Pedosphere 35(6): 931--944, 2025
ISSN 1002-0160/CN 32-1315/P
©2025 Soil Science Society of China
Published by Elsevier B.V. and Science Press
| Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils |
Sabrina FESTA1 , Esteban Emanuel NIETO1, Penélope RAPOSEIRAS ALDORINO1,2, Sara CUADROS-ORELLANA3, José Matías IRAZOQUI4, Claudio QUEVEDO3, Bibiana Marina COPPOTELLI1, Irma Susana MORELLI1,2 |
1 Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de la Plata (CONICET-UNLP), La Plata CP 1900 (Argentina);
2 Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata CP 1900 (Argentina);
3 Facultad de Ciencias Agrarias y Forestales, Centro de Biotecnología de los Recursos Naturales, Universidad Católica del Maule, Talca 3466706 (Chile);
4 Instituto de Investigación de la Cadena Láctea, IdICaL (INTA-CONICET), Rafaela 2300 (Argentina) |
| Corresponding Author:Sabrina FESTA |
| ABSTRACT |
| Bioremediation is an eco-friendly alternative for soil restoration. However, its outcomes are still variable. Different bioremediation strategies were used in a chronically polycyclic aromatic hydrocarbon (PAH)-contaminated soil, and no degradation was achieved. This work attempts to study whether the soil bacterial community has the genetic potential for aromatic compound degradation (ACD). While 16S rRNA metabarcoding of that soil showed a predominance of Proteobacteria, shotgun metagenomics indicated that 99.5% of the sequences were taxonomically assigned to Streptomycetales, and almost all genes related to ACD were assigned to the latter. As comprehension of the composition and metabolic potential of a soil community can be enhanced by exploring enrichment cultures of that soil, a culture approach followed by a shotgun metagenomic analysis was performed. These enrichment cultures were obtained by sequential transfers with pyrene conducted every 7 (r-EFP) and 28 (k-MSP2) d. Both r-EFP and k-MSP2 demonstrated the ability to degrade pyrene and the presence of genes related to ACD. While Pseudomonas and Olivibacter were the predominant genera in r-EFP, Mycobacterium, Chitoniphaga, Bacillus, and Pseudoxanthomonas were predominant in k-MSP2. This study demonstrated the soil bacterial community's potential to degrade PAHs of three and four rings. Therefore, exploration of bioremediation strategies aimed at activating this potential would be worthwhile. It was confirmed that shotgun metagenomics may not fully reveal potential bacterial functions when characterizing impacted soil microbiomes. Additionally, culture-based methods complemented and increased the knowledge obtained from culture-independent approaches, demonstrating their utility for bioprospecting PAH degraders and designing microbiome engineering strategies. |
| Key Words: bioremediation|enrichment culture|pyrene|shotgun metagenomics|Streptomyces |
| Citation: Festa S, Nieto E E, Raposeiras Aldorino P, Cuadros-Orellana S, Irazoqui J M, Quevedo C, Coppotelli B M, Morelli I S. 2025. Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils. Pedosphere. 35(6): 931-944. |
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