Development and applications of microbial ecogenomic indicators for monitoring water quality: report of a workshop assessing the state of the science, research needs and future directions

Comparative Bacteriological and Heavy Metal Toxicity Evaluation of Groundwater Wells Proximal to Pollution Receiving Streams in Ondo City, Nigeria

Background:

Groundwater is the main and easily accessible source of water supply. Aside its over-exploitation problems, groundwater has undergone quality challenges-owing to its proximity to pollution sources.

Methods and Materials:

This study assessed the quality of hand-dug wells situated close to the pollution receiving streams in the Ondo City. Thirty water samples; from fifteen hand-dug wells and fifteen closely associated streams across the city were collected for the study. Physico-chemical, microbial and heavy metals parameters were comparatively analyzed in stream and groundwater samples to assess percolation impact on groundwater quality. Studies were carried out in wet and dry seasons.

Results:

The results obtained from the wells water show that beside temperature and PH, the mean values of other physicochemical parameters like turbidity (111.47 NTU & 68.77 NTU/), total dissolved solid (474.6 mg/l & 68.77mg/l), and electrical conductivity (822.31 µS/cm & 816.79 µS/cm) in both season respectively were above the World Health Organisation (WHO) highest desirable limits. The highest total coliform (T.col) recorded at 11,200 (cfu/100ml) and 11,300 (cfu/100ml) and Faecal coliform at 8,400 (cfu/100ml) and 12,100 (cfu/100ml) for dry and rainy seasons respectively. Highest level of aluminium, cadmium, lead, and chromium concentrations in well water at 1.632mg/l, 0.820mg/l, 0.079mg/l and 0.079mg/l recorded in the rainy season exceeded WHO’s recommendations. Pearson Correlation analysis between well and stream in the dry season shows positive correlation for all water parameters, with strong significance in PH, turbidity, faecal coliform and chromium concentration (0.544, 0.914, 0.414 &0.597) respectively. Similarly, in the rainy season, both well and stream had positive correlations for most parameter tested with significances in turbidity, electrical conductivity, total dissolved solid and cadmium concentration (0.708, 0.775, 0.766&0.655) respectively.

Conclusion:

The major outcome of this research revealed most water samples (well and stream) failed quality assessments. The positive correlations between wells and polluted stream parameters suggested that distance contributed significantly to well contaminations.

Evaluation of five microbial and four mitochondrial DNA markers for tracking human and pig fecal pollution in freshwater

This study systematically evaluated five microbial and four mitochondrial DNA (mtDNA) markers, including sensitivities and specificities under PCR method, and fecal concentrations and decay rates in water under qPCR method. The microbial DNA markers were the three human-associated (BacH, HF183 and B.adolescentis) and two pig-associated (Pig-2-Bac and L.amylovorus), while the mtDNA ones were two human- (H-ND6 and H-ND5) and two pig-associated (P-CytB and P-ND5). All the mtDNA markers showed higher sensitivity (100%) than the microbial ones (84.0-88.8%) except Pig-2-Bac (100%). Specificities of the human mtDNA markers (99.1 and 98.1%) were higher than those of the human-associated microbial ones (57.0-88.8%). But this pattern was not observed in the pig-associated markers where Pig-2-Bac had 100% specificity. The reliability of H-ND6 and H-ND5 was further evidenced to identify locations of the most polluted within the Taihu Lake watershed of China. In general, the microbial DNA markers demonstrated a higher fecal concentration than the mtDNA ones; increasing temperature and sunlight exposure accelerated significantly the decay of all the DNA markers. Results of this study suggest that DNA markers H-ND6, H-ND5, and Pig-2-Bac may be among the best for fecal source tracking in water.

Persistence of mitochondrial DNA markers as fecal indicators in water environments

Mitochondrial DNA (mtDNA) polymerase chain reaction (PCR) technology has recently been developed to identify sources of fecal contamination, but information regarding environmental fate of mtDNA is limited. In this study, quantitative real-time PCR was used to determine the persistence of three species-specific mtDNA markers (human, pig and chicken) in river microcosms under different laboratory conditions and in dialysis tubes incubated in river environments during different seasons. Human feces had a higher abundance of mtDNA marker than pig and chicken feces. A biphasic decay pattern was observed for the mtDNA markers in microcosms incubated in darkness, and T90 (time needed for 90% reduction) ranged from 2.03 to 13.83 d. Each species-specific mtDNA marker persisted for relatively longer time at lower temperatures, and light exposure and predation increased the decay rates. Field experiments showed that the mtDNA markers could survive for longer time in winter (T90: 1.79-4.37 d) than in summer (T90: 0.60-0.75 d). Field application of mtDNA technology indicated that the markers were mainly distributed on the sites near animal breeding plants and had lower abundance in downstream water of the receiving river. This study expands our knowledge of the environmental fate of mtDNA markers and the results may be useful for practical application of the technology in fecal source tracking.

Molecular detection of Penicillium griseofulvum as the coastal pollution indicator

Molecular methods were carried out to detect Penicillium griseofulvum, a dominant species related to heavy metal pollution, which was screened from marine contaminated sediments. Based on differences in internal transcribed spacer (ITS) sequences of Penicillium genus and specific isoamyl alcohol oxidase (IAO) sequences, species-specific primers AS1/RS4 and IAO1/IAO2 of Penicillium griseofulvum were designed and synthesized which were then employed in optimized PCR systems. The detection sensitivities were compared through ordinary PCR and nested-PCR using two pairs of primers, respectively. Both primer pairs could exclusively amplify destined DNA fragment from contaminated environmental samples in our researches. As for primers AS1/RS4, the detection sensitivity for spores (pure spore DNA) could be 10 fg/μl and 10 spores, respectively, and the detection sensitivity for the sediments was 10² spores/0.25 g sediments. While the detection sensitivity of IAO1/IAO2 primers was lower than that of AS1/RS4. Despite the difference in detection sensitivity, it is feasible that the species-specific primers could be used as probes for the detection of environmental pollution dominant species, Penicillium griseofulvum, since the frequency of occurrence and amount of this strain could preferably indicate the pollution degree.

Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution

Advances in microbial source tracking (MST) have largely been driven by the need to comply with water quality standards based on traditional indicator bacteria. Recently, a number of culture-independent, and library-independent methods based on polymerase chain reaction (PCR) have been gaining popularity among source trackers. However, only a limited number of these methods have been successfully used in field applications, primarily due to the fact that many of them are still being developed. In this critical outlook, we examine different viewpoints associated with the practical use of MST to identify critical research gaps, propose a priority-based timeline to address them, and outline emerging technologies that will likely impact the future of source tracking. We propose that it is necessary to consider each of these aspects in order to advance towards a unifying framework in source identification, so that fecal pollution monitoring can be reliably used for comprehensive environmental microbial monitoring, to develop risk assessment models, and to implement and validate adequate management practices.