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 Posted in Asia-Pacific, North America, Research

A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border

 August 24, 2021


doi: 10.3389/fmicb.2021.674214.


eCollection 2021.

Affiliations

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Amity G Zimmer-Faust et al.


Front Microbiol.


.

Abstract

Ocean currents, multiple fecal bacteria input sources, and jurisdictional boundaries can complicate pollution source tracking and associated mitigation and management efforts within the nearshore coastal environment. In this study, multiple microbial source tracking tools were employed to characterize the impact and reach of an ocean wastewater treatment facility discharge in Mexico northward along the coast and across the Southwest United States- Mexico Border. Water samples were evaluated for fecal indicator bacteria (FIB), Enterococcus by culture-based methods, and human-associated genetic marker (HF183) and Enterococcus by droplet digital polymerase chain reaction (ddPCR). In addition, 16S rRNA gene sequence analysis was performed and the SourceTracker algorithm was used to characterize the bacterial community of the wastewater treatment plume and its contribution to beach waters. Sampling dates were chosen based on ocean conditions associated with northern currents. Evidence of a gradient in human fecal pollution that extended north from the wastewater discharge across the United States/Mexico border from the point source was observed using human-associated genetic markers and microbial community analysis. The spatial extent of fecal contamination observed was largely dependent on swell and ocean conditions. These findings demonstrate the utility of a combination of molecular tools for understanding and tracking specific pollutant sources in dynamic coastal water environments.


Keywords:

16S ribosomal DNA analysis; coastal water; droplet digital PCR; microbial source tracking; wastewater.

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures


FIGURE 1



FIGURE 1

Map of sampling locations. (A) Sampling region targeted. (B) Location of specific sites sampled. Map of Imperial Beach region inset. SAB WTP outfall located at site MX2.


FIGURE 2



FIGURE 2

Enterococci by culture (cENT) and ddPCR (dENT) and human marker (HF183 and Lachno3) levels versus distance from the SADB WTP outfall at Punta Bandera. Each event is represented by a different color, with all dates sampled combined per event. On the x-axis location of the SSADB WTP outfall is noted (PB) as is the location of the Tijuana River Estuary (TJR).


FIGURE 3



FIGURE 3

Enterococci (black bars) by culture (cENT) and ddPCR (dENT) and human marker (red bars), HF183 and Lachno3, results for Event 1–4 (A–D) for each day sampled (D1–D3). Gray bars are overlayed on top of sites MX2 (the SADB WTP outfall at Punta Bandera) and SD2 (the Tijuana River Estuary), representing the two non-beach sites. Black dashed lines represent the limit of detection and the red dashed line indicates the single sample beach water quality public health threshold for culturable enterococci of 104 MPN per 100 mL.


FIGURE 4



FIGURE 4

Contributions from potential sources (SADB WTP and Tijuana River) in each sink site using SourceTracker. Sites are arranged from a north to south along the x-axis. (A) SADB WTP included as the only source. (B) SADB WTP and Tijuana River included as potential sources.


FIGURE 5



FIGURE 5

Principal coordinate analysis performed using a Bray–Curtis dissimilarity matrix. Each symbol represents a different sampling event, while each color represents a different site. Three sites north of the United States/Mexico border were chosen to include that represent trends observed. Numbers in parentheses denote % of variation explained by each axis.


FIGURE 6



FIGURE 6

Relative abundances for the 10 most abundant families and genera associated with SADB WTP effluent stream (MX2) and Silver Strand (SD5) samples- representing the unimpacted marine microbial community. Relative abundances are shown at all sites moving south to north along the x-axis. Marine associated taxa are presented on the top and SADB WTP associated taxa are presented on the bottom.


FIGURE 7



FIGURE 7

Correlations between log-normalized microbial indicator (enterococci by culture and ddPCR and human markers, HF183 and Lachno3) results and log-normalized (x + 1) SADB WTP contributions estimated by SourceTracker. Red r-values refer to correlations between data collected at all sites. Black r-values refer to correlations between environmental beach sites only (with the SADB WTP outfall and mixing zone excluded).

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