Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops

Allard, Sarah; Callahan, Mary Theresa; Bui, Anthony; Ferelli, Angela Marie C.; Chopyk, Jessica; Chattopadhyay, Suhana; Mongodin, Emmanuel F.; Micallef, Shirley A.; Sapkota, Amy R.

doi:10.1016/j.scitotenv.2019.02.179

Cited by 31 publications

(21 citation statements)

References 42 publications

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“…This is consistent with previous finding that generic E. coli is a poor fecal indicator in soil from fresh produce field (Ceuppens et al, 2015). Generic E. coli can be present in non-fecal environment and has the ability to proliferate in the environment (Park et al, 2016; Patterson et al, 2018; Allard et al, 2019). The above evidence collectively reinforces the need to explore a suitable generic fecal indicator microorganism of soil.…”

Section: Discussionmentioning

confidence: 99%

Microbial Safety of Dairy Manure Fertilizer Application in Raspberry Production

et al. 2019

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Dairy manure, a by-product in the dairy industry, is also a potential source of nutrients for crops. However, improper application of biological soil amendments of animal origin can be a source of contamination with enteric foodborne pathogens. A 2-year field study was conducted to evaluate impacts of dairy manure fertilizer application on the microbial safety of red raspberry (Rubus idaeus L) production. Fertilizers, including a standard synthetic fertilizer (CON), straight lagoon raw manure (SL), anaerobically digested liquid effluent (DLE), compost (COM) and dairy manure-derived refined fertilizers including ammonium sulfate (AS) and phosphorous solid (PS), were randomly applied in quadruplicate to raspberry plots. Soil, fertilizer, foliar, and raspberry fruit samples were collected during the cropping season for the quantification of indicator microorganisms (total coliform and generic Escherichia coli) and detection of important foodborne pathogens (Shiga toxin-producing E. coli (STEC), Salmonella, and Listeria monocytogenes). Counts of total coliforms in soil were stable over the 2017 cropping season and were not impacted by fertilizer application. In 2018, total coliforms increased with season and soils treated with COM had a significantly higher coliform number than those treated with CON. Both total coliform and generic E. coli in raspberry fruit samples were below the detectable level (3 most probable number/g) regardless of fertilizer types. In both years, no STEC or L. monocytogenes was detected from any of the collected samples regardless of fertilizer treatments. However, Salmonella were detected in some of the fertilizers, including PS (2017), DLE (2018), and SL (2018), which were transferred to soil samples taken directly after application of these fertilizers. Salmonella were not detected in soil samples 2 or 4 months post fertilizer application, foliar, or raspberry fruit samples regardless of fertilizer applications. In summary, one-time application of raw dairy manure or dairy manure-derived fertilizers more than 4 months prior to harvest has no major impact on food safety of red raspberry (6 ft. tall) production in Lynden sandy loam under good agricultural practices.

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Section: Discussionmentioning

confidence: 99%

Microbial Safety of Dairy Manure Fertilizer Application in Raspberry Production

et al. 2019

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“…A recently published study by Allard et al had investigated microbial quality and safety of irrigation water used for produce irrigation and characterized water microbiomes in conjunction with microbiological analyses ( Allard et al, 2019 ). However, it had not investigated associations between microbiomes and presence of foodborne pathogens ( Allard et al, 2019 ). Here, we used random forest analysis to identify microbial families associated with Salmonella and L. monocytogenes isolation.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, seasonal and environmental factors, such as weather, land use adjacent to sampling sites, and concentration of certain chemicals have been shown to affect the microbiome composition ( Van Rossum et al, 2015 ; Payne et al, 2017 ; Wang et al, 2018 ). However, limited data characterizing associations between microbial community composition and foodborne pathogen isolation from agricultural water samples are available ( Allard et al, 2019 ). Thus, the goal of this small-scale study was to (i) characterize bacterial and fungal communities in surface waters collected from six streams in the Northeastern United States over time, and to (ii) investigate potential associations between microbial community composition, environmental factors (e.g., turbidity, water temperature, rainfall), and foodborne pathogen isolation.…”

Section: Introductionmentioning

confidence: 99%

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

2020

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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.

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“…Migratory birds, a kind of wild animals that migrate long distances. They can carry pathogenic microorganisms from one place to another, and spread pathogenic microorganism by excretion [1,2].…”

Section: Introductionmentioning

confidence: 99%

Bacterial Community Research of Migratory Bird in Chifeng, Neimeng via High-Throughput Sequencing

Zheng

Zhu

Guan

et al. 2020

Preprint

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Background: In August 2018, a large number of migratory birds died in Chifeng, Neimeng. We were entrusted by local animal disease prevention and control center to collect the migratory bird epidemic materials and their living environmental water, and in 2019, we collect the local migratory bird stool and their living environmental water again. The bacterial communities in migratory bird epidemic materials, water and aquatic plants are profifiled by high-throughput sequencing of the V3–V4 hypervariable region of 16S rDNA gene.Results: We found that the dominant phylum between migratory bird epidemic materials, water and aquatic plant were Proteobacteia, Bacteroidetes, Firmicutes, Fusobacteria and Verrucomicrobia in 2018. One year later, we found that the dominant phylum between migratory bird stool, water and aquatic plant were Proteobacteia, Firmicutes, Cyanobacteria, Bacteroidetes. The relative abundance among bacterial phylum notably differed between two years. The relative abundance of Fusobacteria and Verrucomicrobia were higher in samples in 2018, while that of Cyanobacteria was higher in water, 2019. The relative abundance of Fusobacteria in migratory bird epidemic materials began to decline in the later period over time. At genus level, the relative abundance of Vibrio, Clostridium and other patnogenic bacteria decreased markedly and disappeared in 2019. The salt content and pH show a downward trend.Conclusions: Differences in diet and geographical location can lead to diversification in migratory bird intestinal flora. It is necessary to pay attention to diversification in intestinal flora of migratory birds, especially the abundance of vibrio in intestine. The overall structure of intestinal flora and relative abundance changes of various species are showed intuitively by 16S rDNA amplicon. But comparing to PCR which using specific primers, the accuracy and sensitivity are relatively poor. In the case of purposeful detection, it can be used in combination with both 16S rDNA amplicon and PCR which using specific primers. They are more accurately, because of supplement each other.

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Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops

Cited by 31 publications

References 42 publications

Microbial Safety of Dairy Manure Fertilizer Application in Raspberry Production

Microbial Safety of Dairy Manure Fertilizer Application in Raspberry Production

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

Bacterial Community Research of Migratory Bird in Chifeng, Neimeng via High-Throughput Sequencing

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