Integrating metagenomics, 16S rRNA gene metabarcoding and culture approaches: a better outlook for functional profiling of a PAH-contaminated soil

FESTA SABRINA, GRANADA MARINA, IRAZOQUI JOSÉ M., QUEVEDO-GALLARDO CLAUDIO, AMADIO ARIEL F. , CUADROS-ORELLANA SARA, COPPOTELLI BIBIANA M., MORELLI IRMA S.

Laussane

Simposio; 18th International Symposium on Microbial Ecology- ISME18,; 2022

ISME International Society of Microbial Ecology

Understanding microbial diversity and function within a contaminated niche is critical for designing bioremediation strategies. This research aimed to assess chronically hydrocarbon contaminated soil bacterial diversity and their aromatic compound degradation (ACD) potential by integrating shotgun metagenomic, 16S rRNA gene metabarcoding and culture approaches. While metabarcoding soil study (Illumina NovaSeq-QIIME2) showed a dominance of Proteobacteria (53,7% relative abundance), metagenomics (Illumina MiSeq-Trimmomatic/Spades/Prodigal/KRAKEN2) indicated that 99,5% of the sequences were taxonomically assigned to Streptomycetales order and that almost all genes related to ACD were assigned to the latter. To inspect other phyla contribution to ACD, a functional prediction was delved by PICRUSt2 and also two culture approaches were used. PICRUSt2 revealed that ACD pathways were mostly found in Alphaproteobacteria, Actinobacteria and Gammaproteobacteria classes. An enrichment culture (r-EF18P) was obtained with pyrene as sole carbon and energy source and a bacterial strain identified as a member of Mycolicibacterium genus (Actinocbacteria), was isolated in pyrene agar plates (S19P6). Both cultures demonstrated the ability to degrade more than 90% of the supplemented pyrene after 21 days of incubation (HPLC-UV). 16S rRNA gene metabarcoding (Illumina NovaSeq-QIIME2) and shotgun metagenomics (Illumina NovaSeq-Trimmomatic/Megahit/CheckM/Prokka/Kaiju) approaches in r-EF18P indicated predominance of Proteobacteria (87,6%) and the presence of genes responsible for the degradation of phenanthrene, 1-hydroxy-2-naphthoic acid and central intermediates mostly assigned to the predominant phyla. Genes coding for a dioxygenase involved in pyrene initial attack was detected in soil, r-EF18P and S19P6 (PCR). Complementing different methodologies enable the recognition of the metabolic potential of soil Proteobacteria related to ACD.