Silent bacteria: Intrinsic bioremediation potential in the sediments of Lake Faro (Messina, Italy)

Alessia Lunetta; Simone Cappello; Salvatore Giacobbe; Gabriella Caruso; Sabrina Patania; Antonietta Specchiulli; Tommaso Scirocco; Monia Renzi; Antonella D'Amore; Maria Genovese; Alessia Lunetta; Simone Cappello; Salvatore Giacobbe; Gabriella Caruso; Sabrina Patania; Antonietta Specchiulli; Tommaso Scirocco; Monia Renzi; Antonella D'Amore; Maria Genovese

doi:10.3934/microbiol.2026015

AIMS Microbiology

2026, Volume 12, Issue 2: 354-376. doi: 10.3934/microbiol.2026015

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Research article

Silent bacteria: Intrinsic bioremediation potential in the sediments of Lake Faro (Messina, Italy)

1.
Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna—Piazza di Porta S. Donato 1, 4126 Bologna (BO), Italy
2.
Institute for Biological Resources and Marine Biotechnologies (IRBIM) section of Messina, National Research Council (CNR-IRBIM), Spianata S. Raineri 86, 98122 Messina, Italy
3.
Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy
4.
PhD School of “Applied Biology and Experimental Medicine”, Faculty of Sciences, University of Messina, Viale F. Stagno D'Alcontres 5, 98166 Messina, Italy
5.
Institute for Biological Resources and Marine Biotechnologies (IRBIM) section of Lesina, Na-tional Research Council (CNR-IRBIM), Via Pola 4, 71010 Lesina (Foggia), Italy
6.
University of Trieste, Via L. Giorgieri, 10, Italy

Received: 27 January 2026 Revised: 27 May 2026 Accepted: 05 June 2026 Published: 22 June 2026

Lake sediments can act as reservoirs for contaminants and host microbial communities with potential roles in natural ecosystem functioning. This study explored the occurrence of hydrocarbon-degrading bacteria, including “silent” hydrocarbon-responsive populations detectable after selective enrichment, in interfacial sediments of Lake Faro, a brackish meromictic basin in Messina, Italy. Sediment samples collected from five stations were chemically characterized and incubated in microcosms enriched with tetradecane, phenanthrene, or crude oil as the sole carbon and energy source. Chemical analyses revealed that hydrocarbons HCs > 12 were below the quantification limit at all stations, while PAHs were detectable at low concentrations. After 80 days of enrichment, microbial abundance increased, especially in tetradecane and crude oil–amended microcosms, and hydrocarbon-degrading bacteria were selectively enriched. Overall, 25 bacterial isolates were obtained, of which 16 were identified by 16S rRNA gene sequencing and assigned to taxa with reported hydrocarbon-degrading potential, including Isoalcanivorax pacificus, Marinobacter hydrocarbonoclasticus, Pseudoalteromonas sp., Vibirio alginolyticus, and Stappia indica. Several strains showed emulsifying activity, with E₂₄ values up to 60%. These findings suggest that Lake Faro sediments host a latent hydrocarbon-responsive bacterial fraction, with intrinsic bioremediation potential and ecological relevance for natural attenuation processes in transitional aquatic ecosystems.
- bioremediation,
- hydrocarbon-degrading bacteria,
- lake sediments,
- microcosms,
- transitional ecosystem
Citation: Alessia Lunetta, Simone Cappello, Salvatore Giacobbe, Gabriella Caruso, Sabrina Patania, Antonietta Specchiulli, Tommaso Scirocco, Monia Renzi, Antonella D'Amore, Maria Genovese. Silent bacteria: Intrinsic bioremediation potential in the sediments of Lake Faro (Messina, Italy)[J]. AIMS Microbiology, 2026, 12(2): 354-376. doi: 10.3934/microbiol.2026015

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Abstract

Lake sediments can act as reservoirs for contaminants and host microbial communities with potential roles in natural ecosystem functioning. This study explored the occurrence of hydrocarbon-degrading bacteria, including “silent” hydrocarbon-responsive populations detectable after selective enrichment, in interfacial sediments of Lake Faro, a brackish meromictic basin in Messina, Italy. Sediment samples collected from five stations were chemically characterized and incubated in microcosms enriched with tetradecane, phenanthrene, or crude oil as the sole carbon and energy source. Chemical analyses revealed that hydrocarbons HCs > 12 were below the quantification limit at all stations, while PAHs were detectable at low concentrations. After 80 days of enrichment, microbial abundance increased, especially in tetradecane and crude oil–amended microcosms, and hydrocarbon-degrading bacteria were selectively enriched. Overall, 25 bacterial isolates were obtained, of which 16 were identified by 16S rRNA gene sequencing and assigned to taxa with reported hydrocarbon-degrading potential, including Isoalcanivorax pacificus, Marinobacter hydrocarbonoclasticus, Pseudoalteromonas sp., Vibirio alginolyticus, and Stappia indica. Several strains showed emulsifying activity, with E₂₄ values up to 60%. These findings suggest that Lake Faro sediments host a latent hydrocarbon-responsive bacterial fraction, with intrinsic bioremediation potential and ecological relevance for natural attenuation processes in transitional aquatic ecosystems.

Acknowledgments

The authors would like to thank the IRBIM-CNR of Messina (Italy) for supporting this study. This study represents partial fulfillment of the requirements for the doctoral thesis of A. Lunetta and A. d'Amore within the international Program “Innovative Technologies and Sustainable Use of Mediterranean Sea Fishery and Biological Re-sources” (FishMed-PhD; www.FishMed-PhD.org) at the University of Bologna. Italy. This study is also a partial result of PhD project of A. Lunetta. The authors are grateful to the Bioscience Research Centre for the support of this study.
This work was financially supported by the National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for tender No. 3138 of 16 December 2021, rectified by Decree n.3175 of 18 December 2021 of Italian Ministry of University and Research funded by the European Union–Next Generation EU (Award Number: Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP B83C22002930006, Project title “National Biodiversity Future Center—NBFC”).
The authors thank Enzo Messina (CNR-IRBIM, Messina) for depositing the sequences.

Conflict of interest

The authors declare no conflict of interest.

Author contributions

Alessia Lunetta: Writing—Original Draft, Methodology, Investigation, Data curation, Formal analysis. Simone Cappello: Resources; Writing-Original Draft; Methodology; Investigation; Data curation; Formal analysis; Funding acquisition; Supervision. Salvatore Giacobbe: Conceptualization; Methodology. Gabriella Caruso: Writing-Original Draft; Data curation; Formal analysis; Sabrina Patania, Antonietta Specchiulli, Tommaso Scirocco, Monia Renzi, Antonella D'Amore: Data curation; Formal analysis. Maria Genovese: Conceptualization; Methodology; Resources; Funding acquisition; Supervision

Data availability

Data presented here are available upon direct request to Dr. Alessia Lunetta (CNR-IRBIM, Messina, Italy). The 16S rRNA gene sequences of the bacterial isolates obtained in this study were deposited in the NCBI GenBank database under the accession numbers reported in Table 5. The remaining data supporting the findings of this study are included within the article.

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