In mid-February 2023, Cyclone Gabrielle caused unprecedented flooding, landslides, and infrastructure damage across large parts of New Zealand's North Island. Following the event, significant public safety concerns were raised regarding the safety of untreated drinking water sourced by groundwater. In the weeks following the event, the first coordinated event response between five organizations (local to national) to assess the impact of widespread flooding on groundwater quality in NZ was initiated. The response consisted in an initial rapid, low-cost sampling for screening a large number of wells for indicator parameters of potential contamination. This was followed by subsequent sampling for a more comprehensive suite of contaminants of wells located in areas where anomalous measurements were identified. This approach provided valuable insights on: fieldwork efficiency, sampling site suitability screening, collection of floodwater or baseline data, the suite of analytes to use, inter-organization involvement and communication, and event-response cost. As current climate predictions for NZ suggest more frequent and more severe storm events, we provide recommendations on pre-event preparedness, event response design, and response activities to inform future similar surveys.

Woodchip denitrifying bioreactors (WDBs) are an established edge-of-field practice for mitigating nitrogen (N) loads in agricultural drainage waters. Of the published 'in-stream' WDB case studies, many have suffered hydraulic failure due to siltation and clogging. In this study we present a very large (450 m3) in-stream WDB of a modular design that sought to incorporate clogging management features. The WDB was designed to provide long-term treatment of dairy land drain water flowing at 6 L/s containing 6 mg nitrate-N/L on average. The hydraulic function of the in-stream WDB and nitrate removal efficacy were determined from monthly monitoring conducted over the first two years of its operation. A 69 % reduction in the equivalent hydraulic conductivity K and 25 % reduction in effective porosity were observed over this time, during which the bioreactor was estimated to have retained at least 2.6 t of sediment. A logarithmic relationship between K x x and sediment load best described the clogging. The average nitrate removal rate was 3.3 +/- 1.0 g N/m3 woodchip/day. Annualised removal rates were 497 and 485 kg N/year, which are on par with performance calculations made during the design phase. Nitrate removal was sensitive to temperature and could be modelled effectively assuming Arrhenius temperature dependence and zero-order reaction. The resulting zero-order nitrate reaction rate for a 20 degrees C reference temperature was 7.93 +/- 4.64 mg N/L/day and the Arrhenius temperature coefficient was 1.06 +/- 0.09. Parameter estimates were within the range of values typically associated with WDBs. The need for longterm monitoring of this in-stream WDB is discussed in the context of testing its modular design functionality for increased operational longevity.

Understanding hydrogeochemical heterogeneity, associated with natural nitrate attenuation, is an integral part of implementing integrated land and water management on a regional or national scale. Redox conditions are a key indicator of naturally occurring denitrification in the groundwater environment, and often used to inform spatial planning and targeted regulation. This work describes the development of a statistical redox condition model for the groundwater environment at a national scale, using spatially variable physiochemical descriptors as predictors. The proposed approach builds on previous work, by complementing the available data with expert knowledge, in the form of synthetic data. Special care is given so that the synthetic data do not overfit and create further imbalances to the training dataset. The predictor dataset is further complemented by the results of a data driven model of the water table developed for this study, which is used both as a predictive parameter and a reference level for groundwater redox condition predictions at different depths. The developed model predicted the redox class for 84% of the samples in the out-of-bag datasets. We also propose an alternative approach for the communication of prediction uncertainty. We use the concept of a discriminate function to identify model classifications that may be ambiguous. Our results show a marked reduction in prediction uncertainty at shallow depths, with uncertainty in reduced environments decreasing from 76 to 12%, and overall uncertainty reduced by approximately 20%, though improvements at greater depths are less pronounced. We conclude that this approach can highlight robust model predictions that are defendable for decision making and can identify areas where monitoring or sampling efforts can be focused for improved outcomes.

Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.

Sand filtration is a cost-effective means of reducing microbial pathogens in drinking-water treatment. Our understand-ing of pathogen removal by sand filtration relies largely on studies of process microbial indicators, and comparative data from pathogens are sparse. In this study, we examined the reductions of norovirus, echovirus, adenovirus, bacte-riophage MS2 and PRD1, Campylobacter jejuni, and Escherichia coli during water filtration through alluvial sand. Dupli-cate experiments were conducted using 2 sand columns (50 cm long, 10 cm diameter) and municipal tap water sourced from chlorine-free untreated groundwater (pH 8.0, 1.47 mM) at filtration rates of 1.1-1.3 m/day. The results were analysed using colloid filtration theory and the HYDRUS-1D 2-site attachment-detachment model. The average log10 reduction values (LRVs) of the normalised dimensionless peak concentrations (Cmax/C0) over 0.5 m were: MS2: 0.28; E. coli: 0.76; C. jejuni: 0.78; PRD1: 2.00; echovirus: 2.20; norovirus: 2.35; and adenovirus: 2.79. The relative reductions largely corresponded to the organisms' isoelectric points rather than their particle sizes or hydrophobicities. MS2 underestimated virus reductions by 1.7-2.5 log, and the LRVs, mass recoveries relative to bromide, collision ef-ficiencies, and attachment and detachment rates differed mostly by similar to 1 order of magnitude. Conversely, PRD1 reduc-tions were comparable with those of all 3 viruses tested, and its parameter values were mostly within the same orders of magnitude. E. coli seemed an adequate process indicator for C. jejuni with similar reductions. Comparative data de-scribing pathogen and indicator reductions in alluvial sand have important implications for sand filter design, risk as-sessments of drinking-water supplies from riverbank filtration and the determination of safe setback distances for drinking-water supply wells.

Groundwater is home to a diverse range of organisms, both small and large, which form a complex ecosystem that helps to purify the water and keep it flowing smoothly. However, much of the processes that occur in this ecosystem are still a mystery and there are many important services that we have yet to fully understand. Our goal is to create a groundwater health index that can be used to monitor the health of groundwater, similar to the macroinvertebrate community index used for surface water systems. We are investigating both the macroinvertebrates and microbial diversity in our research. To gather data, we are collecting groundwater environmental (e)DNA samples and biofilm samples using in-situ biofilm bags from various sites in New Zealand across multiple seasons. We then analyze the water chemistry and sequence data for bacteria, archaea, eukaryotes, and fungi to determine the status of the groundwater source. Our findings show that there is a complex diversity present in both the groundwater itself (e.g., Fig. 1) and the attached microbial biofilm. We have also discovered variations between the attached and groundwater across all sites studied, with significant differences in the Shannon richness indicator in Canterbury. Additionally, we have observed differences in microbial populations depending on the lithology and water chemistry present. Our research aims to identify key species, both micro and macro, that can potentially act as a tool for predicting the health of groundwater. Furthermore, understanding the biological processes occurring in our groundwater may lead to the discovery of beneficial organisms capable of remediation.

Microbial pathogen survival within the environment can be variable and can depend on many criteria, including environmental conditions e.g. oxygen concentration, temperature, pH, sunlight, etc. (e.g., Horswell et al. (2010)). Groundwater has been shown to enable the prolonged survival of pathogenic organisms due to the absence of sunlight and relatively stable temperatures (Cook and Bolster 2007). In other studies, however, survival has been lower in groundwater when compared with a sterile environment (e.g. sterilised groundwater or artificial groundwater) due to the presence of competing organisms and adverse conditions of pH and redox. To elucidate these discrepancies two experiments were designed: The first, hypothesised that, due to Campylobacters' low tolerance to high oxygen levels, survival in oxic (dissolved oxygen (DO) levels over 5 mg per L) would be less than in anoxic groundwater (DO levels below 2 mg per L). The second hypothesised that the survival of the pathogen Salmonella typhimurium , in groundwater, will be enhanced by organic carbon. METHODS Campylobacter experiment: Campylobacter jejuni isolated from the Havelock North drinking water source was used (designated HN16) (Gilpin et al. 2020). To compare the survival of the outbreak strain with type strain Campylobacter , NCTC 11351 was used. Salmonella experiment: For this experiment, environmental isolates were used rather than laboratory strains. Salmonella, isolated from a stream in Wellington, New Zealand, was identified as Salmonella enterica serovar Typhimurium . The Escherichia coli used was a phylogroup A, isolated from stream sediment in Whangarei Falls, New Zealand. Mesocosm experiments were established containing groundwater (oxic and anoxic for Campylobacter experiment and ultrafiltered, groundwater, groundwater amended with 1% or 10% dissolved organic carbon (DOC). pH, dissolved oxygen (DO), and temperature were monitored over the experimental period. The temperature was maintained at 12-14°C during both experiments. Samples (5 mL) of the groundwater from each jar were taken aseptically at set time points over the experimental period. Samples were then serially diluted in sterile peptone water to give a dilution series from 10 -1 to 10 -4 . Samples were analysed by plating onto selective media. RESULTS Campylobacter experiment: The results presented demonstrated differences in the survival of the two Campylobacter strains tested and differences in survival of Campylobacter HN16 depending on groundwater type. Fig. 1 shows the average concentration of Campylobacter strains in groundwater types over time. The results presented are average of three replicates. Over the whole experimental period survival of Campylobacter HN16 was greatest in anoxic groundwater, and only a 1 log reduction was observed (Fig. 1), equating to a 79.6% survival after 16 days. The die-off rate of Campylobacter HN16 in anoxic groundwater was calculated to be 0.0873 days and T90 6.85 days. Salmonella experiment: Die-of rates for Salmonella were similar over the course of the experiment when no or low levels of DOC were present (Fig. 2a). At high levels of DOC, however, Salmonella showed similar survival to the control. After 84 days only a 1 Log decrease was observed. In comparison, E. coli died off at a faster rate than Salmonella in all mesocosms (Fig. 2). It is interesting to note that in the high DOC mesocosms after day 56 counts of E. coli remained at 10 3 per mL until the end of the experiment. Conclusions and significance Both experiments demonstrated the survival of pathogenic microorganisms in varying groundwater conditions. The variation in the outbreak strain Campylobacter compared to the type strain indicated variation within species that may lead to enhanced survival in the environment. The Salmonella experiment indicated the presence of additional organic carbon can enhance the survival of pathogens in groundwater. In addition, the variation between the microbial indicator E. coli and Salmonella provides evidence of differences in the survival of microbes in the environment and indicates caution is needed when considering the survival of pathogens in groundwater if reliance is made on microbial indicator organisms.

The movement of bacterial and viral pathogens through soil and vadose zone and subsequently into groundwater is a major public health concern. There are relatively few studies on the transport and fate of microbes through variably saturated vadose zone media compared with their transport in the soil and saturated groundwater zones. In this study, we investigated the transport of Escherichia coli , F‐RNA bacteriophage MS2, and a conservative solute tracer bromide through three intact vadose zone cores, under saturated (discharge rate ∼100 mm h −1 ) and unsaturated (discharge rate 10 and 0.5 mm h −1 ) flow conditions. The vadose zone media were sandy gravel overlying a sand lens in core 1, a heterogeneous SG mix in core 2, and SG with an open framework gravel lens through the middle of the core in core 3. The three flow regimes resulted in different transport characteristics through each of the cores. As expected, microbial transport through all cores was higher under saturated conditions, compared with unsaturated conditions. Overall, E. coli removal was consistently greater than that of MS2 phage irrespective of core media or flow conditions. There were relatively minor removals (factors of 1–2.5) of both microbes under saturated conditions, reductions of 2–3 orders of magnitude under the high flow unsaturated conditions, and almost complete removal (4 to >5 orders of magnitude) under the low flow unsaturated conditions. The much greater removal of microbes under unsaturated conditions has significant implications and potential benefits for land management decisions.

Anammox is increasingly shown to play a major role in the aquatic nitrogen cycle and can outcompete heterotrophic denitrification in environments low in organic carbon. Given that aquifers are characteristically oligotrophic, anammox may represent a major route for the removal of fixed nitrogen in these environments, including agricultural nitrogen, a common groundwater contaminant.

The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.

Contamination of potable groundwater by human enteric viruses pose serious health risks. Our knowledge about virus subsurface transport relies largely on using bacteriophages as surrogates. Relatively few studies have compared enteric viruses, especially norovirus, with phage surrogates regarding their transport behaviour. Given that bacteriophages and enteric viruses have dissimilar physiochemical properties, differences in their behaviour and interactions in subsurface media and groundwater are possible. Laboratory column studies were conducted to examine the attenuation and transport of norovirus and MS2 bacteriophage in alluvial sand (d10=0.25 mm), and rotavirus, adenovirus and MS2 in alluvial gravel (d10=2 mm) in 2 mM NaCl (pH 6.6–6.9) at pore velocities of 4.6–5.4 m/day. The experimental data were evaluated using colloid filtration theory and HYDRUS-1D two-site attachment-detachment modelling. The log10 reduction values, mass recoveries, attachment efficiencies and irreversible deposition rate constants indicated that compared with MS2, norovirus removal was lower in the alluvial sand and the removal of rotavirus and adenovirus was markedly greater in the alluvial gravel. Modelling suggested virus attachment was reversible, and that the rates of virus detachment were faster than the rates of virus attachment, which favoured free virus transport. Hence, continual virus transport through subsurface media poses health risks if viruses are not inactivated, and virus remobilisation could cause contamination events. Thus, virus transport predictions in subsurface media should incorporate virus attachment reversibility. Some of these observations align with other studies’ findings, but viruses behave very differently in different systems; hence, disparate relationships in other systems have been described, especially in the presence of multivalent cations and organic matter. Our understanding of enteric virus mobility and removal is limited, and data based on bacteriophages may not represent enteric virus behaviour accurately. Thus, further research is needed into enteric virus transport, especially that of norovirus, in different subsurface media under a variety of experimental conditions.

Rapid transmission of contaminants in groundwater can occur in alluvial gravel aquifers that are permeated by highly conductive small-scale open framework gravels (OFGs). This open framework gravel structure and the associated distribution of hydraulic properties is complex, and so assessments of contamination risks in these aquifers are highly uncertain. Geostatistical models, based on lithological data, can be used to quantitatively characterize this structure. These models can then be used to support analyses of the risks of contamination in groundwater systems. However, these geostatistical models are themselves accompanied by significant uncertainty. This is seldom considered when assessing risks to groundwater systems. Geostatistical model uncertainty can be reduced by assimilating information from hydraulic system response data, but this process can be computationally challenging. We developed a sequential conditioning method designed to address these challenges. This method is demonstrated on a transition probability based geostatistical simulation model (TP), which has been shown to be superior for representing the connectivity of high permeability pathways, such as OFGs. The results demonstrate that the common modelling practice of adopting a single geostatistical model may result in realistic predictions being overlooked, and significantly underestimate the uncertainties of groundwater transport predictions. This has important repercussions for uncertainty quantification in general. It also has repercussions if using ensemble-based methods for history matching, since it also relies on geostatistical models to generate prior parameter distributions. This work highlights the need to explore the uncertainty of geostatistical models in the context of the predictions being made.

Woodchip denitrification walls offer a potentially useful way for passive in situ remediation of groundwater nitrate pollution, yet because of the low redox state they induce on the subsurface environment there is an inherent risk they can promote pollution-swapping phenomena. We evaluated pollution-swapping phenomena associated with the first two operational years of a woodchip denitrification wall that is being trialled in a fast-flowing shallow gravel aquifer of quartzo-feldspathic mineralogy. Following burial of woodchip below the water table there was immediate export of dissolved organic carbon (DOC), phosphorus and ammonium into the groundwater. Under the low redox state sustained by labile DOC, the wall initially provided 100% nitrate removal at the expense of acute and localised pollution that occurred in the form of a plume of dissolved iron, manganese and arsenic that were mobilised from the aquifer sediments, in conjunction with methane gas emission. Within one year however, the reactivity of the woodchip wall subsided to support a steady state condition in which nitrate reduction was the terminal electron acceptor process with no measurable methane emission. Having initially functioned as a sink for the potent greenhouse gas nitrous oxide (N2O), evidence is that the woodchip wall is now exporting N2O, albeit at rates less than those associated with productive agricultural land.

A groundwater monitoring network surrounding a pumping well (such as a public water supply) allows for early contaminant detection and mitigation where possible contaminant source locations are often unknown. This numerical study investigates how the contaminant detection probability of a hypothetical sentinel-well monitoring network consisting of one to four monitoring wells is affected by aquifer spatial heterogeneity and dispersion characteristics, where the contaminant source location is randomized. This is achieved through a stochastic framework using a Monte Carlo approach. A single production well is considered that results in converging non-uniform flow close to the well. Optimal network arrangements are obtained by maximizing a weighted risk function that considers true and false positive detection rates, sampling frequency, early detection, and contaminant travel time uncertainty. Aquifer dispersivity is found to be the dominant parameter for the quantification of network performance. For the range of parameters considered, a single monitoring well screening the full aquifer thickness is expected to correctly and timely identify at least 12% of all incidents resulting in contaminants reaching the production well. This proportion increases to a global maximum of 96% for a network consisting of four wells and very dispersive transport conditions. Irrespective of network size and sampling frequency, more dispersive transport conditions result in higher detection rates. Increasing aquifer heterogeneity and decreasing aquifer spatial continuity also lead to higher detection rates, though these effects are diminished for networks of 3 or more wells. Statistical anisotropy has no effect on the network performance. Earlier detection, which is critical for remedial action and supply safety, comes with a significant cost in terms of detection rate, and should be carefully considered when a monitoring network is being designed.

A hydrological framework encompassing nitrogen (N), phosphorus (P) and microbial (E. coli) transfer from land to water was developed to provide a consistent and rapid approach for assessing the potential impacts of land activity on water quality in New Zealand. A flow partition approach was used to route precipitation via surface and subsurface pathways from land to water. The framework included a typology-based inventory that estimates annual yields of transportable N and P from land, a regional-scale spatial layer that attenuates N in groundwater, and literature-based estimates of E. coli concentrations in surface runoff and artificial drainage. Application of the framework in four catchments highlighted the importance of local catchment knowledge of dominant hydrological processes that was needed to ensure flow partitions derived were a realistic representation of transport processes. While the approach was promising, additional refinements are needed to improve process representation (e.g. effects of groundwater lags) and ensure input data (e.g. soil attributes) have appropriate resolution to describe hydrological pathways. We contend that such a framework would provide a consistent and relatively rapid approach for identifying contaminant transfer pathways from land to water that can inform assessments of the potential consequences of land use change and intensification.

Potable groundwater contamination by human enteric viruses poses serious health risks. Our understanding of virus subsurface transport has largely depended on studying bacteriophages as surrogates. Few studies have compared the transport behaviour of enteric viruses, especially norovirus, with phage surrogates. We conducted laboratory column experiments to investigate norovirus and bacteriophage MS2 (MS2) filtration in alluvial sand, and rotavirus, adenovirus and MS2 filtration in alluvial gravel aquifer media in 2 mM NaCl (pH 6.6-6.9) with pore velocities of 4.6-5.4 m/day. The data were analysed using colloid filtration theory and HYDRUS-1D 2-site attachment-detachment modelling. Norovirus removal was somewhat lower than MS2 removal in alluvial sand. The removal of rotavirus and adenovirus was markedly greater than MS2 removal in alluvial gravel. These findings concurred with the logio reduction values, mass recoveries, attachment efficiencies and irreversible deposition rate constants. The modelling results suggested that the MS2 detachment rates were in the same order of magnitude as norovirus, but they were 1 order of magnitude faster than those of rotavirus and adenovirus. The attachment of viruses and MS2 was largely reversible with faster detachment than attachment rates, favouring free virus transport. These findings highlight the risk associated with continual virus transport through subsurface media if viruses are not inactivated and remobilising previously attached viruses could trigger contamination events. Thus, virus attachment reversibility should be considered in virus transport predictions in subsurface media. Further research is needed to compare surrogates with enteric viruses, especially norovirus, regarding their transport behaviours under different experimental conditions. (C) 2021 Elsevier Ltd. All rights reserved.

Monte Carlo uncertainty analysis, model calibration and optimization applications in hydrology, usually involve a very large number of forward transient model solutions, often resulting in computational bottlenecks. Parallel processing can significantly reduce overall simulation time, benefiting from the architecture of modern computers. This work investigates system performance using two realistic flow and transport modeling scenarios, applied to various modeling hardware, to provide information on the expected performance of parallel simulations and inform investment decisions. We investigate how performance, measured in terms of speedup and efficiency, changes with increasing number of parallel processes. We conclude that the maximum performance achieved by parallelization can range from 40% to 100% of the theoretical limit, with the lower increases associated with multi‐CPU servers. The number of parallel processes required to maximize performance is application dependent, and in contrast to common practice, often needs to be significantly larger than the total number of system CPU cores. Further testing is required to better understand how the physical problem being simulated affects the optimal number of parallel processes needed. Finally, when laptops are considered for modeling applications, careful consideration should be given not only to the specifications but also to the intended use designated by the manufacturer.

The vast majority of microorganisms in aquifers live as biofilms on sediment surfaces, which presents significant challenges for sampling as only the suspended microbes will be sampled through normal pumping. The use of a down-well low frequency sonicator has been suggested as a method of detaching microbes from the biofilm and allowing rapid sampling of this community. We developed a portable, easy to use, low-frequency electric sonicator and evaluated its performance for a range of well depths (tested up to 42 m below ground level) and casing types. Three sonicators were characterized in laboratory experiments using a 1 m long tank filled with pea gravel. These included a commercially available pneumatic sonicator, a rotating flexible shaft sonicator, and the prototype electric sonicator. The electric sonicator detached between 56 and 74% of microbes grown on gravel-containing biobags at distances ranging between 2 and 50 cm from the sonicator. The field testing comprises of a total of 55 sampling events from 48 wells located in 4 regions throughout New Zealand. Pre- and post-sonication samples showed an average 33 times increase in bacterial counts. Microbial sequence data showed that the same classes are present in pre- and post-sonicated samples and only slight differences were seen in the proportions present. The sampling process was rapid and the significant increases in bacterial counts mean that microbial samples can be quickly obtained from wells, which permits more detailed analysis than previously possible.