Multiple approaches to microbial source tracking in tropical northern Australia

Spatio-Temporal Variation in the Exceedance of Enterococci in Lake Burley Griffin: An Analysis of 16 Years' Recreational Water Quality Monitoring Data

Recreational waterbodies with high levels of faecal indicator bacteria (FIB) pose health risks and are an ongoing challenge for urban-lake managers. Lake Burley Griffin (LBG) in the Australian Capital city of Canberra is a popular site for water-based recreation, but analyses of seasonal and long-term patterns in enterococci that exceed alert levels (>200 CFU per 100 mL, leading to site closures) are lacking. This study analysed enterococci concentrations from seven recreational sites from 2001-2021 to examine spatial and temporal patterns in exceedances during the swimming season (October-April), when exposure is highest. The enterococci concentrations varied significantly across sites and in the summer months. The frequency of the exceedances was higher in the 2009-2015 period than in the 2001-2005 and 2015-2021 periods. The odds of alert-level concentrations were greater in November, December, and February compared to October. The odds of exceedance were higher at the Weston Park East site (swimming beach) and lower at the Ferry Terminal and Weston Park West site compared to the East Basin site. This preliminary examination highlights the need for site-specific assessments of environmental and management-related factors that may impact the public health risks of using the lake, such as inflows, turbidity, and climatic conditions. The insights from this study confirm the need for targeted monitoring efforts during high-risk months and at specific sites. The study also advocates for implementing measures to minimise faecal pollution at its sources.

Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment

Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs dfrA1, qnrS, sulI and vanB. Significantly elevated levels of the dog faecal marker in stormwater drains at this time also indicated that rainfall led to increased input of dog faecal material from the surrounding catchment. Using 16S rRNA gene amplicon sequencing, several indicator taxa for stormwater contamination such as Arcobacter spp. and Comamonadaceae spp. were identified and the Bayesian SourceTracker tool was used to model the relative impact of specific stormwater drains on the surrounding environment, revealing a heterogeneous contribution of discrete stormwater drains during different periods of the rainfall event, with the microbial signature of one particular drain contributing up to 50% of bacterial community in the seawater directly adjacent. By applying a suite of molecular microbiological approaches, we have precisely pinpointed the causes and point-sources of faecal contamination and other associated microbiological hazards (e.g., ARGs) at an urbanised beach, which has helped to identify the most suitable locations for targeted management of water quality at the beach.

Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem

Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.

Antibiotic Resistance and Sewage-Associated Marker Genes in Untreated Sewage and a River Characterized During Baseflow and Stormflow

Since sewage is a hotspot for antibiotic resistance genes (ARGs), the identification of ARGs in environmental waters impacted by sewage, and their correlation to fecal indicators, is necessary to implement management strategies. In this study, sewage treatment plant (STP) influent samples were collected and analyzed using quantitative polymerase chain reaction (qPCR) to investigate the abundance and correlations between sewage-associated markers (i.e., Bacteroides HF183, Lachnospiraceae Lachno3, crAssphage) and ARGs indicating resistance to nine antibiotics (belonging to aminoglycosides, beta-lactams, sulfonamides, macrolides, and tetracyclines). All ARGs, except bla_VIM, and sewage-associated marker genes were always detected in untreated sewage, and ermF and sul1 were detected in the greatest abundances. intl1 was also highly abundant in untreated sewage samples. Significant correlations were identified between sewage-associated marker genes, ARGs and the intl1 in untreated sewage (τ = 0.488, p = 0.0125). Of the three sewage-associated marker genes, the BIO-ENV procedure identified that HF183 alone best maximized correlations to ARGs and intl1 (τ = 0.590). Additionally, grab samples were collected from peri-urban and urban sites along the Brisbane River system during base and stormflow conditions, and analyzed for Escherichia coli, ARGs, the intl1, and sewage-associated marker genes using quantitative polymerase chain reaction (qPCR). Significant correlations were identified between E. coli, ARGs, and intl1 (τ = 0.0893, p = 0.0032), as well as with sewage-associated marker genes in water samples from the Brisbane River system (τ = 0.3229, p = 0.0001). Of the sewage-associated marker genes and E. coli, the BIO-ENV procedure identified that crAssphage alone maximized correlations with ARGs and intl1 in river samples (τ = 0.4148). Significant differences in E. coli, ARGs, intl1, and sewage-associated marker genes, and by flow condition (i.e., base vs. storm), and site types (peri-urban vs. urban) combined were identified (R = 0.3668, p = 0.0001), where percent dissimilarities between the multi-factorial groups ranged between 20.8 and 11.2%. Results from this study suggest increased levels of certain ARGs and sewage-associated marker genes in stormflow river water samples compared to base flow conditions. E. coli, HF183 and crAssphage may serve as potential indicators of sewage-derived ARGs under stormflow conditions, and this merits further investigation. Data presented in this study will be valuable to water quality managers to understand the links between sewage pollution and ARGs in urban environments.

Identification the source of fecal contamination for geographically unassociated samples with a statistical classification model based on support vector machine

The bacterial diversity and corresponding biological significance revealed by high-throughput sequencing contribute massive information to source tracking of fecal contamination. The performances of classification models on predicting the fecal source of geographical local and foreign samples were examined herein, by applying support vector machine (SVM) algorithm. Random forest (RF) and Adaboost were applied for comparison as well. Discriminatory sequences were selected from Clostridiale, Bacteroidales, or Lactobacillales bacterial groups using extremely randomized trees (ExtraTrees). 1.51-12.64% of the unique sequences in the original library composed the representative markers, and they contributed 70% of the discrepancies between source microbiomes. The overall accuracy of the SVM model and the RF model on local samples was 96.08% and 98.04%, respectively, higher than that of the Adaboost (90.20%). As for the non-local samples, the SVM assigned most of the fecal samples into the correct category while several false-positive judgments occurred in closely related groups. The results in this paper suggested that the SVM was a time-saving and accurate method for fecal source tracking in contaminated water body with the potential capability of executing tasks based on geographically unassociated samples, and underlined the necessity of qPCR analysis for accurate detection of human source pollution.

Occurrence of a human-associated microbial source tracking marker and its relationship with faecal indicator bacteria in an urban estuary

One of the main impacts of urban sprawl in rapidly growing countries has been contamination of coastal environments by waterborne pathogens, posing a critical risk to ecosystem and human health. Microbial source tracking (MST) has been a robust tool to identify the origin of these pathogens globally. This study compared the occurrence of a human-associated Bacteroides marker (BT-α) with faecal indicator bacteria (FIB) in an urban estuary (Golden Horn, Istanbul, Turkey). Faecal coliform (culture method), enterococci (both culture and qPCR method) concentrations and physicochemical variables were compared with the BT-α concentrations in monthly collected samples for a year (n = 108). Enterococci concentrations detected by culture and qPCR were positively correlated (r = 0·86, P < 0·01) suggesting that qPCR can be an alternative method for monitoring. BT-α marker was positive for 30% of the samples and positively correlated with enterococci (r = 0·61 and r = 0·64 for culture and qPCR methods respectively, P < 0·01). Rainfall had a moderate positive correlation with all faecal/MST indicators suggesting combined sewer overflows also severely impacted estuarine water quality. The high FIB and BT-α concentrations at upper estuary suggested that faecal pollution mainly originated from the peri-urban settlements around two creeks entering the estuary.

Microbial quality of wild shellfish in a tropical estuary subject to treated effluent discharge

Elevated faecal indicator levels in beaches around Darwin Harbour including near effluent outfalls have led to concerns about the safety of popular, locally harvested aquatic foods. To address these concerns, the impact of treated effluent discharge on the microbial quality of aquatic foods was assessed using culture-based and molecular tools. Seawater, shellfish (mangrove snails Telescopium and Nerita balteata, the local black lip oyster Saccostrea cucullata) and mud crabs (Scylla serrata) were collected from 13 sites close (impacted) and distal (reference) to two effluent discharge locations, in creeks and coastal areas. Sampling occurred over two dry seasons and one wet season. E. coli, typical sewage related pathogens, Salmonella and norovirus, and the molecular faecal marker Bacteroides, as well as naturally occurring marine bacteria, Vibrio parahaemolyticus and Vibrio vulnificus were tested in biota. E. coli and faecal coliforms were measured in water in water. The highest concentration of faecal coliforms in water was from the Buffalo Creek discharge site. At sites located in creeks including reference creeks, the highest concentrations of faecal coliforms in water were measured in the wet season compared to the dry season, whereas in coastal sites, no or only few (<10) faecal coliforms were detected. E. coli concentrations in both snail species were significantly higher in the wet season compared to the dry season (P < 0.0001) at both the treated effluent discharge sites and reference sites with some samples exceeding the acceptable Australian and New Zealand Food Standards (ANZFS) level based on E. coli levels in bivalves. E. coli concentrations in all of the S. cucullata samples were either below the detection limit or below the ANZFS limit for E. coli. No E. coli exceedances occurred in cooked mud crabs although low E. coli levels were measured in 3 cooked mud crab samples. Only one shellfish sample (T. telescopium) was positive for Salmonella. Norovirus and Bacteroides were not detected in any of the shellfish samples tested. V. parahaemolyticus and V. vulnificus were significantly more prevalent in shellfish samples during the wet season. Twelve virulent strains of V. parahaemolyticus were detected in T. telescopium and two in N. balteata. There was no significant difference in V. parahaemolyticus prevalence between sites. V. parahaemolyticus was detected in cooked S. serrata samples from three sites in the wet season and once in the 2016 dry season. V. vulnificus was detected in both T. telescopium and N. balteata, but not in any of the S. cucullata samples. One cooked crab meat sample from a reference site was positive for V. vulnificus. The prevalence of V. vulnificus was significantly higher at the reference sites compared to the discharge or potential impact sites. The lack of correlation between E. coli and targeted faecal pathogens in biota confirm that traditional faecal markers are not suitable surrogates for faecal pollution, at least not in the tropics. The higher prevalence of E. coli, V. parahaemolyticus and V. vulnificus in biota during the wet season compared to the dry season irrespective of treated sewage influence suggests that marine snails should not be harvested and consumed from creeks during the wet season. Any future aquaculture involving shellfish should consider these data when developing appropriate shellfish quality assurance protocols and for making decisions on where to situate farms.

Compositional and temporal stability of fecal taxon libraries for use with SourceTracker in sub-tropical catchments

Characterization of microbial communities using high-throughput amplicon sequencing is an emerging approach for microbial source tracking of fecal pollution. This study used SourceTracker software to examine temporal and geographical variability of fecal bacterial community profiles to identify pollutant sources in three freshwater catchments in sub-tropical Australia. Fecal bacterial communities from 10 animal species, humans, and composite wastewater samples from six sewage treatment plants were characterized and compared to freshwater samples using Illumina amplicon sequencing of the V5-V6 regions of the 16S rRNA gene. Source contributions were calculated in SourceTracker using new fecal taxon libraries as well as previously generated libraries to determine the effects of geographic and temporal variability on source assignments. SourceTracker determined 16S rRNA bacterial communites within freshwater samples, shared taxonomic similarities to that of wastewater at low levels (typically <3%). SourceTraker also predicted occasional fecal detection of deer and flying fox sources in the water samples. No significant differences in source contributions were observed within sequences from current and previously characterized fecal samples (P ≥ 0.107). However, significant differences were observed between previously characterized and newly characterized source communities (ANOSIM P ≤ 0.001), which shared <15% community composition. Results suggest temporal instability of fecal taxon libraries among tested sources and highlight continual evaluation of community-based MST using confirmatory qPCR analyses of marker genes.

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.

Ecological patterns in the skin microbiota of frogs from tropical Australia

The microbiota of frog skin can play an important role in protecting against diseases and parasites. The frog skin microbial community represents a complex mix of microbes that are promoted by the chemical environment of the frog skin and influenced by the animal's immediate past environment. The microbial communities of six species of frogs sampled from the campus of Charles Darwin University (CDU) were more similar within species than between species. The microbiota of the introduced cane toad (Rhinella marina) was most dissimilar among the species. Pairwise comparisons showed that the microbial communities of each species were different, except for the terrestrial Litoria nasuta and the arboreal L. rothii. The microbial communities of the six species were not related to ecological habit (arboreal or terrestrial), and neither was the alpha diversity of the microbes. The core microbes (defined as being on ≥90% of individuals of a species or group) were significantly different among all species, although 89 microbial operational taxonomic units (OTUs) were core microbes for all six species at CDU. Two species, Rhinella marina and Litoria rothii, were sampled at additional sites approximately 10 and 30 km from CDU. The microbial communities and the core OTU composition were different among the sites, but there were nevertheless 194 (R. marina) and 181 (L. rothii) core OTUs present at all three sites. Thus, the core microbiota varied with respect to geographic range and sample size.

Fecal source identification using random forest

BACKGROUND

Clostridiales and Bacteroidales are uniquely adapted to the gut environment and have co-evolved with their hosts resulting in convergent microbiome patterns within mammalian species. As a result, members of Clostridiales and Bacteroidales are particularly suitable for identifying sources of fecal contamination in environmental samples. However, a comprehensive evaluation of their predictive power and development of computational approaches is lacking. Given the global public health concern for waterborne disease, accurate identification of fecal pollution sources is essential for effective risk assessment and management. Here, we use random forest algorithm and 16S rRNA gene amplicon sequences assigned to Clostridiales and Bacteroidales to identify common fecal pollution sources. We benchmarked the accuracy, consistency, and sensitivity of our classification approach using fecal, environmental, and artificial in silico generated samples.

RESULTS

Clostridiales and Bacteroidales classifiers were composed mainly of sequences that displayed differential distributions (host-preferred) among sewage, cow, deer, pig, cat, and dog sources. Each classifier correctly identified human and individual animal sources in approximately 90% of the fecal and environmental samples tested. Misclassifications resulted mostly from false-positive identification of cat and dog fecal signatures in host animals not used to build the classifiers, suggesting characterization of additional animals would improve accuracy. Random forest predictions were highly reproducible, reflecting the consistency of the bacterial signatures within each of the animal and sewage sources. Using in silico generated samples, we could detect fecal bacterial signatures when the source dataset accounted for as little as ~ 0.5% of the assemblage, with ~ 0.04% of the sequences matching the classifiers. Finally, we developed a proxy to estimate proportions among sources, which allowed us to determine which sources contribute the most to observed fecal pollution.

CONCLUSION

Random forest classification with 16S rRNA gene amplicons offers a rapid, sensitive, and accurate solution for identifying host microbial signatures to detect human and animal fecal contamination in environmental samples.

Fecal pollution: new trends and challenges in microbial source tracking using next-generation sequencing

In this minireview, we expand upon traditional microbial source tracking (MST) methods by discussing two recently developed, next-generation-sequencing (NGS)-based MST approaches to identify sources of fecal pollution in recreational waters. One method defines operational taxonomic units (OTUs) that are specific to a fecal source, e.g., humans and animals or shared among multiple fecal sources to determine the magnitude and likely source association of fecal pollution. The other method uses SourceTracker, a program using a Bayesian algorithm, to determine which OTUs have contributed to an environmental community based on the composition of microbial communities in multiple fecal sources. Contemporary NGS-based MST tools offer a promising avenue to rapidly characterize fecal source contributions for water monitoring and remediation efforts at a broader and more efficient scale than previous molecular MST methods. However, both NGS methods require optimized sequence processing methodologies (e.g. quality filtering and clustering algorithms) and are influenced by primer selection for amplicon sequencing. Therefore, care must be taken when extrapolating data or combining datasets. Furthermore, traditional limitations of library-dependent MST methods, including differential decay of source material in environmental waters and spatiotemporal variation in source communities, remain to be fully understood. Nevertheless, increasing use of these methods, as well as expanding fecal taxon libraries representative of source communities, will help improve the accuracy of these methods and provide promising tools for future MST investigations.

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints

The general consensus is that the abundance of tap water bacteria is greatly influenced by water purification and distribution. Those bacteria that are released from biofilm in the distribution system are especially considered as the major potential risk for drinking water bio-safety. For the first time, this full-scale study has captured and identified the proportional contribution of the source water, treated water, and distribution system in shaping the tap water bacterial community based on their microbial community fingerprints using the Bayesian "SourceTracker" method. The bacterial community profiles and diversity analyses illustrated that the water purification process shaped the community of planktonic and suspended particle-associated bacteria in treated water. The bacterial communities associated with suspended particles, loose deposits, and biofilm were similar to each other, while the community of tap water planktonic bacteria varied across different locations in distribution system. The microbial source tracking results showed that there was not a detectable contribution of source water to bacterial community in the tap water and distribution system. The planktonic bacteria in the treated water was the major contributor to planktonic bacteria in the tap water (17.7-54.1%). The particle-associated bacterial community in the treated water seeded the bacterial community associated with loose deposits (24.9-32.7%) and biofilm (37.8-43.8%) in the distribution system. In return, the loose deposits and biofilm showed a significant influence on tap water planktonic and particle-associated bacteria, which were location dependent and influenced by hydraulic changes. This was revealed by the increased contribution of loose deposits to tap water planktonic bacteria (from 2.5% to 38.0%) and an increased contribution of biofilm to tap water particle-associated bacteria (from 5.9% to 19.7%) caused by possible hydraulic disturbance from proximal to distal regions. Therefore, our findings indicate that the tap water bacteria could possibly be managed by selecting and operating the purification process properly and cleaning the distribution system effectively.

Application of SourceTracker for Accurate Identification of Fecal Pollution in Recreational Freshwater: A Double-Blinded Study

The efficacy of SourceTracker software to attribute contamination from a variety of fecal sources spiked into ambient freshwater samples was investigated. Double-blinded samples spiked with ≤5 different sources (0.025-10% vol/vol) were evaluated against fecal taxon libraries characterized by next-generation amplicon sequencing. Three libraries, including an initial library (17 nonlocal sources), a blinded source library (5 local sources), and a composite library (local and nonlocal sources), were used with SourceTracker. SourceTracker's predictions of fecal compositions in samples were made, in part, based on distributions of taxa within abundant genera identified as discriminatory by discriminant analyses but also using a large percentage of low abundance taxa. The initial library showed poor ability to characterize blinded samples, but, using local sources, SourceTracker showed 91% accuracy (31/34) at identifying the presence of source contamination, with two false positives for sewage and one for horse. Furthermore, sink predictions of source contamination were positively correlated (Spearman's ρ ≥ 0.88, P < 0.001) with spiked source volumes. Using the composite library did not significantly affect sink predictions ( P > 0.79) compared to those made using the local sources alone. Results of this study indicate that geographically associated fecal samples are required for SourceTracker to assign host sources accurately.

Emerging opportunities for developing a diversified land sector economy in Australia’s northern savannas

We explore sustainable land sector opportunities for Australia’s 1.2 million km2 northern savanna rangelands where extensive beef cattle pastoralism is the predominant contemporary land use. Our focal region is characterised by mean annual rainfall exceeding 600 mm, ecologically bountiful wet season water availability followed by 6–8 months of surface water deficit, mostly nutrient-poor soils, internationally significant biodiversity and carbon stock values, very extensive dry season fires in pastorally unproductive settings, a sparse rural population (0.14 persons km–2) comprising a high proportion of Indigenous people, and associated limited infrastructure. Despite relatively high beef cattle prices in recent seasons and property values escalating at a spectacular ~6% p.a. over the past two decades, long-term economics data show that, for most northern regions, typical pastoral enterprises are unprofitable and carry significant debt. Pastoral activities can also incur very significant environmental impacts on soil and scarce dry season water resources, and greenhouse gas emissions, which currently are not accounted for in economic sustainability assessments. Over the same period, the conservation sector (including National Parks, Indigenous Protected Areas) has been expanding rapidly and now occupies 25% of the region. Since 2012, market-based savanna burning projects aimed at reducing greenhouse gas emissions occur over a further 25%. Returns from nature-based tourism focussed particularly on maintaining intact freshwater systems and associated recreational fishing opportunities dwarf returns from pastoralism. The growth of these latter industries illustrates the potential for further development of profitable ‘ecosystem services’ markets as part of a more environmentally and socially sustainable diversified regional land sector economy. We outline some of the imminent challenges involved with, and opportunities for developing, this new industry sector.

Physicochemical Factors Influence the Abundance and Culturability of Human Enteric Pathogens and Fecal Indicator Organisms in Estuarine Water and Sediment

To assess fecal pollution in coastal waters, current monitoring is reliant on culture-based enumeration of bacterial indicators, which does not account for the presence of viable but non-culturable or sediment-associated micro-organisms, preventing effective quantitative microbial risk assessment (QMRA). Seasonal variability in viable but non-culturable or sediment-associated bacteria challenge the use of fecal indicator organisms (FIOs) for water monitoring. We evaluated seasonal changes in FIOs and human enteric pathogen abundance in water and sediments from the Ribble and Conwy estuaries in the UK. Sediments possessed greater bacterial abundance than the overlying water column, however, key pathogenic species (Shigella spp., Campylobacter jejuni, Salmonella spp., hepatitis A virus, hepatitis E virus and norovirus GI and GII) were not detected in sediments. Salmonella was detected in low levels in the Conwy water in spring/summer and norovirus GII was detected in the Ribble water in winter. The abundance of E. coli and Enterococcus spp. quantified by culture-based methods, rarely matched the abundance of these species when measured by qPCR. The discrepancy between these methods was greatest in winter at both estuaries, due to low CFU's, coupled with higher gene copies (GC). Temperature accounted for 60% the variability in bacterial abundance in water in autumn, whilst in winter salinity explained 15% of the variance. Relationships between bacterial indicators/pathogens and physicochemical variables were inconsistent in sediments, no single indicator adequately described occurrence of all bacterial indicators/pathogens. However, important variables included grain size, porosity, clay content and concentrations of Zn, K, and Al. Sediments with greater organic matter content and lower porosity harbored a greater proportion of non-culturable bacteria (including dead cells and extracellular DNA) in winter. Here, we show the link between physicochemical variables and season which govern culturability of human enteric pathogens and FIOs. Therefore, knowledge of these factors is critical for accurate microbial risk assessment. Future water quality management strategies could be improved through monitoring sediment-associated bacteria and non-culturable bacteria. This could facilitate source apportionment of human enteric pathogens and FIOs and direct remedial action to improve water quality.

A High-Throughput DNA-Sequencing Approach for Determining Sources of Fecal Bacteria in a Lake Superior Estuary

Current microbial source-tracking (MST) methods, employed to determine sources of fecal contamination in waterways, use molecular markers targeting host-associated bacteria in animal or human feces. However, there is a lack of knowledge about fecal microbiome composition in several animals and imperfect marker specificity and sensitivity. To overcome these issues, a community-based MST method has been developed. Here, we describe a study done in the Lake Superior-Saint Louis River estuary using SourceTracker, a program that calculates the source contribution to an environment. High-throughput DNA sequencing of microbiota from a diverse collection of fecal samples obtained from 11 types of animals (wild, agricultural, and domesticated) and treated effluent (n = 233) was used to generate a fecal library to perform community-based MST. Analysis of 319 fecal and environmental samples revealed that the community compositions in water and fecal samples were significantly different, allowing for the determination of the presence of fecal inputs and identification of specific sources. SourceTracker results indicated that fecal bacterial inputs into the Lake Superior estuary were primarily attributed to wastewater effluent and, to a lesser extent, geese and gull wastes. These results suggest that a community-based MST method may be another useful tool for determining sources of aquatic fecal bacteria.

A case study characterizing animal fecal sources in surface water using a mitochondrial DNA marker

Water quality impairment by fecal waste in coastal watersheds is a public health issue. The present study provided evidence for the use of a mitochondrial (mtDNA) marker to detect animal fecal sources in surface water. The accurate identification of fecal pollution is based on the notion that fecal microorganisms preferentially inhabit a host animal's gut environment. In contrast, mtDNA host-specific markers are inherent to eukaryotic host cells, which offers the advantage by detecting DNA from the host rather than its fecal bacteria. The present study focused on sampling water presumably from non-point sources (NPS), which can increase bacterial and nitrogen concentrations to receiving water bodies. Stream sampling sites located within the Piscataqua River Watershed (PRW), New Hampshire, USA, were sampled from a range of sites that experienced nitrogen inputs such as sewer and septic systems and suburban runoff. Three mitochondrial (mtDNA) gene marker assays (human, bovine, and canine) were tested from surface water. Nineteen sites were sampled during an 18-month period. Analyses of the combined single and multiplex assay results showed that the proportion of occurrence was highest for bovine (15.6%; n = 77) compared to canine (5.6%; n = 70) and human (5.7%; n = 107) mtDNA gene markers. For the human mtDNA marker, there was a statistically significant relationship between presence vs. absence and land use (Fisher's test p = 0.0031). This result was evident particularly for rural suburban septic, which showed the highest proportion of presence (19.2%) compared to the urban sewered (3.3%), suburban sewered (0%), and agricultural (0%) as well as forested septic (0%) sites. Although further testing across varied land use is needed, our study provides evidence for using the mtDNA marker in large watersheds.

Bacteroidales markers for microbial source tracking in Southeast Asia

The island city country of Singapore served as a model to validate the use of host-associated Bacteroidales 16S rRNA gene marker assays for identifying sources of fecal pollution in the urban tropical environment of Southeast Asia. A total of 295 samples were collected from sewage, humans, domesticated animals (cats, dogs, rabbits and chicken), and wild animals (birds, monkeys and wild boars). Samples were analyzed by real time PCR using five human-associated assays (HF183-SYBR Green, HF183, BacHum, BacH and B. thetaiotaomicron α-1-6, mannanase (B. theta), one canine-associated assay (BacCan), and a total Bacteroidales assay (BacUni). The best performing human-associated assay was B. theta with a diagnostic sensitivity of 69% and 100% in human stool and sewage, respectively, and a specificity of 98%. BacHum achieved the second highest sensitivity and specificity for human stool at 65% and 91%, respectively. The canine-associated Bacteroidales assay (BacCan) had a sensitivity and specificity above 80% and was validated for tracking fecal pollution from dogs. BacUni demonstrated a sensitivity and specificity of 100% for mammals, thus BacUni was confirmed for total Bacteroidales detection in the region. We showed for the first time that rabbit fecal samples cross-react with human-associated assays (HF183-SYBR Green, HF183, BacHum and BacH) and with BacCan. Our findings regarding the best performing human-associated assays differ from those reported in Bangladesh and India, which are geographically close to Southeast Asia, and where HF183 and BacHum were the preferred assays, respectively.

Frogs host faecal bacteria typically associated with humans

Tree frogs commonly access drinking water tanks; this may have human health implications. Although amphibians might not be expected to host mammalian faecal indicator bacteria (FIB), it is possible that they may have human FIB on their skin after exposure to human waste. We collected faeces and skin wash from green tree frogs (Litoria caerulea) from a natural environment, a suburban site, and a suburban site near a creek occasionally contaminated with sewage effluent. We used molecular techniques to test for FIB that are routinely used to indicate human faecal contamination. Enterococci colonies were isolated from both faecal and skin wash samples, and specific markers (Enterococcus faecium and Bacteroides thetaiotaomicron) were found in frog faeces, demonstrating that these markers are not human- or mammalian-specific. Bacteroides thetaiotaomicron was detected in frogs from both natural and urban sites, but E. faecium was only associated with the sewage impacted site.

Multiple approaches to assess the safety of artisanal marine food in a tropical estuary

In this study, metal and metalloid concentrations and pathogens were measured in shellfish at different locations in a tropical estuary, including sites impacted by sewage and industry. Oyster, mangrove snails and mud snails did not exceed Australian and New Zealand Food Standards maximum levels for copper, lead or estimated inorganic arsenic at any site although copper concentrations in oysters and mud snails exceeded generally expected levels at some locations. Bacterial community composition in shellfish was species-specific regardless of location and different to the surrounding water and sediment. In the snails Telescopium telescopium, Terebralia palustris and Nerita balteata, some bacterial taxa differed between sites, but not in Saccostrea cucullata oysters. The abundance of potential human pathogens was very low and pathogen abundance or diversity was not associated with site classification, i.e. sewage impact, industry impact and reference.

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling

Urban estuaries around the world are experiencing contamination from diffuse and point sources, which increases risks to public health. To mitigate and manage risks posed by elevated levels of contamination in urban waterways, it is critical to identify the primary water sources of contamination within catchments. Source tracking using microbial community fingerprints is one tool that can be used to identify sources. However, results derived from this approach have not yet been evaluated using independent datasets. As such, the key objectives of this investigation were: (1) to identify the major sources of water responsible for bacterial loadings within an urban estuary using microbial source tracking (MST) using microbial communities; and (2) to evaluate this method using a 3-dimensional hydrodynamic model. The Yarra River estuary, which flows through the city of Melbourne in South-East Australia was the focus of this study. We found that the water sources contributing to the bacterial community in the Yarra River estuary varied temporally depending on the estuary's hydrodynamic conditions. The water source apportionment determined using microbial community MST correlated to those determined using a 3-dimensional hydrodynamic model of the transport and mixing of a tracer in the estuary. While there were some discrepancies between the two methods, this investigation demonstrated that MST using bacterial community fingerprints can identify the primary water sources of microorganisms in an estuarine environment. As such, with further optimization and improvements, microbial community MST has the potential to become a powerful tool that could be practically applied in the mitigation of contaminated aquatic systems.

Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification

Sources of fecal indicator bacteria are difficult to identify in watersheds that are impacted by a variety of non-point sources. We developed a molecular source tracking test using the PhyloChip microarray that detects and distinguishes fecal bacteria from humans, birds, ruminants, horses, pigs and dogs with a single test. The multiplexed assay targets 9001 different 25-mer fragments of 16S rRNA genes that are common to the bacterial community of each source type. Both random forests and SourceTracker were tested as discrimination tools, with SourceTracker classification producing superior specificity and sensitivity for all source types. Validation with 12 different mammalian sources in mixtures found 100% correct identification of the dominant source and 84-100% specificity. The test was applied to identify sources of fecal indicator bacteria in the Russian River watershed in California. We found widespread contamination by human sources during the wet season proximal to settlements with antiquated septic infrastructure and during the dry season at beaches during intense recreational activity. The test was more sensitive than common fecal indicator tests that failed to identify potential risks at these sites. Conversely, upstream beaches and numerous creeks with less reliance on onsite wastewater treatment contained no fecal signal from humans or other animals; however these waters did contain high counts of fecal indicator bacteria after rain. Microbial community analysis revealed that increased E. coli and enterococci at these locations did not co-occur with common fecal bacteria, but rather co-varied with copiotrophic bacteria that are common in freshwaters with high nutrient and carbon loading, suggesting runoff likely promoted the growth of environmental strains of E. coli and enterococci. These results indicate that machine-learning classification of PhyloChip microarray data can outperform conventional single marker tests that are used to assess health risks, and is an effective tool for distinguishing numerous fecal and environmental sources of pathogen indicators.

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments-a Review

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.

Large Differences in Bacterial Community Composition among Three Nearby Extreme Waterbodies of the High Andean Plateau

The high Andean plateau or Altiplano contains different waterbodies that are subjected to extreme fluctuations in abiotic conditions on a daily and an annual scale. The bacterial diversity and community composition of those shallow waterbodies is largely unexplored, particularly, of the ponds embedded within the peatland landscape (i.e., Bofedales). Here we compare the small-scale spatial variability (<1 m) in bacterial diversity and community composition between two of those ponds with contrasting apparent color, using 454 pyrosequencing of the 16S rRNA gene. Further, we compared the results with the nearest (80 m) main lagoon in the system to elucidate the importance of different environmental factors such as salinity and the importance of these ponds as a source of shared diversity. Bacterial diversity was higher in both ponds than in the lagoon and community composition was largely different among them and characterized by very low operational taxonomic unit sharing. Whereas the “green” pond with relatively low dissolved organic carbon (DOC) concentration (33.5 mg L^-1) was dominated by Proteobacteria and Bacteroidetes, the one with extreme DOC concentration (424.1 mg L^-1) and red hue was dominated by Cyanobacteria. By contrast, the lagoon was largely dominated by Proteobacteria, particularly by Gammaproteobacteria. A large percentage (47%) of all reads was unclassified suggesting the existence of large undiscovered bacterial diversity. Our results suggest that even at the very small-scale spatial range considered, local environmental factors are important in explaining differences in bacterial community composition in those systems. Further, our study highlights that Altiplano peatland ponds represent a hitherto unknown source of microbial diversity.

Evaluation of Techniques for Measuring Microbial Hazards in Bathing Waters: A Comparative Study

Recreational water quality is commonly monitored by means of culture based faecal indicator organism (FIOs) assays. However, these methods are costly and time-consuming; a serious disadvantage when combined with issues such as non-specificity and user bias. New culture and molecular methods have been developed to counter these drawbacks. This study compared industry-standard IDEXX methods (Colilert and Enterolert) with three alternative approaches: 1) TECTA™ system for E. coli and enterococci; 2) US EPA’s 1611 method (qPCR based enterococci enumeration); and 3) Next Generation Sequencing (NGS). Water samples (233) were collected from riverine, estuarine and marine environments over the 2014–2015 summer period and analysed by the four methods. The results demonstrated that E. coli and coliform densities, inferred by the IDEXX system, correlated strongly with the TECTA™ system. The TECTA™ system had further advantages in faster turnaround times (~12 hrs from sample receipt to result compared to 24 hrs); no staff time required for interpretation and less user bias (results are automatically calculated, compared to subjective colorimetric decisions). The US EPA Method 1611 qPCR method also showed significant correlation with the IDEXX enterococci method; but had significant disadvantages such as highly technical analysis and higher operational costs (330% of IDEXX). The NGS method demonstrated statistically significant correlations between IDEXX and the proportions of sequences belonging to FIOs, Enterobacteriaceae, and Enterococcaceae. While costs (3,000% of IDEXX) and analysis time (300% of IDEXX) were found to be significant drawbacks of NGS, rapid technological advances in this field will soon see it widely adopted.

Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters

Faecal contamination of recreational waters is an increasing global health concern. Tracing the source of the contaminant is a vital step towards mitigation and disease prevention. Total 16S rRNA amplicon data for a specific environment (faeces, water, soil) and computational tools such as the Markov-Chain Monte Carlo based SourceTracker can be applied to microbial source tracking (MST) and attribution studies. The current study applied artificial and in-laboratory derived bacterial communities to define the potential and limitations associated with the use of SourceTracker, prior to its application for faecal source tracking at three recreational beaches near Port Phillip Bay (Victoria, Australia). The results demonstrated that at minimum multiple model runs of the SourceTracker modelling tool (i.e. technical replicates) were required to identify potential false positive predictions. The calculation of relative standard deviations (RSDs) for each attributed source improved overall predictive confidence in the results. In general, default parameter settings provided high sensitivity, specificity, accuracy and precision. Application of SourceTracker to recreational beach samples identified treated effluent as major source of human-derived faecal contamination, present in 69% of samples. Site-specific sources, such as raw sewage, stormwater and bacterial populations associated with the Yarra River estuary were also identified. Rainfall and associated sand resuspension at each location correlated with observed human faecal indicators. The results of the optimised SourceTracker analysis suggests that local sources of contamination have the greatest effect on recreational coastal water quality.

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways.

A short review of fecal indicator bacteria in tropical aquatic ecosystems: knowledge gaps and future directions

Given the high numbers of deaths and the debilitating nature of diseases caused by the use of unclean water it is imperative that we have an understanding of the factors that control the dispersion of water borne pathogens and their respective indicators. This is all the more important in developing countries where significant proportions of the population often have little or no access to clean drinking water supplies. Moreover, and notwithstanding the importance of these bacteria in terms of public health, at present little work exists on the persistence, transfer and proliferation of these pathogens and their respective indicator organisms, e.g., fecal indicator bacteria (FIB) such as Escherichia coli and fecal coliforms in humid tropical systems, such as are found in South East Asia or in the tropical regions of Africa. Both FIB and the waterborne pathogens they are supposed to indicate are particularly susceptible to shifts in water flow and quality and the predicted increases in rainfall and floods due to climate change will only exacerbate the problems of contamination. This will be furthermore compounded by the increasing urbanization and agricultural intensification that developing regions are experiencing. Therefore, recognizing and understanding the link between human activities, natural process and microbial functioning and their ultimate impacts on human health are prerequisites for reducing the risks to the exposed populations. Most of the existing work in tropical systems has been based on the application of temperate indicator organisms, models and mechanisms regardless of their applicability or appropriateness for tropical environments. Here, we present a short review on the factors that control FIB dynamics in temperate systems and discuss their applicability to tropical environments. We then highlight some of the knowledge gaps in order to stimulate future research in this field in the tropics.