Microbial Source Tracking of Fecal Indicating Bacteria in Coral Reef Waters, Recreational Waters, and Groundwater of Saipan by Real-Time Quantitative PCR

Grey and harbor seals in France (mainland and Saint-Pierre et Miquelon): microbial communities and identification of a microbial source tracking seal marker

Introduction

Seals, protected wild marine mammals, are widely found in waters around the world. However, rising concerns about their increasing numbers in some areas have led to potential worries regarding microbiological contamination of coastal areas by their feces, which could impact bathing and shellfish-harvesting activities. To the best of our knowledge, no study has been conducted on the bacterial and RNA viral communities present in the feces of both grey and harbor seals, which are the two main seal species observed in mainland France and overseas.

Methods

Fecal bacterial (n = 132) and RNA viral (n = 40) communities of seals were analyzed using 16S rRNA gene amplicon high-throughput sequencing and viral RNA sequencing methods, respectively. In addition, to identify the specific characteristics of seal fecal microbial communities compared to other animal fecal microbial communities that may also contaminate coastal areas, the bacterial communities of seals were compared to those of wild waterbirds and breeding animals (i.e., cattle and pigs) which could be present in upstream catchments of coastal areas. Finally, ANCOM was used to identify unique and seal-associated Amplicon Sequence Variants (ASVs), aiming to develop a Microbial Source Tracking (MST) bacterial qPCR marker associated with seals.

Results and discussion

The bacterial communities of grey and harbor seals were not found to be significantly different and were characterized by a predominance of Firmicutes, including the genera Clostridium sensu stricto 1 and Peptoclostridium, followed by Fusobacteriota with the genus Fusobacterium, and Bacteroidota with the genus Bacteroides. However, variations in bacterial communities between sites and individuals were observed. Similar observations were made for the RNA viral communities being characterized by a predominance of Picobirnaviridae (44% of total reads) and Astroviridae (15%). This study successfully developed a sensitive (89.8%) and specific (97.1%) MST qPCR marker targeting grey seal-associated bacteria belonging to the Bifidobacteriaceae family. This marker can be used to identify potential fecal contamination of coastal areas by seals and complements the MST toolboxes of markers already developed for humans, wild birds and livestock.

Fecal Impairment Framework, A New Conceptual Framework for Assessing Fecal Contamination in Recreational Waters

Fecal pollution of surface water is a pervasive problem that negatively affects waterbodies concerning both public health and ecological functions. Current assessment methods monitor fecal indicator bacteria (FIB) to identify pollution sources using culture-based quantification and microbial source tracking (MST). These types of information assist stakeholders in identifying likely sources of fecal pollution, prioritizing them for remediation, and choosing appropriate best management practices. While both culture-based quantification and MST are useful, they yield different kinds of information, potentially increasing uncertainty in prioritizing sources for management. This study presents a conceptual framework that takes separate human health risk estimates based on measured MST and E. coli concentrations as inputs and produces an estimate of the overall fecal impairment risk as its output. The proposed framework is intended to serve as a supplemental screening tool for existing monitoring programs to aid in identifying and prioritizing sites for remediation. In this study, we evaluated the framework by applying it to two primarily agricultural watersheds and several freshwater recreational beaches using existing routine monitoring data. Based on a combination of E. coli and MST results, the proposed fecal impairment framework identified four sites in the watersheds as candidates for remediation and identified temporal trends in the beach application. As these case studies demonstrate, the proposed fecal impairment framework is an easy-to-use and cost-effective supplemental screening tool that provides actionable information to managers using existing routine monitoring data, without requiring specialized expertize.

Microbe-sediment interactions in Great Lakes recreational waters: Implications for human health risk

Microbial assessments of recreational water have traditionally focused on culturing or DNA-based approaches of the planktonic water column, omitting influence from microbe-sediment relationships. Sediment (bed and suspended) has been shown to often harbour levels of bacteria higher than the planktonic phase. The fate of suspended sediment (SS) bacteria is extensively related to transport dynamics (e.g., deposition) of the associated sediment/floc. When hydraulic energy allows, SS will settle, introducing new (potentially pathogenic) organisms to the bed. With turbulence, including waves, currents and swimmers, the risk of human ingestion is elevated due to resuspension of bed sediment and associated microbes. This research used multiplex nanofluidic reverse transcriptase quantitative PCR on RNA of bacteria associated with bed and SS to explore the active bacteria in freshwater shorelines. Bacterial genes of human health concern regarding recreational water use were targeted, such as faecal indicator bacteria (FIB), microbial source tracking genes and virulence factors from waterborne pathogens. Results indicate avian sources (i.e., gulls, geese) to be the largest nonpoint source of FIB associated with sediment in Great Lakes shorelines. This research introduces a novel approach to microbial water quality assessments and enhances our understanding of microbe-sediment dynamics and the quality of freshwater beaches.

Detection and impact of sewage pollution on South Kohala's coral reefs, Hawai'i

Sewage pollution from on-site sewage disposal systems and injection wells is impacting coral reefs worldwide. Our study documented the presence and impact of sewage on South Kohala's coral reefs, on Hawai'i Island, through benthic water quality and macroalgal sampling (fecal indicator bacteria, nutrients, δ¹⁵N macroalgal tissue), NO₃^- stable isotope mixing models, water motion measurements, and coral reef surveys. Sewage pollution was moderate on the offshore reef from benthic seeps, and water motion mixed and diluted it across the benthos. These conditions likely contribute to the dominance of turf algae cover, and the severity and prevalence of growth anomalies and algal overgrowth on corals. Use of multiple indicators and studying water motion was necessary to assess sewage pollution and identify environmental drivers associated with impaired coral health conditions. Methods used in this study can be utilized by natural resource managers to identify and reduce anthropogenic stressors to coral reefs.

Fecal indicator bacteria levels at a marine beach before, during, and after the COVID-19 shutdown period and associations with decomposing seaweed and human presence

Studies are limited that evaluate seaweed as a source of bacteria to beach waters. The objective of the current study was to evaluate whether seaweed, along with humans and other animals, could be the cause of beach advisories due to elevated levels of enterococci. The monitoring period occurred a year prior to and through the COVID-19 beach shutdown period, which provided a unique opportunity to evaluate bacteria levels during prolonged periods without recreational activity. Samples of water, sediment, and seaweed were measured for enterococci by culture and qPCR, in addition to microbial source tracking by qPCR of fecal bacteria markers from humans, dogs, and birds. During periods of elevated enterococci levels in water, these analyses were supplemented by chemical source tracking of human-associated excretion markers (caffeine, sucralose, acetaminophen, ibuprofen, and naproxen). Results show that enterococci with elevated levels of human fecal markers persist in the seaweed and sediment and are the likely contributor to elevated levels of bacteria to the nearshore waters. During the shutdown period the elevated levels of enterococci in the sediment were isolated to the seaweed stranding areas. During periods when the beaches were open, enterococci were distributed more uniformly in sediment across the supratidal and intertidal zones. It is hypothesized from this study that human foot traffic may be responsible for the spread of enterococci throughout these areas. Overall, this study found high levels of enterococci in decomposing seaweed supporting the hypothesis that decomposing seaweed provides an additional substrate for enterococci to grow.

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

Protection of Water Resources from Agriculture Pollution: An Integrated Methodological Approach for the Nitrates Directive 91-676-EEC Implementation

Nitrogen is a vital nutrient helpful to plants and crop growth. However, among the leading causes of water resources pollution is the excess nitrogen from agricultural sources. In European Union countries, the Nitrates Directive has been approved to reduce this problem monitoring of water bodies with regard to nitrate concentrations, designation of Nitrate Vulnerable Zones (NVZs), and establishing codes of good agricultural practices and measures to prevent and reduce water pollution from nitrates. In light of this, we propose an integrated methodological approach to better manage a environmental issue as the perimeter of NVZs with the prospective that our approach could be used in the future by other member states representing a Best Practice in that direction. The methodology is based on data integration applied in a GIS environment. Different available data representing the knowledge of the territory were harmonised, systematised and georeferenced, in order to increase the environmental framework, preserve the contamination of the water resource and give indications on the measures to be implemented to apply in the best way possible the Nitrates Directive. Finally, it was also possible to overcome the infringement procedure in progress for Italy and the Puglia region and proceed to new designation of NVZs.

Integrated analyses of fecal indicator bacteria, microbial source tracking markers, and pathogens for Southeast Asian beach water quality assessment

The degradation of coastal water quality from fecal pollution poses a health risk to visitors at recreational beaches. Fecal indicator bacteria (FIB) are a proxy for fecal pollution; however the accuracy of their representation of fecal pollution health risks at recreational beaches impacted by non-point sources is disputed due to non-human derivation. This study aimed to investigate the relationship between FIB and a range of culturable and molecular-based microbial source tracking (MST) markers and pathogenic bacteria, and physicochemical parameters and rainfall. Forty-two marine water samples were collected from seven sampling stations during six events at two tourist beaches in Thailand. Both beaches were contaminated with fecal pollution as evident from the GenBac3 marker at 88%-100% detection and up to 8.71 log₁₀ copies/100 mL. The human-specific MST marker human polyomaviruses JC and BK (HPyVs) at up to 4.33 log₁₀ copies/100 mL with 92%-94% positive detection indicated that human sewage was likely the main contamination source. CrAssphage showed lower frequencies and concentrations; its correlations with the FIB group (i.e., total coliforms, fecal coliforms, and enterococci) and GenBac3 diminished its use as a human-specific MST marker for coastal water. Human-specific culturable AIM06 and SR14 bacteriophages and general fecal indicator coliphages also showed less sensitivity than the human-specific molecular assays. The applicability of the GenBac3 endpoint PCR assay as a lower-cost prescreening step prior to the GenBac3 qPCR assay was supported by its 100% positive predictive value, but its limited negative predictive values required subsequent qPCR confirmation. Human enteric adenovirus and Vibrio cholerae were not found in any of the samples. The HPyVs related to Vibrio parahaemolyticus, Vibrio vulnificus, and 5-d rainfall records, all of which were more prevalent and concentrated during the wet season. More monitoring is therefore recommended during wet periods. Temporal differences but no spatial differences were observed, suggesting the need for a sentinel site at each beach for routine monitoring. The exceedance of FIB water quality standards did not indicate increased prevalence or concentrations of the HPyVs or Vibrio spp. pathogen group, so the utility of FIB as an indicator of health risks at tropical beaches maybe challenged. Accurate assessment of fecal pollution by incorporating MST markers could lead to developing a more effective water quality monitoring plan to better protect human health risks in tropical recreational beaches.