Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California

Abstract

Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens originating from agricultural activities such as Shiga Toxin-producing E. coli (STEC) in such sediments remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley was sampled over a nine-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and comparable to the functional and taxonomic diversity observed in soils. With our sequencing effort (~4 Gbp per library), we were unable to detect any pathogenic Escherichia coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low pathogen abundance. Further, no significant differences were detected in the abundance of human- or cow-specific gut microbiome sequences compared to upstream, more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, a high baseline level of metagenomic reads encoding antibiotic resistance genes (ARGs) was found in all samples and was significantly higher compared to ARG reads in metagenomes from other environments, suggesting that these communities may be natural reservoirs of ARGs. Overall, our metagenomic results revealed that creek sediments are not a major sink for anthropogenic runoff and the public health risk associated with these sediment microbial communities may be low.\n\nIMPORTANCECurrent agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food and water-borne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health is assessed by culture-based tests for the intestinal bacterium, E. coli. However, the accuracy of these traditional methods (e.g., low quantification, and false positive signal when PCR-based) and their suitability for sediments remains unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the U.S. in order to assess how agricultural runoff affects the native microbial communities and if the presence of STEC in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.