Integrated site-specific quantification of faecal bacteria and detection of DNA markers in faecal contamination source tracking as a microbial risk tracking tool in urban Lake ecosystems

The presence of feacal-derived pathogens in water is responsible for several infectious diseases and deaths worldwide. As a solution, sources of fecal pollution in waters must be accurately assessed, properly determined and strictly controlled. However, the exercise has remained challenging due to the existing overlapping characteristics by different members of faecal coliform bacteria and the inadequacy of information pertaining to the contribution of seasonality and weather condition on tracking the possible sources of pollution. There are continued ef forts to improve the Faecal Contamination Source Tracking(FCST) techniques such as Microbial Source Tracking(MST). This study aimed to make contribution to MST by evaluating the efficacy of combining site specific quantification of faecal contamination indicator bacteria and detection of DNA markers while accounting for seasonality and weather conditions' eff ects in tracking the major sources of faecal contamination in a freshwater system(Donghu Lake, China). The results showed that the use of cyd gene in addition to lacZ and uidA genes differentiates E. coli from other closely related faecal bacteria. The use of selective media increases the pollution source tracking accuracy. BSA addition boosts PCR detection and increases FCST efficiency. Seasonality and weather variability also influence the detection limit for DNA markers.

Assembly process and source tracking of microbial communities in sediments of Dongting Lake

●Soil erosion resulted in homogenization of bacterial communities in the watershed.●Microbial community heterogeneity among erosion sites made soil tracing possible.●Assembly process results showed that the tracking results can achieve high precision.●Dryland was the main source of sediment deposition based on the result of FEAST.Sediment source tracing can accurately provide a theoretical basis for controlling soil erosion effectively,by identifying the most serious types of land use.Traditional sediment tracing methods are based on physical,chemical,biological,and composite fingerprinting,which have not included microbes.As high-throughput sequencing becomes more prevalent,microorganisms can provide more information than what we think.Thus,whether the microorganism can also be used as a special fingerprint factor for sediment source identification during soil erosion,we have tested it by using microbial source tracking tool FEAST to quantify the microbe contribution from five types of eroded land(including dryland,urban,paddy field,forest and grassland)to the depositional areas(Niubitan)in the Yuanjiang basin.The source microbial community in the erosive area was heterogeneous,and assembly process analysis further demonstrated that the source tracking results could reach higher accuracy.The results of FEAST showed that dryland(35.50%),urban(17.21%),paddy field(8.14%),and forest(1.07%)were the major contributors to Niubitan.Our results follow the general soil erosion rules and prove its validity.Taken together,a new perspective is provided by these results for tracing sediment sources in erosion-sedimentary systems.

The spatial variation of soil bacterial community assembly processes affects the accuracy of source tracking in ten major Chinese cities

Urban soils harbor billions of bacterial cells and millions of species.However,the distribution patterns and assembly processes of bacterial communities remain largely uncharacterized in urban soils.It is also unknown if we can use the bacteria to track soil sources to certain cities and districts.Here,Illumina MiSeq sequencing was used to survey soil bacterial communities from 529 random plots spanning 61 districts and 10 major cities in China.Over a 3,000 km range,community similarity declined with increasing geographic distance(Mantel r=0.62),and community composition was clustered by city(R^(2)=0.50).Within cities(<100 km),the aforementioned biogeographic patterns were weakened.Process analysis showed that homogenizing dispersal and dispersal limitation dominated soil bacterial assembly at small and large spatial scales,respectively.Accordingly,the probabilities of accurately tracking random soil sources to certain cities and districts were 90.0% and 66.7%,respectively.When the tested samples originated from cities that were more than 1,265 km apart,the soil sources could be identified with nearly 100% accuracy.Overall,this study demonstrates the strong distance-decay relationship and the clear geographic zoning of urban soil bacterial communities among cities.The varied importance of different community assembly processes at multiple spatial scales strongly affects the accuracy of microbial source tracking.

Validation of Bacteroidales-based microbial source tracking markers for pig fecal pollution and their application in two rivers of North China

In China,pig feces is the predominant source of excrement produced b y animal husbandry.Improper use or direct discharge of pig feces can result in contamination of natural water systems.Microbial source tracking(MST)technology can identify the sources of fecal pollution in environmental water,and contribute to the management of pig fecal pollution by local environmental protection agencies.However,the accuracy of such assays can be context-dependent,and they have not been comprehensively evaluated under Chinese conditions.We aimed to compare the performance of five previously reported nig-specific MST assays(PF,Pig-Bac 1 STBR,Pig-Bac2 SYBR,Pig-1-Bac TaqMan,and Pig-2-Bac TaqMan,which are based on Bacteroidales 16S rRNA gene markers)and apply them in two rivers of North China.We collected a total of 173 fecal samples from pigs,cows,goats,chickens,humans,and horses across China.The PF assay optimized in this study showed outstanding qualitative performance and achieved 100%specificity and sensitivity.However,the two SYBR green qPCR assays(Pig-Bac1 SYBR and Pig-Bac2 SYBR)cross-reacted with most non-pig fecal samples.In contrast,both the Pig-l-Bac TaqMan and Pig-2-Bacr TaqMan assays gave 100%specificity and sensitivity.Of these,the Pig-2-Bac TaqMan assay showed higher reproducibility.Our results regarding the specificity of these pig-specific MST assays differ from those reported in Thailand,Japan,and America.Using the PF and Pig-2-Bac TaqMan assays,a field test comparing the levels of pig fecal pollution in rivers near a pig farm before and after comprehensive environmental pollution governance indicated that pig fecal pollution was effectively controlled at this location.

Bernoulli particle flter with observer altitude for maritime radiation source tracking in the presence of measurement uncertainty

For maritime radiation source target tracking in particular electronic counter measures（ECM）environment,there exists two main problems which can deteriorate the tracking performance of traditional approaches.The frst problem is the poor observability of the radiation source.The second one is the measurement uncertainty which includes the uncertainty of the target appearing/disappearing and the detection uncertainty（false and missed detections）.A novel approach is proposed in this paper for tracking maritime radiation source in the presence of measurement uncertainty.To solve the poor observability of maritime radiation source target,using the radiation source motion restriction,the observer altitude information is incorporated into the bearings-only tracking（BOT）method to obtain the unique target localization.Then the two uncertainties in the ECM environment are modeled by the random fnite set（RFS）theory and the Bernoulli fltering method with the observer altitude is adopted to solve the tracking problem of maritime radiation source in such context.Simulation experiments verify the validity of the proposed approach for tracking maritime radiation source,and also demonstrate the superiority of the method compared with the traditional integrated probabilistic data association（IPDA）method.The tracking performance under different conditions,particularly those involving different duration of radiation source opening and switching-off,indicates that the method to solve our problem is robust and effective.

Using Host-Specificity of Cryptosporidium to Understand Contaminant Sources, Seasonality, and Human Health Risk in Three Watersheds of Differing Land-Use

Three tributaries of the Grand River watershed (Ontario, Canada), each representing different watershed types (urban, agricultural/rural, and mixed land-use) were examined to understand the spatial, temporal, and host-source distribution of the waterborne pathogen, Cryptosporidium. Cryptosporidium was frequently found throughout the study (73%, 65/89) with occurrence and concentrations observed to be similar among the varying watershed types. However, applying advanced genotyping techniques, marked differences in dominant host sources could be observed in each watershed. The agricultural/rural and mixed land-use watersheds were dominated by genotypes typically associated with cattle (i.e., C. andersoni), while the urban watershed had the highest diversity of Cryptosporidium genotypes with a variety of wildlife as the common source of contamination (e.g., muskrat and cervine genotypes). A similar seasonal trend observed in the urban, agricultural, and mixed land-use watershed suggests that factors beyond specific land use activities (e.g. autumn manure spreading) may influence the timing and concentration of Cryptosporidium in these streams. Corresponding genotyping results provided additional insight into source inputs during these seasonal peaks, indicating that wildlife may be important seasonal contributors to Cryptosporidium contamination in these streams. Despite the abundance of Cryptosporidium in these watersheds, most of the genotypes observed were of limited human health importance. This study provides evidence regarding the significance of including genotyping results into studies examining waterborne Cryptosporidium. Using this technique can provide a greater understanding of the risk to the population using water sources, as well as provide insight into the probable sources and timing of contamination. This ancillary information can contribute to implementation of targeted management strategies to further protect sources of drinking water and recreation areas.

Tracking PCB Contamination in Ontario Great Lakes Tributaries: Development of Methodologies and Lessons Learned for Watershed Based Investigations

Project Trackdown is an investigative environmental program aimed at tracking sources of polychlorinated biphenyl (PCB) contamination in Great Lakes tributaries. The program uses a multimedia weight of evidence approach for identifying sources of PCBs to the environment. PCB concentrations in environmental media (sediment, water, suspended sediment and soil), passive samplers and/or exposed biota (mussels, young-of-the-year fish and benthic invertebrates) are used in combination to evaluate bioavailability and identify local anomalies within a tributary. These lines of evidence can be assessed with simple chemometric techniques and fingerprinting of PCB congener profiles, and, combined with anecdotal information such as land use history and tributary alterations, may be used to identify ongoing and locally controllable sources of PCBs to the Great Lakes. The program was successful at developing environmental triggers to differentiate potential source areas from background PCB conditions in urban areas, allowing efforts to focus on identifying active ongoing sources of PCB contamination. Project Trackdown has been carried out in three tributaries to Lake Ontario (Cataraqui River, Etobicoke Creek and Twelve Mile Creek) and two tributaries that flow into the Detroit River (Turkey Creek and Little River). Local ongoing PCB sources have been identified in four projects, leading to abatement or remediation measures. As a collaborative initiative between the Ontario Ministry of the Environment and Environment Canada, Project Trackdown has successfully identified several PCB sources leading to substantial cleanup efforts aimed ultimately at reducing PCB contamination to the Great Lakes.

Tracking a Severe Pollution Event in Beijing in December 2016 with the GRAPES–CUACE Adjoint Model

We traced the adjoint sensitivity of a severe pollution event in December 2016 in Beijing using the adjoint model of the GRAPES–CUACE（Global/Regional Assimilation and Prediction System coupled with the China Meteorological Administration Unified Atmospheric Chemistry Environmental Forecasting System）. The key emission sources and periods affecting this severe pollution event are analyzed. For comaprison, we define 2000 Beijing Time 3 December 2016 as the objective time when PM2.5 reached the maximum concentration in Beijing. It is found that the local hourly sensitivity coefficient amounts to a peak of 9.31 μg m^–3 just 1 h before the objective time, suggesting that PM2.5 concentration responds rapidly to local emissions. The accumulated sensitivity coefficient in Beijing is large during the 20-h period prior to the objective time, showing that local emissions are the most important in this period.The accumulated contribution rates of emissions from Beijing, Tianjin, Hebei, and Shanxi are 34.2%, 3.0%, 49.4%,and 13.4%, respectively, in the 72-h period before the objective time. The evolution of hourly sensitivity coefficient shows that the main contribution from the Tianjin source occurs 1–26 h before the objective time and its peak hourly contribution is 0.59 μg m^-3 at 4 h before the objective time. The main contributions of the Hebei and Shanxi emission sources occur 1–54 and 14–53 h, respectively, before the objective time and their hourly sensitivity coefficients both show periodic fluctuations. The Hebei source shows three sensitivity coefficient peaks of 3.45, 4.27, and 0.71 μg m^–3 at 4, 16, and 38 h before the objective time, respectively. The sensitivity coefficient of the Shanxi source peaks twice, with values of 1.41 and 0.64 μg m^–3 at 24 and 45 h before the objective time, respectively. Overall, the adjoint model is effective in tracking the crucial sources and key periods of emissions for the severe pollution event.

Microbial diversity accumulates in a downstream direction in the Three Gorges Reservoir

Organic and inorganic materials migrate downstream and have important roles in regulating environmental health in the river networks.However,it remains unclear whether and how a mixture of materials(i.e.,microbial species)from various upstream habitats contribute to microbial community coalescence upstream of a dam.Here we track the spatial variation in microbial abundance and diversity in the Three Gorges Reservoir based on quantitative PCR and 16 S rRNA gene high-throughput sequencing data.We further quantitatively assess the relative contributions of microbial species from mainstem,its tributaries,and the surrounding riverbank soils to the area immediately upstream of the Three Gorges Dam(TGD).We found an increase of microbial diversity and the convergent microbial distribution pattern in areas immediately upstream of TGD,suggesting this area become a new confluence for microbial diversity immigrating from upstream.Indeed,the number of shared species increased from upstream to TGD but unique species decreased,indicating immigration of various sources of microbial species overwhelms local environmental conditions in structuring microbial community close to TGD.By quantifying the sources of microbial species close to TGD,we found little contribution from soils as compared to tributaries,especially for sites closer to TGD,suggesting tributary microbes have greater influence on microbial diversity and environmental health in the Three Gorges Reservoir.Collectively,our results suggest that tracking microbial geographic origin and evaluating accumulating effects of microbial diversity shed light on the ecological processes in microbial communities and provide information for regulating aquatic ecological health.