Prokaryotic community structure and predicted metabolism associated with hydrocarbon degradation in marine sediments from the Northwest Coast of Baja California, Mexico

Abstract

Purpose

The coastal environment is a fragile ecosystem exposed to anthropogenic pressures, including pollution. Microbial ecology studies have demonstrated the importance of microbial metabolism in marine sediments to maintain nutrient cycling; however, recalcitrant contaminants such as polycyclic aromatic hydrocarbons (PAHs) could affect these microbial communities. This study aimed to investigate the diversity of microbial communities on marine sediments from the North Occidental Coast of Baja California, Mexico (NOCBC) and their potential aromatic hydrocarbon catabolic pathways.

Materials and methods

During the Southern California Bight Oceanographic Campaign, sediment samples were collected in September 2018 from 33 coastal sites from the Tijuana-San Diego border to Punta Banda Cape, Ensenada (Mexico). The samples were analyzed for grain size, total PAHs, and organic carbon (OC) concentrations. Next, the bacterial communities were identified using Illumina high-throughput sequencing of 16S rRNA genes, and hydrocarbonoclastic function was inferred using PICRUSt2.

Results

According to Canadian and EPA guidelines for marine sediments, the total PAH concentration from the samples suggested a low pollution impact. Sequence analysis identified 27 phyla and 36 candidate divisions across the sampled sediments. The dominant phyla were Pseudomonadota, Bacteroidota, Planctomycetota, and Crenarchaeota. At the family level, the most prominent were Piscirickettsiaceae, OM60, Flavobacteriaceae, Pirellulaceae, and Cenarchaeaceae. The key genera were identified as Nitrosopumilus, Lutimonas, and Desulfococcus; nine Amplicon Sequence Variants (ASVs) represented the core microbiome across the sites, comprising about 7.68% of the total reads. The predictive functional analysis detected 47 principal pathways involved in hydrocarbon degradation, including catechol, protocatechuate, and aerobic toluene degradation routes.

Conclusions

Our data suggest the presence of hot spots for aromatic degradative pathways in those sampling sites near cities, where a significant proportion of aromatic hydrocarbon-degrading microorganisms may be present. This study represents the first census of the prokaryotic communities from marine sediments of NOCBC, which harbors diverse communities with hydrocarbonoclastic potential. These results could provide constructive guidelines on ecosystem management and pollution mitigation actions.