Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation
Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustaina...
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| Published in | Environmental pollution (1987) Vol. 317; p. 120772 |
|---|---|
| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Elsevier Ltd
15.01.2023
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60–100%) and HMs removal (21–100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.
[Display omitted]
•Highly polluted sediments' microbiome enriched for PAH- and HM-remediating bacteria.•Two new Alcanivorax and Halomonas strains isolated show high bioremediation yields.•Metagenome assembly unveiled their novel genomic assets for PAH and HM remediation.•Possible use for efficient bioremediation of sites mixedly polluted by PAHs and HMs. |
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| AbstractList | Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs. Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs. Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60–100%) and HMs removal (21–100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs. [Display omitted] •Highly polluted sediments' microbiome enriched for PAH- and HM-remediating bacteria.•Two new Alcanivorax and Halomonas strains isolated show high bioremediation yields.•Metagenome assembly unveiled their novel genomic assets for PAH and HM remediation.•Possible use for efficient bioremediation of sites mixedly polluted by PAHs and HMs. |
| ArticleNumber | 120772 |
| Author | Pepi, Milva Joaquim van Zyl, Leonardo Golyshin, Peter N. Dell’Anno, Antonio Dell’Anno, Filippo Buschi, Emanuela Rastelli, Eugenio Sansone, Clementina Ianora, Adrianna Cannavacciuolo, Antonio Trindade, Marla de Pascale, Donatella Brunet, Christophe |
| Author_xml | – sequence: 1 givenname: Filippo surname: Dell’Anno fullname: Dell’Anno, Filippo email: filippo.dellanno@szn.it organization: Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121, Naples, Italy – sequence: 2 givenname: Leonardo surname: Joaquim van Zyl fullname: Joaquim van Zyl, Leonardo email: lvanzyl@uwc.ac.za organization: Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa – sequence: 3 givenname: Marla orcidid: 0000-0002-2478-0270 surname: Trindade fullname: Trindade, Marla email: ituffin@uwc.ac.za organization: Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa – sequence: 4 givenname: Emanuela surname: Buschi fullname: Buschi, Emanuela email: emanuela.buschi@szn.it organization: Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy – sequence: 5 givenname: Antonio surname: Cannavacciuolo fullname: Cannavacciuolo, Antonio email: antonio.cannavacciuolo@szn.it organization: Department of Integrative Marine Ecology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy – sequence: 6 givenname: Milva surname: Pepi fullname: Pepi, Milva email: milva.pepi@szn.it organization: Department of Integrative Marine Ecology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy – sequence: 7 givenname: Clementina orcidid: 0000-0002-3007-8154 surname: Sansone fullname: Sansone, Clementina email: clementina.sansone@szn.it organization: Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121, Naples, Italy – sequence: 8 givenname: Christophe orcidid: 0000-0003-1435-358X surname: Brunet fullname: Brunet, Christophe email: brunet@szn.it organization: Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121, Naples, Italy – sequence: 9 givenname: Adrianna orcidid: 0000-0002-6511-5517 surname: Ianora fullname: Ianora, Adrianna email: ianora@szn.it organization: Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121, Naples, Italy – sequence: 10 givenname: Donatella surname: de Pascale fullname: de Pascale, Donatella email: donatella.depascale@szn.it organization: Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121, Naples, Italy – sequence: 11 givenname: Peter N. orcidid: 0000-0002-5433-0350 surname: Golyshin fullname: Golyshin, Peter N. email: p.golyshin@bangor.ac.uk organization: Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, UK – sequence: 12 givenname: Antonio surname: Dell’Anno fullname: Dell’Anno, Antonio email: a.dellanno@univpm.it organization: Department of Life and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy – sequence: 13 givenname: Eugenio surname: Rastelli fullname: Rastelli, Eugenio email: eugenio.rastelli@szn.it organization: Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy |
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| Keywords | Next-generation sequencing Bioremediation Marine biotechnology Polycyclic aromatic hydrocarbons Heavy metals |
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| SubjectTerms | Alcanivorax Bacteria - genetics Bacteria - metabolism bacterial culture Biodegradation, Environmental Bioremediation coasts Geologic Sediments - microbiology Halomonas Heavy metals Hydrocarbons - metabolism lead Marine biotechnology Metals, Heavy - metabolism microbiome Microbiota naphthalene Next-generation sequencing petroleum Petroleum - analysis pollution Polycyclic aromatic hydrocarbons Polycyclic Aromatic Hydrocarbons - metabolism species |
| Title | Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation |
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