Research Article: Variability in metagenomic samples from the Puget Sound: Relationship to temporal and anthropogenic impacts

Date Published: February 13, 2018

Publisher: Public Library of Science

Author(s): James C. Wallace, Jessica E. Youngblood, Jesse A. Port, Alison C. Cullen, Marissa N. Smith, Tomomi Workman, Elaine M. Faustman, Peter E. Larsen.


Whole-metagenome sequencing (WMS) has emerged as a powerful tool to assess potential public health risks in marine environments by measuring changes in microbial community structure and function in uncultured bacteria. In addition to monitoring public health risks such as antibiotic resistance determinants, it is essential to measure predictors of microbial variation in order to identify natural versus anthropogenic factors as well as to evaluate reproducibility of metagenomic measurements.This study expands our previous metagenomic characterization of Puget Sound by sampling new nearshore environments including the Duwamish River, an EPA superfund site, and the Hood Canal, an area characterized by highly variable oxygen levels. We also resampled a wastewater treatment plant, nearshore and open ocean sites introducing a longitudinal component measuring seasonal and locational variations and establishing metagenomics sampling reproducibility. Microbial composition from samples collected in the open sound were highly similar within the same season and location across different years, while nearshore samples revealed multi-fold seasonal variation in microbial composition and diversity. Comparisons with recently sequenced predominant marine bacterial genomes helped provide much greater species level taxonomic detail compared to our previous study. Antibiotic resistance determinants and pollution and detoxification indicators largely grouped by location showing minor seasonal differences. Metal resistance, oxidative stress and detoxification systems showed no increase in samples proximal to an EPA superfund site indicating a lack of ecosystem adaptation to anthropogenic impacts. Taxonomic analysis of common sewage influent families showed a surprising similarity between wastewater treatment plant and open sound samples suggesting a low-level but pervasive sewage influent signature in Puget Sound surface waters. Our study shows reproducibility of metagenomic data sampling in multiple Puget Sound locations while establishing baseline measurements of antibiotic resistance determinants, pollution and detoxification systems. Combining seasonal and longitudinal data across these locations provides a foundation for evaluating variation in future studies.

Partial Text

Microorganisms are ubiquitously distributed throughout the earth, creating unique environmental microbiomes that reflect habitat type and conditions [1, 2]. Coastal microbiomes are particularly vulnerable to changing habitat conditions because they are at the interface of land-sea interactions. Increasing urbanization and the changing climate are putting stress on coastal ecosystems [3–5] and have the potential to alter microbiome community structure and function [6–8]. These changes in the microbial community can include increased pathogenicity and antibiotic resistance and have the potential to impact human health and wellbeing [9–12]. In addition to addressing human health concerns, changes in microbial community can serve as early indicators of human impact and environmental degradation [7, 13]. Aquatic environments are particularly relevant because they act as reservoirs for environmental pollutants [4, 10, 14], making the composition of these microbial communities of special importance for understanding the bidirectional relationship between humans and microbes.

Proteobacteria are found in every environment and include the largest and most diverse division among prokaryotes and the majority of agricultural, industrial and medical relevant organisms [40]. As shown in S2 Table, Puget Sound metagenomic microbial communities were predominantly composed of the phylum Proteobacteria, ranging from approximately 47% in the freshwater WWTP-1 effluent to over 67% in in the JBP-2 sample at the mouth of the Duwamish River. The two next most abundant phyla were Bacteroidetes (38%) in the Duwamish River HHP-2 sample and Actinobacteria (28%) in the WWTP-2 sample. The phylum Firmicutes, which contains human pathogenic genera such as Streptococcus, was found mainly in WWTP samples (3.3%-7.8%) and at less than 0.5% abundance in all other samples.

This is the first study to introduce longitudinal sampling of Puget Sound nearshore and open sound surface waters and wastewater treatment effluent using WMS methods. At a minimum, it helps establish baseline data in Puget Sound describing microbial community and function leading to a better understanding of descriptors of healthy versus abnormal or human-impacted ecosystems. Overall, we found a highly similar microbial community structure for geographically disparate open sound sites sampled in the same season one year apart. We also saw distinct seasonal and local sampling site variability relating to taxonomy, species diversity, predominant species, antibiotic resistance determinants and anthropogenic indicators.




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