scholarly journals Microbial Source Tracking of Fecal Pollution on Kabushima Beach Utilizing Genetic Markers

2018 ◽  
Vol 41 (4) ◽  
pp. 97-105
Author(s):  
Yuki TANAKA ◽  
Junichi YAGUCHI
Keyword(s):  
Genetic Markers ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Source Tracking

scholarly journals Identifying Host Sources of Fecal Pollution: Diversity of Escherichia coli in Confined Dairy and Swine Production Systems

2005 ◽  
Vol 71 (10) ◽  
pp. 5992-5998 ◽  
Author(s):  
Zexun Lu ◽  
David Lapen ◽  
Andrew Scott ◽  
Angela Dang ◽  
Edward Topp
Keyword(s):  
Escherichia Coli ◽  
Dairy Farm ◽  
Sampling Strategy ◽  
Farming Systems ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Source Tracking ◽  
E Coli ◽  
Repetitive Extragenic Palindromic Pcr ◽  
Repetitive Extragenic Palindromic

ABSTRACT Repetitive extragenic palindromic PCR fingerprinting of Escherichia coli is one microbial source tracking approach for identifying the host source origin of fecal pollution in aquatic systems. The construction of robust known-source libraries is expensive and requires an informed sampling strategy. In many types of farming systems, waste is stored for several months before being released into the environment. In this study we analyzed, by means of repetitive extragenic palindromic PCR using the enterobacterial repetitive intergenic consensus primers and comparative analysis using the Bionumerics software, collections of E. coli obtained from a dairy farm and from a swine farm, both of which stored their waste as a slurry in holding tanks. In all fecal samples, obtained from either barns or holding tanks, the diversity of the E. coli populations was underrepresented by collections of 500 isolates. In both the dairy and the swine farms, the diversity of the E. coli community was greater in the manure holding tank than in the barn, when they were sampled on the same date. In both farms, a comparison of stored manure samples collected several months apart suggested that the community composition changed substantially in terms of the detected number, absolute identity, and relative abundance of genotypes. Comparison of E. coli populations obtained from 10 different locations in either holding tank suggested that spatial variability in the E. coli community should be accounted for when sampling. Overall, the diversity in E. coli populations in manure slurry storage facilities is significant and likely is problematic with respect to library construction for microbial source tracking applications.

scholarly journals Evaluation of Bovine Feces-Associated Microbial Source Tracking Markers and Their Correlations with Fecal Indicators and Zoonotic Pathogens in a Brisbane, Australia, Reservoir

2013 ◽  
Vol 79 (8) ◽  
pp. 2682-2691 ◽  
Author(s):  
W. Ahmed ◽  
T. Sritharan ◽  
A. Palmer ◽  
J. P. S. Sidhu ◽  
S. Toze
Keyword(s):  
Host Specificity ◽  
Water Samples ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Decay Rates ◽  
Source Tracking ◽  
Content Type ◽  
Zoonotic Pathogens ◽  
Maximum Value ◽  
Bovine Feces

ABSTRACTThis study was aimed at evaluating the host specificity and host sensitivity of two bovine feces-associated bacterial (BacCow-UCD and cowM3) and one viral [bovine adenovirus (B-AVs)] microbial source tracking (MST) markers by screening 130 fecal and wastewater samples from 10 target and nontarget host groups in southeast Queensland, Australia. In addition, 36 water samples were collected from a reservoir and tested for the occurrence of all three bovine feces-associated markers along with fecal indicator bacteria (FIB),Campylobacterspp.,Escherichia coliO157, andSalmonellaspp. The overall host specificity values of the BacCow-UCD, cowM3, and B-AVs markers to differentiate between bovine and other nontarget host groups were 0.66, 0.88, and 1.00, respectively (maximum value of 1.00). The overall host sensitivity values of these markers, however, in composite bovine wastewater and individual bovine fecal DNA samples were 0.93, 0.90, and 0.60, respectively (maximum value of 1.00). Among the 36 water samples tested, 56%, 22%, and 6% samples were PCR positive for the BacCow-UCD, cowM3, and B-AVs markers, respectively. Among the 36 samples tested, 50% and 14% samples were PCR positive for theCampylobacter16S rRNA andE. coliO157rfbEgenes, respectively. Based on the results, we recommend that multiple bovine feces-associated markers be used if possible for bovine fecal pollution tracking. Nonetheless, the presence of the multiple bovine feces-associated markers along with the presence of potential zoonotic pathogens indicates bovine fecal pollution in the reservoir water samples. Further research is required to understand the decay rates of these markers in relation to FIB and zoonotic pathogens.

scholarly journals Microbial source tracking in highly vulnerable karst drinking water resources

2017 ◽  
Vol 16 (1) ◽  
pp. 138-149 ◽  
Author(s):  
D. Diston ◽  
R. Robbi ◽  
A. Baumgartner ◽  
R. Felleisen
Keyword(s):  
Water Resources ◽  
16S Rrna ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Source Tracking ◽  
Microbial Water Quality ◽  
Marker Selection ◽  
Drinking Water Resources ◽  
Selection For ◽  
Culture Dependent

Abstract Water resources situated in areas with underlying karst geology are particularly vulnerable to fecal pollution. In such vulnerable systems, microbial source tracking (MST) methods are useful tools to elucidate the pathways of both animal and human fecal pollution, leading to more accurate water use risk assessments. Here, we describe the application of a MST toolbox using both culture-dependent bacteriophage and molecular-dependent 16S rRNA assays at spring and well sites in the karstic St Imier Valley, Switzerland. Culture-dependent and molecular-dependent marker performance varied significantly, with the 16S rRNA assays displaying greater sensitivity than their phage counterpart; HF183 was the best performing human wastewater-associated marker while Rum2Bac was the best performing ruminant marker. Differences were observed in pollution regimes between the well and spring sampling sites, with the spring water being more degraded than the well site. Our results inform the choice of marker selection for MST studies and highlight differences in microbial water quality between well and spring karst sites.

scholarly journals Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach

2021 ◽  
Vol 12 ◽  
Author(s):  
Amine M. Boukerb ◽  
Cyril Noël ◽  
Emmanuelle Quenot ◽  
Bernard Cadiou ◽  
Julien Chevé ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Source Tracking ◽  
Human Pathogens ◽  
Bird Droppings ◽  
Environmental Pathogens

Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their comparison to other sources and develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers to detect such pollution. Thus, by using 16S rRNA amplicon high-throughput sequencing, the aims of this study were (i) to explore and compare fecal bacterial communities from wild waterbirds (i.e., six families and 15 species, n = 275 samples) to that of poultry, cattle, pigs, and influent/effluent of wastewater treatment plants (n = 150 samples) and (ii) to develop new MST markers for waterbirds. Significant differences were observed between wild waterbirds and the four other groups. We identified 7,349 Amplicon Sequence Variants (ASVs) from the hypervariable V3–V4 region. Firmicutes and Proteobacteria and, in a lesser extent, Actinobacteria and Bacteroidetes were ubiquitous while Fusobacteria and Epsilonbacteraeota were mainly present in wild waterbirds. The clustering of samples in non-metric multidimensional scaling (NMDS) ordination indicated a by-group clustering shape, with a high diversity within wild waterbirds. In addition, the structure of the bacterial communities was distinct according to bird and/or animal species and families (Adonis R2 = 0.13, p = 10–4, Adonis R2 = 0.11, p = 10–4, respectively). The Analysis of Composition of Microbiomes (ANCOM) showed that the wild waterbird group differed from the others by the significant presence of sequences from Fusobacteriaceae (W = 566) and Enterococcaceae (W = 565) families, corresponding to the Cetobacterium (W = 1427) and Catellicoccus (W = 1427) genera, respectively. Altogether, our results suggest that some waterbird members present distinct fecal microbiomes allowing the design of qPCR MST markers. For instance, a swan- and an oystercatcher-associated markers (named Swan_2 and Oyscab, respectively) have been developed. Moreover, bacterial genera harboring potential human pathogens associated to bird droppings were detected in our dataset, including enteric pathogens, i.e., Arcobacter, Clostridium, Helicobacter, and Campylobacter, and environmental pathogens, i.e., Burkholderia and Pseudomonas. Future studies involving other wildlife hosts may improve gut microbiome studies and MST marker development, helping mitigation of yet unknown fecal pollution sources.

Performance of host-associated genetic markers for microbial source tracking in China

2020 ◽  
Vol 175 ◽  
pp. 115670 ◽  
Author(s):  
Yang Zhang ◽  
Renren Wu ◽  
Kairong Lin ◽  
Yishu Wang ◽  
Junqing Lu
Keyword(s):  
Genetic Markers ◽  
Microbial Source Tracking ◽  
Source Tracking

Fecal Pollution, Public Health, and Microbial Source Tracking

2014 ◽  
pp. 1-32 ◽  
Author(s):  
Jill R. Stewart ◽  
Jorge W. Santo Domingo ◽  
Timothy J. Wade
Keyword(s):  
Public Health ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Source Tracking

scholarly journals Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer

2020 ◽  
Vol 184 ◽  
pp. 116211
Author(s):  
Jessica Hinojosa ◽  
Jemima Green ◽  
Fabiola Estrada ◽  
Jonathan Herrera ◽  
Troy Mata ◽  
...  
Keyword(s):  
Land Use ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Primary Sources ◽  
Source Tracking ◽  
Edwards Aquifer

Relationships among microbial indicators of fecal pollution, microbial source tracking markers, and pathogens in Costa Rican coastal waters

2021 ◽  
Vol 188 ◽  
pp. 116507
Author(s):  
Adriana González-Fernández ◽  
Erin M. Symonds ◽  
Javier F. Gallard-Gongora ◽  
Bonnie Mull ◽  
Jerzy O. Lukasik ◽  
...  
Keyword(s):  
Coastal Waters ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Costa Rican ◽  
Source Tracking ◽  
Microbial Indicators
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