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Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

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Dell’ Anno, Filippo, Rastelli, Eugenio, Sansone, Clementina, Brunet, Christophe, Ianora, Adrianna, Dell’ Anno, Antonio·2021·Microorganisms
DOI 10.3390/microorganisms9081695PMC PMC8400010
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Abstract

Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.

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  • Bacteria that break down hydrocarbons, such as Pseudomonas and Bacillus species, produce enzymes such as hydroxylases and dioxygenases that break down petroleum compounds.

    “Bacteria that break down hydrocarbons, such as Pseudomonas and Bacillus species, make enzymes such as hydroxylases and dioxygenases that break down petroleum compounds [26,86,87].”

    From Harnessing bacterial consortia for effective bioremediation: targeted removal of heavy metals, hydrocarbons, and persistent pollutants (2025) · cites this paper as [86]

    The Introduction names Pseudomonas and Bacillus among bacteria involved in bioremediation, and Section 3 reports that Bacillus subtilis enhanced crude-oil degradation. Sections 2 and 6 describe dioxygenases and alkane hydroxylase in bacterial hydrocarbon-degradation pathways, including a dioxygenase implicated in Pseudomonas. The copy does not establish that Bacillus produces the specified enzymes. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Bacteria that break down hydrocarbons, such as Pseudomonas and Bacillus species, produce enzymes such as hydroxylases and dioxygenases that break down petroleum compounds.

    “Bacteria that break down hydrocarbons, such as Pseudomonas and Bacillus species, make enzymes such as hydroxylases and dioxygenases that break down petroleum compounds [26,86,87].”

    From Harnessing bacterial consortia for effective bioremediation: targeted removal of heavy metals, hydrocarbons, and persistent pollutants (2025) · cites this paper as [87]

    The Introduction (page unavailable) names Pseudomonas and Bacillus among bacteria involved in bioremediation. Sections 2 and 6 describe dioxygenases and alkane hydroxylases in bacterial hydrocarbon degradation, and Section 6 links a dioxygenase to a Pseudomonas strain. Our copy does not establish that Bacillus produces either named enzyme for this purpose. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Microbial consortia can tackle complex pollutants more effectively than single strains, leading to more complete mineralization and fewer harmful byproducts.

    “These consortia can tackle complex pollutants more effectively than single strains, leading to more complete mineralization and fewer harmful byproducts [86,87].”

    From Harnessing bacterial consortia for effective bioremediation: targeted removal of heavy metals, hydrocarbons, and persistent pollutants (2025) · cites this paper as [86]

    Section 6 (page unavailable) says synthetic microbial consortia could be engineered for the complete breakdown of pollutants that require enzymes a single strain may lack. It presents this as a prospect, not a demonstrated increase in mineralization. Section 7 (page unavailable) warns about risks from incomplete biotransformation but does not establish that consortia produce fewer harmful byproducts. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Microbial consortia can tackle complex pollutants more effectively than single strains, leading to more complete mineralization and fewer harmful byproducts.

    “These consortia can tackle complex pollutants more effectively than single strains, leading to more complete mineralization and fewer harmful byproducts [86,87].”

    From Harnessing bacterial consortia for effective bioremediation: targeted removal of heavy metals, hydrocarbons, and persistent pollutants (2025) · cites this paper as [87]

    Section 6 says synthetic microbial consortia could be engineered for complete breakdown of pollutants that require enzymes rarely found in a single strain. It presents this as a future possibility, not an established comparative result, and does not report more complete mineralization or fewer harmful byproducts. Section 7 instead warns that incomplete biotransformation could increase ecotoxicological risk. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • Antioxidant-producing microorganisms can mitigate ARG enrichment and dissemination by reducing ROS levels, limiting genetic mutations and plasmid-mediated ARG transfer.

    “Recent studies have demonstrated that antioxidant-producing microorganisms can mitigate ARG enrichment and dissemination by reducing ROS levels, thereby limiting genetic mutations and plasmid-mediated ARG transfer in microbial communities [87,302].”

    From Harnessing bacterial consortia for effective bioremediation: targeted removal of heavy metals, hydrocarbons, and persistent pollutants (2025) · cites this paper as [87]

    The Introduction describes microorganisms used to remediate contaminated sediments and mentions fungal production of catalases and peroxidases, but not antibiotic resistance genes. Searches for antioxidant-producing microorganisms, ROS, ARG dissemination, mutations, and plasmid-mediated transfer found no passage addressing the claimed mechanism. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Dell’ Anno, F., Rastelli, E., Sansone, C., Brunet, C., Ianora, A., & Dell’ Anno, A.
Affiliations
  • Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
  • Stazione Zoologica Anton Dohrn (IT)
  • Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
ORCID
Venue
Microorganisms
Publisher
MDPI AG
Published
2021-08-10
Volume
9
Issue
8
Pages
1695
ISSN
2076-2607 (ISSN-L)
DOI
10.3390/microorganisms9081695
PMC
PMC8400010
OpenAlex
W3187655492
Cited by
194
References
1
Citations by year
2026: 42 · 2025: 52 · 2024: 39 · 2023: 31 · 2022: 30
FWCI
1.22
Type
journal article
Language
en
Open access
Licence
Locations
  • Microorganisms (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Università Politecnica delle Marche (Università Politecnica delle Marche) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
Italian 582 Ministry for Education, University and Research and Comitato Interministeriale di Programma-583 zione Economica (C62F16000170001)
Topics
  • Physical Sciences › Environmental Science › Pollution › Microbial bioremediation and biosurfactants
  • Physical Sciences › Environmental Science › Pollution › Oil Spill Detection and Mitigation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Steroid Chemistry and Biochemistry
Keywords
petroleum hydrocarbons, marine sediment contamination, bioremediation, bacteria, fungi, microalgae, hydrocarbon-degrading microorganisms, omics approaches, marine sediment, oil pollution

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