Microbial transport into groundwater from irrigation: Comparison of two irrigation practices in New Zealand

Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria

Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.

Particle fractionation controls Escherichia coli release from solid manure

Bacteria transport through soil is a complex process particularly when the cells are released from solid manures and co-transported with particles. This study focuses on understanding of the Escherichia coli release from different particle fractions (0.25-, 0.5-, 1-, and 2-mm) of solid manure and evaluating different influent boundary conditions during cell release from manure and when a solid manure is applied to the soil. The 0.25-mm and 2-mm particle sizes resulted a greater cell release compared to 0.5-mm and 1-mm fractions (p < 0.05). The shape and magnitude of the cell release curves (CRCs) from the original manure bulk were mainly influenced by the two 0.25-mm and 2-mm fractions, respectively. The arithmetic mean for normalizing the CRCs and the time variable- based normalized CRCs for the manure-treated soil were the robust variables in evaluation of the experimental data. However, a single maximum bacteria concentration could provide the realistic dataset for the modeling process. Evaluation of the root-mean-squared-error and Akaike criterion showed that the two- and three-parametric models are recommended for simulating the cell release from solid manure in comparison with one parametric models. This study also suggests considering separate microbial release evaluations, with regards to influent concentration, for manure and manure-treated soils to propose best management practices for controlling bacteria pollution. Further research will reveal the key roles of different woody components and soluble material ratios for the various solid manures in bacteria release.

Seventy years of data from the world's longest grazed and irrigated pasture trials

Pastures are the most widespread land use, globally. The Winchmore trials were established in 1948–1949 in Canterbury, New Zealand and examined either different rates of phosphorus (P) fertiliser on the same irrigation schedule (Fertiliser trial), or different irrigation scheduling at the same rate of P application (Irrigation trial). About 96,000 records of soil chemistry and physical data and pasture yield and botanical composition are available along with nearly 7000 soil samples. These data have been used in 475 publications that have explored topics as diverse as: improvements in sheep, dairy and deer production; the efficacy and scheduling of irrigation; improvements in pasture and crop production; agronomic and environmental soil and water research; and entomology. In addition to above topics, these data are invaluable for calibrating models to predict long-term issues like the accumulation of soil carbon or contaminants like cadmium and informing policy on climate change and agricultural practices. The data and soil samples are available for use and may yet yield discoveries, unforeseen 70 years ago.

Measurement(s)	phosphorus • cadmium • soil moisture • composition of soil • acidity of soil • total biomass yield • porosity of soil • hydraulic conductivity • temperature of soil
Technology Type(s)	colorimetry • inductively coupled plasma-atomic emission spectrometry • gravimetric analysis • pH meter • Calculation • ring infiltrometer • Thermometer Device
Factor Type(s)	fertiliser application rate • irrigation scheduling • year of data collection
Sample Characteristic - Environment	farm soil • pasture • irrigation ditch • leachate
Sample Characteristic - Location	New Zealand

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12996692

How can we improve understanding of faecal indicator dynamics in karst systems under changing climatic, population, and land use stressors? - Research opportunities in SW China

Human exposure to water contaminated with faeces is a leading cause of worldwide ill-health. Contaminated water can be transmitted rapidly in karst terrain as a result of the connectivity of surface and groundwater systems, high transmissivity of aquifers over large areas, and well-developed underground conduit systems. Faecal indicator organisms (FIOs) are the most widely-used indicator of faecal contamination and microbial water quality; however, the conceptualisation of FIO risk and associated sources, pathways, and survival dynamics of FIOs in karst landscapes requires a degree of modification from traditional conceptual models of FIO fate and transfer in non-karst systems. While a number of reviews have provided detailed accounts of the state-of-the-science concerning FIO dynamics in catchments, specific reference to the uniqueness of karst and its influence on FIO fate and transfer is a common omission. In response, we use a mixed methods approach of critical review combined with a quantitative survey of 372 residents of a typical karst catchment in the southwest China karst region (SWCKR) to identify emerging research needs in an area where much of the population lives in poverty and is groundwater dependent. We found that the key research needs are to understand: 1) overland and subsurface FIO export pathways in karst hydrology under varying flow conditions; 2) urban and agricultural sources and loading in mixed land-use paddy farming catchments; 3) FIO survival in paddy farming systems and environmental matrices in karst terrain; 4) sediment-FIO interactions and legacy risk in karst terrain; and 5) key needs for improved hydrological modelling and risk assessment in karst landscapes. Improved knowledge of these research themes will enable the development of evidence-based faecal contamination mitigation strategies for managing land and water resources in the SWCKR, which is highly vulnerable to climate change impacts on water supply and quality of water resources.

A simple method of transport parameter estimation for slug injecting tracer tests in porous media

Slug (instantaneous injection) tracer tests can be used effectively to determinate solute transport parameters in porous media such as pore velocities and dispersivities, which are usually estimated with curve-fitting methods. This study proposes a simple method to estimate conservative and reactive solute transport parameters in one-, two- and three- dimensional domains with uniform flow fields based on peak times of slug tracer tests. This method requires fewer measured data than traditional curve-fitting methods. The accuracy of the method depends on the time-interval of measurement that is the time interval used in collecting observed concentrations of solutes. The error of the pore velocity estimate is very small (less than 3%) even for a relatively large time-interval of measurement. The error of the dispersivity estimate increases with the time-interval (Δt) of measurement significantly. For 1-D case, the relative error increases from 0.29% at ∆t of 0.1 min to 17.12% at ∆t of 6 min. Such an error can be reduced by refining the time-interval of measurement near the actual peak time of breakthrough curves. The error of the dispersivity estimate decreases when the retardation factor increases. The first-order decay rate constant in the liquid hardly influences the accuracies of both pore velocity and dispersivity estimates. The proposed method is applied on laboratory sand column tests. The results indicate that the estimated pore velocities and dispersivities are almost the same to that of the curves-fitting method. This method can be employed easily by scientists and practitioners for parameter estimations in laboratory column experiments if advection-dispersion equation is applicable. This method can also be used for parameter estimation of heat transport in a laboratory column experiment if a slug heat source is injected into a porous media with the presence of a uniform flow field. Limitations of the study have also been addressed.

Retention modes of manure-fecal coliforms in soil under saturated hydraulic condition

Manures are important soil nutrient conditioners and source of several pathogenic bacteria that potentially contribute to groundwater and surface water pollution. The best management practices need a solid understanding of manure sources, concentrations, and strategies to limit the number of bacteria in natural soil environment. In this study, a series of soil column experiments were conducted to investigate how bacteria mobility can potentially be influenced by retention mechanisms while moving through undisturbed saturated soil. This was assessed by bacteria retention profiles and mobility indices including the maximum transported (C_max-T) and retained (C_max-R) concentrations, filtration coefficient (λ_f) and the maximum depth of bacteria transport (Z_max). Three different soil samples (sandy, loamy and silty clay loam) were enriched with three types of manures (cow, sheep, and poultry), placed on top of three soil columns (16 cm diameter, 30 cm height) with an equivalent of 10 Mg ha^-1 (dry basis) summing up to a total of 36 columns. Leaching was performed under saturated steady-state conditions (i.e., 1.62 cm min^-1) for a duration of 4 pore volumes. After percolation, soil columns were sliced into six 5-cm interval layers and slices were characterized for retained bacteria. Results showed irregular exponential or quasi-exponential bacteria retention profiles for cow and sheep manures, whereas uniform-shaped profiles occurred for poultry manure. The latter variant also switched to exponential shape for the sandy soil at the highest and lowest C_max-T and C_max-R values due to higher pore water velocity. The λ_f and the Z_max values were also found to be affected by soil texture and manure origin. The λ_f was higher for poultry manure due to higher free-cell transport of bacteria most probably induced by higher amount of soluble mobile components. However, the greater amounts of transported wooden materials released from cow and sheep manures acted as harbors for bacteria. Accordingly, the filtration rate decreased and tailing effects for bacteria transport increased. The results also suggest that the practices and strategies for using manures could be optimized according to the respective transport behavior to manage the bacteria retention with respect to soil and manure types to reduce soil and water pollution.

Fecal source tracking methods to elucidate critical sources of pathogens and contaminant microbial transport through New Zealand agricultural watersheds - A review

In New Zealand, there is substantial potential for microbial contaminants from agricultural fecal sources to be transported into waterways. The flow and transport pathways for fecal contaminants vary at a range of scales and is dependent on chemical, physical and biological attributes of pathways, soils, microorganisms and landscape characteristics. Understanding contaminant transport pathways from catchment to stream can aid water management strategies. It is not practical, however to conduct direct field measurement for all catchments on the fate and transport of fecal pathogens due to constraints on time, personnel, and material resources. To overcome this problem, fecal source tracking can be utilised to link catchment characteristics to fecal signatures identifying critical sources. In this article, we have reviewed approaches to identifying critical sources and pathways for fecal microorganisms from agricultural sources, and make recommendations for the appropriate use of these fecal source tracking (FST) tools.

Tracking effluent discharges in undisturbed stony soil and alluvial gravel aquifer using synthetic DNA tracers

With the intensification of human activities, fresh water resources are increasingly being exposed to contamination from effluent disposal to land. Thus, there is a greater need to identify the sources and pathways of water contamination to enable the development of better mitigation strategies. To track discharges of domestic effluent into soil and groundwater, 10 synthetic double-stranded DNA (dsDNA)³ tracers were developed in this study. Laboratory column experiment and field groundwater and soil lysimeter studies were carried out spiking DNA with oxidation-pond domestic effluent. The selected DNA tracers were compared with a non-reactive bromide (Br) tracer with respect to their relative mass recoveries, speeds of travel and dispersions using the method of temporal moments. In intact stony soil and gravel aquifer media, the dsDNA tracers typically showed earlier breakthrough and less dispersion than the Br tracer, and underwent mass reduction. This suggests that the dsDNA tracers were predominantly transported through the network of larger pores or preferential flow paths. Effluent tracking experiments in soil and groundwater demonstrated that the dsDNA tracers were readily detectable in effluent-contaminated soil and groundwater using quantitative polymerase chain reaction. DNA tracer spiked in the effluent at quantities of 36μg was detected in groundwater 37m down-gradient at a concentration 3-orders of magnitude above the detection limit. It is anticipated it could be detected at far greater distances. Our findings suggest that synthetic dsDNA tracers are promising for tracking effluent discharges in soils and groundwater but further studies are needed to investigate DNA-effluent interaction and the impact of subsurface environmental conditions on DNA attenuation. With further validation, synthetic dsDNA tracers, especially when multiple DNA tracers are used concurrently, can be an effective new tool to track effluent discharge in soils and groundwater, providing spatial estimation on the presence or absence of contamination sources and pathways.

Concentrations of Campylobacter spp., Escherichia coli, Enterococci, and Yersinia spp. in the Feces of Farmed Red Deer in New Zealand

Intensive deer farming can cause environmental issues, mainly by its impact on soils and water quality. In particular, there is a risk to the microbial quality of water, as high quantities of suspended sediment and fecal bacteria can enter into water systems. The feces of farmed red deer (, = 206) from Canterbury and Southland, New Zealand, were analyzed with regard to the presence of spp., , enterococci, and spp.. Enterococci and were isolated from all samples, with mean concentrations of 4.5 × 10 (95% CI 3.5 × 10, 5.6 10) and 1.3 × 10 (95% CI 1.1 × 10, 1.5 × 10) per gram of dry feces, respectively. spp. were isolated from 27 fecal samples, giving an overall prevalence of 13.1%. isolation rates were variable within and between regions (Canterbury 7.95% [95% CI 2-14%], Southland 16.95% [95% CI 10-24%]). Five out of 42 composite samples were positive for , and one sample for The overall prevalence ranges on a per-animal basis were therefore 2.43 to 11.17% and 0.49 to 2.91%, respectively. This study is the first to quantify the concentration of spp. present in healthy deer farmed in New Zealand. Deer feces are a potential source of human campylobacteriosis, with all genotypes isolated also previously observed among human cases. The fecal outputs from deer should be regarded as potentially pathogenic to humans and therefore be appropriately managed.