://doi.org/10.1038/ismej.2015.175
Wang W, Shao Z (2012) Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11–3. Appl Microbiol Biotechnol 94(2):437–448. https://doi.org/10.1007/s00253-011-3818-x
Wang B, Lai Q, Cui Z, Tan T, Shao Z (2008) A pyrene-degrading consortium from deep-sea sediment of the West Pacific and its key member Cycloclasticus sp. P1. Environ Microbiol 10(8):1948–1963. https://doi.org/10.1111/j.1462-2920.2008.01611.x
Wang W, Wang L, Shao Z (2018) Polycyclic aromatic hydrocarbon (PAH) degradation pathways of the obligate marine PAH degrader Cycloclasticus sp. strain P1. Appl Environ Microbiol 84(21):e01261-18. https://doi.org/10.1128/AEM.01261-18
Wei R, Zimmermann W (2017) Microbial enzymes for the recycling of recalcitrant petroleum-based plastics: how far are we? Microb Biotechnol 10(6):1308–1322. https://doi.org/10.1111/1751-7915.12710
Won N-I, Kim K-H, Kang JH, Park SR, Lee HJ (2017) Exploring the impacts of anthropogenic disturbance on seawater and sediment microbial communities in Korean coastal waters using metagenomics analysis. Int J Environ Res Public Health 14(2):130. https://doi.org/10.3390/ijerph14020130
Yoshida S, Hiraga K, Takehana T, Taniguchi I, Yamaji H, Maeda Y, Toyohara K, Miyamoto K, Kimura Y, Oda K (2016) A bacterium that degrades and assimilates poly(ethylene terephthalate). Science 351(6278):1196–1199. https://doi.org/10.1126/science.aad6359
Yun SH, Choi C-W, Lee S-Y, Lee YG, Kwon J, Leem SH, Chung YH, Kahng H-Y, Kim SJ, Kwon KK, Kim SI (2014) Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1. PLoS ONE 9(3):e90812. https://doi.org/10.1371/journal.pone.0090812
Zadjelovic V, Chhun A, Quareshy M, Silvano E, Hernandez-Fernaud JR, Aguilo-Ferretjans MM, Bosch R, Dorador C, Gibson MI, Christie-Oleza JA (2020a) Beyond oil degradation: enzymatic potential of Alcanivorax to degrade natural and synthetic polyesters. Environ Microbiol 22(4):1356–1369. https://doi.org/10.1111/1462-2920.14947
Zadjelovic V, Gibson MI, Dorador C, Christie-Oleza JA (2020b) Genome of Alcanivorax sp. 24: a hydrocarbon degrading bacterium isolated from marine plastic debris. Mar Genomics 49:100686. https://doi.org/10.1016/j.margen.2019.05.001
Zhang X, Ye X, Chai W, Lian XY, Zhang Z (2016) New metabolites and bioactive actinomycins from marine-derived Streptomyces sp. ZZ338. Mar Drugs 14(10). https://doi.org/10.3390/md14100181
Zhang W, Ding W, Li Y-X, Tam C, Bougouffa S, Wang R, Pei B, Chiang H, Leung P, Lu Y, Sun J, Fu H, Bajic VB, Liu H, Webster NS, Qian P-Y (2019) Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nat Commun 10(1):517. https://doi.org/10.1038/s41467-019-08463-z
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We thank Daniel Mayer Martínez for drawings, and Shirley Elizabeth Ainsworth Gore and David Santiago Castañeda Carreón for bibliography assistance.
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This research was funded by the National Council of Science and Technology of Mexico—Mexican Ministry of Energy—Hydrocarbon Trust, project 201441. This is a contribution of the Gulf of Mexico Research Consortium (CIGoM).
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LM-M and LP-L conceived the idea. LM-M, SM-L and LP-L performed the literature search, data analysis, wrote the manuscript and approved the final version. LP-L coordinated the IBt-L4-CIGoM group.
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Muriel-Millán, L.F., Millán-López, S. & Pardo-López, L. Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics. Appl Microbiol Biotechnol 105, 7171–7185 (2021). https://doi.org/10.1007/s00253-021-11569-4
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DOI: https://doi.org/10.1007/s00253-021-11569-4