The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation

Abstract

Surface water used for produce production is a potential source of pre-harvest contamination with foodborne pathogens. Decisions on how to mitigate food safety risks associated with pre-harvest water use currently rely on generic Escherichia coli -based water quality tests, although multiple studies have suggested that E. coli levels are not a suitable indicator of the food safety risks under all relevant environmental conditions. Hence, improved understanding of spatiotemporal variability in surface water microbiota composition is needed to facilitate identification of alternative or supplementary indicators that co-occur with pathogens. To this end, we aimed to characterize the composition of bacterial and fungal communities in the sediment and water fractions of 68 agricultural water samples collected from six New York streams. We investigated potential associations between the composition of microbial communities, environmental factors and Salmonella and/or Listeria monocytogenes isolation. We found significantly different composition of fungal and bacterial communities among sampled streams and among water fractions of collected samples. This indicates that geography and the amount of sediment in a collected water sample may affect its microbial composition, which was further supported by identified associations between the flow rate, turbidity, pH and conductivity, and microbial community composition. Lastly, we identified specific microbial families that were weakly associated with the presence of Salmonella or Listeria monocytogenes , however, further studies on samples from additional streams are needed to assess whether identified families may be used as indicators of pathogen presence.

Correlation of Salmonella enterica and Listeria monocytogenes in Irrigation Water to Environmental Factors, Fecal Indicators, and Bacterial Communities

“…and L. monocytogenes in irrigation ponds, respectively. The diverse and complex composition of microbial communities in irrigation water are associated with environmental conditions and water sources ( Gu et al, 2019b ; Chung et al, 2020 ). The sample size ( n = 96) performed for high-throughput sequencing in this study might be limited to cover the comprehensive microbial communities.…”

Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes

“…Similar to other freshwater ecosystems [50][51][52], study lakes were dominated by a 'core' group of relatively abundant taxa that exhibited temporal turnover. Exiguobacterium (Firmicutes) was the most overall relatively abundant taxon in the study (5.7%) and was collected from a majority of lakes and times with the exception of February samples from BL1 bottom and BL2 top and bottom.…”

It’s a Long Way to the Tap: Microbiome and DNA-Based Omics at the Core of Drinking Water Quality

“…On the other hand, surface waters are more affected by seasonal and environmental factors, such as weather and temperature, and thus, the concentration of certain chemicals is more variable. Being groundwater and surface water ecosystems with different characteristics, the microbial communities are also different [9]. For instance, groundwater has been shown to harbor microorganisms belonging to the Candidate Phyla Radiation (CPR) and even ultra-small bacteria (see Section 2.2) [10,11].…”