Development of a multiplex droplet digital PCR assay for simultaneous detection and quantification of Escherichia coli, E. marmotae, and E. ruysiae in water samples.

Escherichia coli are widely used by water quality managers as Fecal Indicator Bacteria, but current quantification methods do not differentiate them from benign, environmental Escherichia species such as E. marmotae (formerly named cryptic clade V) or E. ruysiae (cryptic clades III and IV).

Draft genome sequences of spp. isolates from New Zealand environmental sources.

is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500 isolates including newly described species, namely , and , obtained from diverse environmental sources to assist with improved public health risk assessments.

High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments.

Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp.

Survival, mobilization, and transport of Escherichia coli from sheep faeces.

Aims: This study looked at the survival, mobilization, and transport of Escherichia coli from sheep faeces over an extended period, which was then repeated for all four seasons.

Methods And Results: Rain simulation was used to measure E. coli mobilization directly from faecal pats and subsequent transport across a soil surface.

Escherichia coli runoff from sheep and dairy cow grazed pasture: A plot scale simulation.

Animal agriculture is recognized as a key source of fecal microbial impacts on water quality and associated risks to human health. Most of the research effort has focused on losses of fecal microbes from cow/cattle feces with little research effort on sheep fecal risks. The literature on fecal microbial risks from pasture is complicated by the fact that experiments are carried out in different environments leading to difficulties in making direct comparisons between sheep and cow/cattle losses from pasture areas.

A Heuristic Method for Determining Changes of Source Loads to Comply with Water Quality Limits in Catchments.

A common land and water management task is to determine where and by how much source loadings need to change to meet water quality limits in receiving environments. This paper addresses the problem of quantifying changes in loading when limits are specified in many locations in a large and spatially heterogeneous catchment, accounting for cumulative downstream impacts. Current approaches to this problem tend to use either scenario analysis or optimization, which suffer from difficulties of generating scenarios that meet the limits, or high complexity of optimization approaches.

Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture.

The production of dairy, meat, and fiber by ruminant animals relies on the biological processes occurring in soils, forage plants, and the animals' rumens. Each of these components has an associated microbiome, and these have traditionally been viewed as distinct ecosystems. However, these microbiomes operate under similar ecological principles and are connected via water, energy flows, and the carbon and nitrogen nutrient cycles.

Variability of Concentrations in Rivers during Base-Flow Conditions in New Zealand.

concentrations in rivers are known to vary considerably. Much research has focused on storm events and the relationships between fecal microbe concentrations and flows. However, there is still considerable variability in microbial concentrations during base-flow conditions, and little research has been conducted to understand this short-term variability in rivers.

Transcriptome Changes of , and O157:H7 Laboratory Strains in Response to Photo-Degraded DOM.

In this study, we investigated gene expression changes in three bacterial strains ( C3000, O157:H7 B6914, and ATCC 29212), commonly used as indicators of water quality and as control strains in clinical, food, and water microbiology laboratories. Bacterial transcriptome responses from pure cultures were monitored in microcosms containing water amended with manure-derived dissolved organic matter (DOM), previously exposed to simulated sunlight for 12 h. We used RNA sequencing (RNA-seq) and quantitative real-time reverse transcriptase (qRT-PCR) to compare differentially expressed temporal transcripts between bacteria incubated in microcosms containing sunlight irradiated and non-irradiated DOM, for up to 24 h.

Development and evaluation of the bacterial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model.

The Agricultural Policy/Environmental eXtender (APEX) is a watershed-scale water quality model that includes detailed representation of agricultural management. The objective of this work was to develop a process-based model for simulating the fate and transport of manure-borne bacteria on land and in streams with the APEX model. The bacteria model utilizes manure erosion rates to estimate the amount of edge-of-field bacteria export.

Modeling the interannual variability of microbial quality metrics of irrigation water in a Pennsylvania stream.

Knowledge of the microbial quality of irrigation waters is extremely limited. For this reason, the US FDA has promulgated the Produce Rule, mandating the testing of irrigation water sources for many farms. The rule requires the collection and analysis of at least 20 water samples over two to four years to adequately evaluate the quality of water intended for produce irrigation.

Modeling fate and transport of fecally-derived microorganisms at the watershed scale: State of the science and future opportunities.

Natural waters serve as habitat for a wide range of microorganisms, a proportion of which may be derived from fecal material. A number of watershed models have been developed to understand and predict the fate and transport of fecal microorganisms within complex watersheds, as well as to determine whether microbial water quality standards can be satisfied under site-specific meteorological and/or management conditions. The aim of this review is to highlight and critically evaluate developments in the modeling of microbial water quality of surface waters over the last 10 years and to discuss the future of model development and application at the watershed scale, with a particular focus on fecal indicator organisms (FIOs).

Mapping of Escherichia coli Sources Connected to Waterways in the Ruamahanga Catchment, New Zealand.

Rivers and streams in New Zealand are natural with free access and used by many people for swimming and fishing. However, pastoral farming with free grazing animals is a common land use in New Zealand and faecal microorganisms from them often end up in waterways. These microorganisms can seriously affect human and animal health if ingested.

Predicting microbial water quality with models: Over-arching questions for managing risk in agricultural catchments.

The application of models to predict concentrations of faecal indicator organisms (FIOs) in environmental systems plays an important role for guiding decision-making associated with the management of microbial water quality. In recent years there has been an increasing demand by policy-makers for models to help inform FIO dynamics in order to prioritise efforts for environmental and human-health protection. However, given the limited evidence-base on which FIO models are built relative to other agricultural pollutants (e.

A farm-scale risk-index for reducing fecal contamination of surface waters.

There is increasing recognition of the adverse impacts of agricultural practices on microbial water quality leading to increased expectation on farmers to manage environmental impacts on water quality. Therefore, farmers require a tool to help them prioritize mitigations targeted at reducing fecal contamination of surface water. A farm-scale risk-index was developed from modeled data on the predicted losses of from selected farm practices.

Differences in the fecal concentrations and genetic diversities of Campylobacter jejuni populations among individual cows in two dairy herds.

Dairy cows have been identified as common carriers of Campylobacter jejuni, which causes many of the human gastroenteritis cases reported worldwide. To design on-farm management practices that control the human infection sourced from dairy cows, the first step is to acquire an understanding of the excretion patterns of the cow reservoir. We monitored the same 35 cows from two dairy farms for C.

A model framework to assess the effect of dairy farms and wild fowl on microbial water quality during base-flow conditions.

There is concern regarding microbial water quality in many pastoral catchments in New Zealand which are home to numerous livestock and wild animals. Information on microbial impacts on water quality from these animals is scarce. A framework is needed to summarise our current knowledge and identify gaps at the scale of an individual farm.

Differential behaviour of Escherichia coli and Campylobacter spp. in a stream draining dairy pasture.

The faecal indicator bacterium Escherichia coli and thermotolerant Campylobacter spp., which are potentially pathogenic, were investigated in the Toenepi Stream draining a pastoral catchment dominated by dairying. Bacteria concentrations were monitored routinely at fortnightly intervals over 12 months and intensively during storm events to compare the transport dynamics of bacterial indicator and pathogen under varying hydro-meteorological conditions.

Lyophilization prior to direct DNA extraction from bovine feces improves the quantification of Escherichia coli O157:H7 and Campylobacter jejuni.

Lyophilization was used to concentrate bovine feces prior to DNA extraction and analysis using real-time PCR. Lyophilization significantly improved the sensitivity of detection compared to that in fresh feces and was associated with reliable quantification of both Escherichia coli O157:H7 and Campylobacter jejuni bacteria present in feces at concentrations ranging between 2 log(10) and 6 log(10) CFU g(-)(1).

Interaction of Escherichia coli and soil particles in runoff.

A laboratory-scale model system was developed to investigate the transport mechanisms involved in the horizontal movement of bacteria in overland flow across saturated soils. A suspension of Escherichia coli and bromide tracer was added to the model system, and the bromide concentration and number of attached and unattached E. coli cells in the overland flow were measured over time.

Erosion and subsequent transport state of Escherichia coli from cowpats.

Processes by which fecal bacteria enter overland flow and their transportation state to surface waters are poorly understood, making the effectiveness of measures designed to intercept this pathway, such as vegetated buffer strips, difficult to predict. Freshly made and aged (up to 30 days) cowpats were exposed to simulated rainfall, and samples of the cowpat material and runoff were collected. Escherichia coli in the runoff samples were separated into attached (to particles) and unattached fractions, and the unattached fraction was analyzed to determine if the cells were clumped.