Ni Chadhain, S. M. | bioRxiv Science

bioRxiv2026

Fecal Contributors to an Urbanized Estuary Identified by a Multi-Species qPCR Approach

Coastal waters often experience fecal contamination from human (e.g., septic systems, wastewater treatment catchments and outfalls) and non-human (e.g., wildlife, domesticated pets, and livestock) origins, posing human health risks through contaminated fisheries and recreational waters. Quantitative PCR (qPCR) methods can identify and quantify fecal origins for their management by targeting Bacteroides, a dominant group of gastrointestinal bacteria with high host specificity. This study identified major contributors and drivers of fecal contamination to Mobile Bay, Alabama, an urbanized estuary in the southern United States. We utilized a multi-species qPCR source tracking approach targeting total Bacteroides and human-, pig-, dog-, cow-, and fowl-associated Bacteroides. Water samples and environmental parameters were collected over one year from 13 sites that represent a range of potential fecal inputs common to coastal waters. Human-associated feces were a consistent major contributor to the system (positive in 82% of samples), with localized inputs from pig (wild or domestic) and dog. Freshwater discharge and nitrogen constituents were good predictors of Bacteroides concentrations in this system, while areas with impervious surfaces and developed land cover may be contributing elevated fecal indicator levels. The multi-species qPCR source tracking approach described in this study can be implemented in other watersheds to support the development of better detection, identification, and fecal management strategies for community health of coastal areas.

microbiology↗

bioRxiv2018

Assessment of the petroleum hydrocarbon biodegradation potential of the sediment microbial community from an urban fringing tidal marsh of Northern New England.

We assessed the impact of dodecane, n- hexane and gasoline on the microbial diversity of chronically polluted fringing tidal marsh sediment from the Great Bay Estuary of New Hampshire. Dilution cultures containing saturated alkane concentrations were sampled at zero, one and 10 days, and alkB and cyp153A1 alkane hydroxylase gene libraries and 16S rRNA sequences were analyzed. The initial sediment had the most diverse alkane hydroxylase sequences and phylogenetic composition whereas treated sediments became less functionally and phylogenetically diverse with alkane substrates apparently enriching a few dominant taxa. All 1-and 10-day samples were dominated by Pseudomonas- type alkane hydroxylase sequences except in dodecane treatments where primarily Rhodococcus--type alkane hydroxylases were detected. 16S rRNA profiling revealed that the Gammaproteobacteria, particularly Pseudomonas, dominated all one day samples, especially the n- hexane and gasoline treatments (63.2 and 47.2% respectively) and the 10-day n- hexane treatment (which contained 60.8% Pseudomonas and 18.6%Marinobacter). In contrast, the 10 days of dodecane treatment enriched for Actinobacteria (26.2% Rhodococcus and 32.4%Mycobacterium) and gasoline treatment enriched for Firmicutes (29.7%; mainly Bacillus, Lysinibacillus and Rumelibacillus). Our data indicate that fringing tidal marshes contain microbial communities with alkane-degrading abilities similar to larger meadow marshes, and support the hypothesis that alkane exposure reduces the functional and phylogenetic diversity of microbial communities in an alkane-specific manner. Further research to evaluate the ability of such fringing marsh communities to rebound to pre-pollutant diversity levels should be conducted to better assess the threat of petroleum to these habitats.

microbiology↗