Biochemical and Genomic Characterization of the Cypermethrin-Degrading and Biosurfactant-Producing Bacterial Strains Isolated from Marine Sediments of the Chilean Northern Patagonia

Abstract

Pesticides cause severe environmental damage to marine ecosystems. In the last ten years, cypermethrin has been extensively used as an antiparasitic pesticide in the salmon farming industry located in Northern Patagonia. The objective of this study was the biochemical and genomic characterization of cypermethrin-degrading and biosurfactant-producing bacterial strains isolated from cypermethrin-contaminated marine sediment samples collected in southern Chile (MS). Eleven strains were isolated by cypermethrin enrichment culture techniques and were identified by 16S rDNA gene sequencing analyses. The highest growth rate on cypermethrin was observed in four isolates (MS13, MS15a, MS16, and MS19) that also exhibited high levels of biosurfactant production. Genome sequence analyses of these isolates revealed the presence of genes encoding components of bacterial secondary metabolism, and the enzymes esterase, pyrethroid hydrolase, and laccase, which have been associated with different biodegradation pathways of cypermethrin. These novel cypermethrin-degrading and biosurfactant-producing bacterial isolates have a biotechnological potential for biodegradation of cypermethrin-contaminated marine sediments, and their genomes contribute to the understanding of microbial lifestyles in these extreme environments.

Keywords: biodegradation capacities; biosurfactants; cypermethrin; marine sediments.

Figure 1

Map of sampling site, geographical position, colony morphologies, phylogeny, and biodiversity of cypermethrin-degrading and biosurfactant-producing bacterial strains isolated from the Chilean Northern Patagonia samples. (a) Map of the sampling sites in the Manao Bay: samples were collected from marine sediments at 25 m depth. The asterisk indicates salmon farming center. Crosses mark the three sampling sites. (b) Colony morphology, in TSA medium, of cypermethrin-degrading and biosurfactant-producing bacterial strains isolated by enrichment using cypermethrin as the sole carbon and energy source. (c) Phylogenetic tree of cypermethrin-degrading and biosurfactant-producing bacterial strains isolated from the Northern Patagonia; black circles indicate cypermethrin-degrading and biosurfactant-producing isolated bacterial strains. Red circles indicate strains selected for genomic analysis.

Figure 2

Scanning electron microscopy of cypermethrin-degrading and biosurfactant-producing bacterial strains. Cells tended to occur in pairs. The formation of inter-cellular bonds is highlighted in strain MS16.

Figure 3

Biosynthetic gene clusters for secondary metabolites and cypermethrin degradation genes in isolated bacteria and reference strains. ¹ Soil contaminated with fuel. ² Rhizosphere of plants grown in soil contaminated with polychlorinated biphenyls (PCBs). ³ Groundwater of pea rhizoplane (Pisum sativum L.). ⁴ Deep-sea in the Fiji Sea. * Secondary metabolites identified through antiSMASH5.0 database and ** in silico analysis using a search by homology approach.

Figure 4

Proposed pathway of cypermethrin biodegradation based on the presence of esterase, laccase, and carboxylesterase-encoding genes in the genomes of MS13, MS16, MS15a, and MS19 isolates. Adapted from ¹Bhatt et al. [23], ²Zhan et al. [24], and ³Gangola et al. [17].