Application of phylogenetic microarray analysis to discriminate sources of fecal pollution

Conventional methods for fecal source tracking typically use single biomarkers to systematically identify or exclude sources. High-throughput DNA sequence analysis can potentially identify all sources of microbial contaminants in a single test by measuring the total diversity of fecal microbial communities. In this study, we used phylogenetic microarray analysis to determine the comprehensive suite of bacteria that define major sources of fecal contamination in coastal California. Fecal wastes were collected from 42 different populations of humans, birds, cows, horses, elk, and pinnipeds. We characterized bacterial community composition using a DNA microarray that probes for 16S rRNA genes of 59,316 different bacterial taxa. Cluster analysis revealed strong differences in community composition among fecal wastes from human, birds, pinnipeds, and grazers. Actinobacteria, Bacilli, and many Gammaproteobacteria taxa discriminated birds from mammalian sources. Diverse families within the Clostridia and Bacteroidetes taxa discriminated human wastes, grazers, and pinnipeds from each other. We found 1058 different bacterial taxa that were unique to either human, grazing mammal, or bird fecal wastes. These OTUs can serve as specific identifier taxa for these sources in environmental waters. Two field tests in marine waters demonstrate the capacity of phylogenetic microarray analysis to track multiple sources with one test.     

Principal component analysis for the identification of pollution sources in mussel survey by trace metals

Summary Principal component analysis has been applied to analyze the correlation matrix obtained from a 8 × 43 data matrix. The 8 trace metals are Mn, Co, Ni, Cu, Zn, Cd, Hg, Ph, which are contained in the soft part of mussels (Mytilus galloprovincialis Lamarck). Mussels were sampled from two sites in the Gulf of Trieste. In both samples, 76–78% of the total variance is explained by the four principal components. The orthogonally rotated factor matrix indicates that Co and Ni are bonded to the first principal component and Cd and Pb to the first (site 2) or second principal component (site 1). The origin of trace metals in the soft part of mussels from the Gulf of Trieste is discussed.

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Analyse der Hauptkomponenten zur Identifizierung der Verunreinigungsursachen von Muscheln über die Spurenmetalle

Zusammenfassung Die Analyse der Hauptkomponenten wurde auf die Korrelationsmatrix, die aus der 8 × 43-Datenmatrix hervorgeht, angewandt. Diese 8 Spurenmetalle sind Mn, Co, Ni, Cu, Zn, Cd, Hg, Pb, die im Fleisch der Miesmuscheln (Mytilus galloprovincialis Lamarck) gefunden worden sind. Die Miesmuscheln stammen aus zwei Gegenden des Golfes von Triest. Vier Hauptkomponenten erklären 76–78 % der totalen Varianz der beiden Stichproben. Die orthogonale-rotierte Faktorenmatrix zeigt, daß Co und Ni an die erste Hauptkomponente und Cd und Pb an die erste (Lage 2) oder an die zweite Hauptkomponente (Lage 1) gebunden sind. Die Herkunft der Spurenmetalle im Muschelfleisch aus dem Golf von Triest wird diskutiert.

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L. Felician is the author of the statistical analysis for site 1 as a part of his thesis in Commodity Science, Faculty of Economics, University of Trieste- L. Gabrielli Favretto is the author of the statistical analysis of the data for site 2. All authors contributed to the rest of the paper     

Principal component analysis for the identification of pollution sources in mussel survey by trace metals

Principal component analysis has been applied to analyze the correlation matrix obtained from a 8 X 43 data matrix. The 8 trace metals are Mn, Co, Ni, Cu, Zn, Cd, Hg, Pb, which are contained in the soft part of mussels (Mytilus galloprovincialis Lamarck). Mussels were sampled from two sites in the Gulf of Trieste. In both samples, 76-78% of the total variance is explained by the four principal components. The orthogonally rotated factor matrix indicates that Co and Ni are bonded to the first principal component and Cd and Pb to the first (site 2) or second principal component (site 1). The origin of trace metals in the soft part of mussels from the Gulf of Trieste is discussed.     

Decay of Bacteroidales genetic markers in relation to traditional fecal indicators for water quality modeling of drinking water sources

The implementation of microbial fecal source tracking (MST) methods in drinking water management is limited by the lack of knowledge on the transport and decay of host-specific genetic markers in water sources. To address these limitations, the decay and transport of human (BacH) and ruminant (BacR) fecal Bacteroidales 16S rRNA genetic markers in a drinking water source (Lake R?dasj?n in Sweden) were simulated using a microbiological model coupled to a three-dimensional hydrodynamic model. The microbiological model was calibrated using data from outdoor microcosm trials performed in March, August, and November 2010 to determine the decay of BacH and BacR markers in relation to traditional fecal indicators. The microcosm trials indicated that the persistence of BacH and BacR in the microcosms was not significantly different from the persistence of traditional fecal indicators. The modeling of BacH and BacR transport within the lake illustrated that the highest levels of genetic markers at the raw water intakes were associated with human fecal sources (on-site sewers and emergency sewer overflow). This novel modeling approach improves the interpretation of MST data, especially when fecal pollution from the same host group is released into the water source from different sites in the catchment.     

Tiered approach for identification of a human fecal pollution source at a recreational beach: case study at Avalon Bay,Catalina Island,California

Recreational marine beaches in California are posted as unfit for swimming when the concentration of fecal indicator bacteria (FIB) exceeds any of seven concentration standards. Finding and mitigating sources of shoreline FIB is complicated by the many potential human and nonhuman sources of these organisms and the complex fate and transport processes that control their concentrations. In this study, a three-tiered approach is used to identify human and nonhuman sources of FIB in Avalon Bay, a popular resort community on Catalina Island in southern California. The first and second tiers utilize standard FIB tests to spatially isolate the FIB signal, to characterize the variability of FIB over a range of temporal scales, and to measure FIB concentrations in potential sources of these organisms. In the third tier, water samples from FIB "hot spots" and sources are tested for human-specific bacteria Bacteroides/Prevotella and enterovirus to determine whether the FIB are from human sewage or from nonhuman sources such as bird feces. FIB in Avalon Bay appear to be from multiple, primarily land-based, sources including bird droppings, contaminated subsurface water, leaking drains, and runoff from street wash-down actvities. Multiple shoreline samples and two subsurface water samples tested positive for human-specific bacteria and enterovirus, suggesting that at least a portion of the FIB contamination is from human sewage.     

Hyperspectral fluorescence imaging using violet LEDs as excitation sources for fecal matter contaminate identification on spinach leaves

Food safety in the production of fresh produce for human consumption is a worldwide issue and needs to be addressed to decrease foodborne illnesses and resulting costs. Hyperspectral fluorescence imaging coupled with multivariate image analysis techniques for detection of fecal contaminates on spinach leaves (Spinacia oleracea) was evaluated. Violet fluorescence excitation was provided at 405 nm and light emission was recorded from 464 to 800 nm. Partial least square discriminant analysis and wavelength ratio methods were compared for detection accuracy for fecal contamination. Fluorescence emission profiles of spinach leaves were monitored over a 27 days storage period; peak emission blue-shifts were observed over the storage period accompanying a color change from green to green–yellow–brown hue. The PLSDA model developed correctly detected fecal contamination on 100 % of relatively fresh green spinach leaves used in this investigation, which also had soil contamination. The PLSDA model had 19 % false positives for non-fresh post storage leaves. A wavelength ratio technique using four wavebands (680, 688, 703 and 723 nm) was successful in identifying 100 % of fecal contaminates on both fresh and non-fresh leaves. An on-line fluorescence imaging inspection system for fecal contaminant detection has potential to allow fresh produce producers to reduce foodborne illnesses and prevent against the associated economic losses.     

Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution

Diffuse sources of human fecal pollution allow for the direct discharge of waste into receiving waters with minimal or no treatment. Traditional culture-based methods are commonly used to characterize fecal pollution in ambient waters, however these methods do not discern between human and other animal sources of fecal pollution making it difficult to identify diffuse pollution sources. Human-associated quantitative real-time PCR (qPCR) methods in combination with low-order headwatershed sampling, precipitation information, and high-resolution geographic information system land use data can be useful for identifying diffuse source of human fecal pollution in receiving waters. To test this assertion, this study monitored nine headwatersheds over a two-year period potentially impacted by faulty septic systems and leaky sanitary sewer lines. Human fecal pollution was measured using three different human-associated qPCR methods and a positive significant correlation was seen between abundance of human-associated genetic markers and septic systems following wet weather events. In contrast, a negative correlation was observed with sanitary sewer line densities suggesting septic systems are the predominant diffuse source of human fecal pollution in the study area. These results demonstrate the advantages of combining water sampling, climate information, land-use computer-based modeling, and molecular biology disciplines to better characterize diffuse sources of human fecal pollution in environmental waters.     

Locating sources of surf zone pollution: a mass budget analysis of fecal indicator bacteria at Huntington Beach, California

The surf zone is the unique environment where ocean meets land and a place of critical ecological, economic, and recreational importance. In the United States, this natural resource is increasingly off-limits to the public due to elevated concentrations of fecal indicator bacteria and other contaminants, the sources of which are often unknown. In this paper, we describe an approach for calculating mass budgets of pollutants in the surf zone from shoreline monitoring data. The analysis reveals that fecal indicator bacteria pollution in the surf zone at several contiguous beaches in Orange County, California, originates from well-defined locations along the shore, including the tidal outlets of the Santa Ana River and Talbert Marsh. Fecal pollution flows into the ocean from the Santa Ana River and Talbert Marsh outlets during ebb tides and from there is transported parallel to the shoreline by wave-driven surf zone currents and/or offshore tidal currents, frequently contaminating >5 km of the surf zone. The methodology developed here for locating and quantifying sources of surf zone pollution should be applicable to a wide array of contaminants and coastal settings.     

食品重金属污染来源的研究进展

食品重金属污染严重危害食品安全。文中结合国内外研究现状,从食品原材料、食品加工制作、食品贮藏销售3个方面综述了食品重金属污染的来源,以期为探寻当前食品重金属残留的产生因素,并制订具体的防控措施提供参考。     

A procedural approach for the identification of sources of uncertainty associated with GM quantification and real-time quantitative PCR measurements

Estimation of measurement uncertainty is important as it provides objective evidence that an assay or instrument is ‘fit for purpose’, and is a requirement for accreditation to ISO17025. Technological developments within the bioanalytical laboratory have progressed rapidly in the past few years. However, the measurement science associated with these technologies has not yet fully matured. The provision of a full measurement uncertainty budget is often difficult because of a lack of standardised approaches and the constraints associated with time, finances and expertise. A procedural approach for the identification of factors that can account for measurement uncertainty in quantification of genetically modified (GM) ingredients using real-time quantitative PCR is presented here. This example illustrates an approach for the identification of factors that can be applied to related assays concerned with GM quantification, can be utilised as part of existing uncertainty approaches, and can provide the basis for making quantitative estimates of uncertainty that will contribute towards a full measurement uncertainty budget.     

大型水生植物在水污染治理中的应用研究进展

近年来随着将大型水生植物运用在水污染治理中,通过长时间研究发现,其可以通过自身生长代谢吸收氮、磷等水体营养物质,从而实现降解有机污染物。而进一步针对大型水生植物在水污染治理中应用研究进展展开分析,对于促进我国水污染治理会起到诸多帮助。基于此,本文首先将会针对大型水生植物及生态功能展开概述,而后针对大型水生植物在生态系统污水处理中应用研究进展与现状展开分析,进而针对大型水生植物种类选择及搭配展开研究,旨为相关人员提供参考帮助。     

Incidence of the enterococcal surface protein (esp) gene in human and animal fecal sources

The occurrence of the enterococcal surface protein (esp) gene in the opportunistic pathogens Enterococcus faecalis and E. faecium is well-documented in clinical research. Recently, the esp gene has been proposed as a marker of human pollution in environmental waters; however, information on its relative incidence in various human and animal fecal sources is limited. We have determined the occurrence of the esp gene in enterococci from human (n=64) and animal (n=233) fecal samples by polymerase chain reaction using two primer sets: one presumably specific for E. faecium (esp(fm)) and the other for both E. faecalis and E. faecium (esp(fs/fm)). We believe that this research is the first to explore the use of esp(fs/fm) for the detection of human waste in natural environmental settings. The incidence in human sources was 93.1% esp(fm) and 100% esp(fs/fm) in raw sewage influent; 30% for both esp(fm) and esp(fs/fm) in septic waste; and 0% esp(fm) and 80% esp(fs/fm) in active pit toilets. The overall occurrence of the gene in animal feces was 7.7% (esp(fs/fm)) and 4.7% (esp(fm)); animal types with positive results included dogs (9/43, all esp(fm)), gulls (10/34, esp(fs/fm); 2/34, esp(fm)), mice (3/22, all esp(fs/fm)), and songbirds (5/55, all esp(fs/fm)). The esp gene was not detected in cat (0/34), deer (0/4), goose (0/18), or raccoon (0/23) feces. The inconsistent occurrence, especially in septic and pit toilet sewage, suggests a low statistical power of discrimination between animal and human sources, which means a large number of replicates should be collected. Both esp(fm) and esp(fs/fm) were common in raw sewage, but neither one efficiently differentiated between animal and other human sources.