Dave Bachoon - Academia.edu (original) (raw)

Papers by Dave Bachoon

Research paper thumbnail of Tracking the sources of Leptospira and nutrient flows in two urban watersheds of Puerto Rico

Environmental Monitoring and Assessment

Research paper thumbnail of Environmental risk assessment for fecal contamination sources in urban and peri-urban estuaries, in Escambia and Santa Rosa counties, FL, USA

Environmental Monitoring and Assessment, Jun 21, 2023

Research paper thumbnail of Potential rates of methanogenesis in peat and marl sawgrass wetlands in the Florida Everglades

Research paper thumbnail of Rapid detection of human fecal contamination in estuarine environments by PCR targeting of Bifidobacterium adolescentis

Journal of Microbiological Methods, 2007

Detection of Bifidobacterium adolescentis was used as an effective genetic marker of human fecal ... more Detection of Bifidobacterium adolescentis was used as an effective genetic marker of human fecal contamination in Georgia estuaries. Enterococci enumerations on mEI media indicated that a tributary to the Little Satilla River with 516 CFU/100 ml was the most polluted of all the rivers tested. Extracted DNA from eight river water samples was subjected to a two-step nested PCR protocol using genus and species specific primers for Bifidobacterium spp. and B. adolescentis. B. adolescentis was detected from extracted DNA in Dunbar River, Black Bank Creek, and in a Little Satilla River tributary which demonstrates the presence of human fecal contamination in these three rivers. In the five other estuaries tested including West Point-Federica River and the Altamaha River, which both had less than 16 CFU/100 ml of enterococci, B. adolescentis was not detected.

Research paper thumbnail of Identifying the primary sources of fecal contamination along the beaches and rivers of Trinidad

Journal of Water and Health, Mar 13, 2020

The aim of this study was to identify the main sources of fecal pollution at popular beaches and ... more The aim of this study was to identify the main sources of fecal pollution at popular beaches and rivers in the island of Trinidad. Escherichia coli enumeration and microbial source tracking (MST) were used to identify the primary sources of fecal bacteria contamination at the sites. Nineteen sites exceeded USEPA water quality standards for safe recreational use. Highest levels of fecal contamination were recorded on the central and west coasts of the island and included Brickfield River (4,839 MPN 100 ml À1), Orange Valley Bay (2,406.6 MPN 100 ml À1) and Chaguaramas Bay (1,921.2 MPN 100 ml À1). MST detected human (HF183) fecal pollution at ∼63%, birds at ∼67%, chicken at ∼36% and cattle (BacCow) at ∼34% of the sites. MST is a useful and rapid method for identifying major sources of fecal pollution in rivers and beaches. In Trinidad water bodies, the main sources of fecal pollution were humans and birds. The large number of sites with elevated levels of fecal pollution detected is particularly alarming and represents a serious public health risk.

Research paper thumbnail of RNA recovery and detection of mRNA by RT-PCR from preserved prokaryotic samples

Fems Microbiology Letters, Jul 1, 2001

The effectiveness of maintaining prokaryotic RNA in Synechococcus and Pseudomonas cells, fixed in... more The effectiveness of maintaining prokaryotic RNA in Synechococcus and Pseudomonas cells, fixed in 96% ethanol, 4% paraformaldehyde, or suspended in RNAlater, and held in cold storage for 3 months was compared. Fluorometric determination of the RNA extracted from Synechococcus and Pseudomonas cells indicated that the cell storage treatments tested were equally effective at maintaining their total RNA content. There was not any detectable decrease in the quantity of RNA isolated from the preserved samples during storage. Intact mRNA transcripts of the RuBisCO (rbcL) and nir genes were detected by reverse transcriptase-polymerase chain reaction (RT-PCR) from preserved bacterial cells throughout 3 months of storage. In contrast, RT-PCR failed to amplify the mRNA of the rbcL and nitrite reductase genes in unfixed and/or unpreserved bacterial samples, suggesting that bacterial mRNA can be well maintained during a prolonged storage when cells are preserved properly. In addition, RNAlater is a useful reagent for the storage and maintenance of high quality RNA in unfrozen samples.

Research paper thumbnail of The presence of atrazine and atrazine-degrading bacteria in the residential, cattle farming, forested and golf course regions of Lake Oconee

Journal of Applied Microbiology, Jun 9, 2011

To assess the concentration of atrazine in Lake Oconee and develop a qPCR assay as a potential ma... more To assess the concentration of atrazine in Lake Oconee and develop a qPCR assay as a potential marker for the presence of atrazine-degrading bacteria indicating atrazine contamination. Water and sediment samples were collected from the Oconee Lake at four golf course sites, two residential sites, one cattle farming site and a forested site. Atrazine concentration at the study sites was determined using an ELISA kit and indicated the presence of atrazine from 0·72 ppb at the forested sites to 1·84 ppb at the golf course sites. QPCR results indicate the presence of atzA gene (atrazine chlorohydrolase) from 1·51 × 10(2) gene copies at the residential sites to 3·31 × 10(5) gene copies per 100 ml of water at the golf course regions of the lake and correlated (r = 0·64) with atrazine concentration. Sediment samples had higher atzA gene copies compared with the water samples (P < 0·05). Atrazine concentration and the highest quantity of atzA gene were detected in the golf course regions of the lake. Overall, atrazine concentration monitored in Lake Oconee was below the Environment Protection Agency (EPA) regulatory standards. Quantitative PCR is an efficient technique for assessing the presence of atrazine catabolism gene as a functional marker for atrazine-degrading bacteria and the presence of atrazine contamination.

Research paper thumbnail of Microbial community assessment in oil-impacted salt marsh sediment microcosms by traditional and nucleic acid-based indices

Journal of Microbiological Methods, Jul 1, 2001

The effect of oil amendment in salt marsh sediment microcosms was examined by most probable numbe... more The effect of oil amendment in salt marsh sediment microcosms was examined by most probable number MPN , DNA-hybridization with domain-specific oligonucleotide probes and whole community 16S rDNA-hybridizations. Gas Ž. chromatography GCrMS analysis of oil residues in sediments from microcosms after 3 months of operation showed that the quantity of petroleum hydrocarbons was lower in microcosms amended with oil compared to microcosms amended with Ž. Ž oil q plant detritus. Bacterial numbers total-MPN increased in all experimental microcosms amended with plant detritus,. oil, and oil q plant detritus. In comparison to the intact sediment, the proportions of oil-degrading bacteria increased) 100-fold in the oil amended microcosm and) 10-fold in the plant detritus and the oil q plant detritus amended microcosms. DNA-hybridizations with Bacteria, Archaea and Eukarya oligonucleotide probes indicated few changes in the petroleum contaminated sediment community profile. In contrast, rDNA-hybridizations indicated that the bacterial community profile of the oil-impacted sediments, after 1 month of exposure, was significantly different from the control sediment.

Research paper thumbnail of Detection of <i>Brucella suis</i>, <i>Campylobacter jejuni</i>, and <i>Escherichia coli</i> Strains in Feral Pig (<i>Sus scrofa</i>) Communities of Georgia

Vector-borne and Zoonotic Diseases, Jul 1, 2018

Feral pigs (Sus scrofa) are an environmentally destructive invasive species that act as a reservo... more Feral pigs (Sus scrofa) are an environmentally destructive invasive species that act as a reservoir for zoonotic pathogens. The aim of this study was to determine the presence of Brucella suis, Campylobacter jejuni, and of Escherichia coli in feces of feral pigs from Georgia. Fecal samples were collected from 87 feral pigs from forested and agricultural regions of Georgia. DNA was extracted from the fecal samples and quantitative PCR (qPCR) was used to screen for each of the four pathogens. The qPCR assays indicated that B. suis and eaeA-containing strains of E. coli was present in about 22% and 28% of the samples, respectively. C. jejuni was undetected in any of the feral pig fecal samples. The incidence of B. suis was higher in the pigs from forested region, whereas E. coli strains possessing eaeA gene incidence was higher in the pigs from agricultural regions. In Georgia, feral pigs harbor infectious agents and are a growing threat to the transmission of pathogens to native wildlife, humans, and food crops.

Research paper thumbnail of Quantification of enterococci and bifidobacteria in Georgia estuaries using conventional and molecular methods

Water Research, Aug 1, 2008

Fecal pollution is a serious threat to the estuarine environment along the Georgia coast. Culture... more Fecal pollution is a serious threat to the estuarine environment along the Georgia coast. Culture-dependant and molecular methodologies were utilized to compare and evaluate the abundance of fecal indicator bacteria in four Georgia estuaries (Darien River, Frederica River, Gulley Hole Creek, and St. Marys River). The functionality of enterococci and bifidobacteria as indicator organisms in marine environments was assessed, as well as Bifidobacterium adolescentis densities. At each study site, enterococci were enumerated as colony forming units (CFU) on mEI agar. For quantitative polymerase chain reaction (qPCR), genus-and species-specific primer sets were used to quantify bifidobacteria and B. adolescentis as 16S rRNA gene copies and enterococci as tuf gene copies. A high correlation (r ¼ 0.925) was observed between CFU and qPCR enumeration of enterococci. Enterococci densities in the estuarine rivers ranged from 3-449 CFU/100 ml on mEI plates and 4.58-5.39 Log 10 gene copies/100 ml by qPCR. Bifidobacteria densities ranged from 3.62-4.14 Log 10 gene copies/100 ml and suggested the Frederica River as least affected by fecal bacteria and the Darien River as most affected by fecal pollution. A correlation of 0.46 was observed among qPCR densities of enterococci and bifidobacteria at all sample sites. Quantitative polymerase chain reaction detection of B. adolescentis was a rapid (i.e., less than 2 h) indicator of presumptive human fecal pollution and suggested that Gulley Hole Creek, the Darien River, and the St. Marys River were affected by fecal bacteria derived from a human source. Gulley Hole Creek and the Darien River had the highest levels of fecal pollution detected in the studied estuaries. Molecular quantification of bifidobacteria may be a more accurate method of determining immediate health risks associated with fecal pollution in estuarine water than traditional and contemporary assessments of enterococci.

Research paper thumbnail of Detection of Campylobacter jejuni Presence in Trinidad’s Aquatic Environments

Water Air and Soil Pollution, Jun 1, 2022

Research paper thumbnail of Detection of verotoxin producing Escherichia coli in marine environments of the Caribbean

Marine Pollution Bulletin, Nov 1, 2013

Research paper thumbnail of Remote sensing of the biological dynamics of large-scale salt evaporation ponds

International Symposium on Remote Sensing of Environment, 1992

Optical properties of salt evaporation ponds associated with Exportadora de Sal, a salt productio... more Optical properties of salt evaporation ponds associated with Exportadora de Sal, a salt production company in Baja California Sur, Mexico, were analyzed using a combination of spectroradiometer and extracted pigment data, and Landsat-5 Thematic Mapper imagery. ...

Research paper thumbnail of Tracking human faecal contamination in tropical reservoirs in Puerto Rico

Lakes and Reservoirs: Research and Management, Nov 6, 2008

Using a combination of chemical and microbiological (culture-dependent and-independent) approache... more Using a combination of chemical and microbiological (culture-dependent and-independent) approaches, sources of human faecal contamination were identified in two water reservoirs in Puerto Rico-Guajataca and La Plata. Fluorescence from optical brighteners (OB)-commonly found in laundry detergents-was used as an indicator of contamination from septic systems and other household discharges. Traditional indicators of faecal contamination (e.g. Escherichia coli; faecal enterococci) were enumerated, and human faecal contamination was confirmed through detection of Bifidobacterium adolescentis utilizing polymerase chain reaction (PCR)-based analyses. For Guajataca Reservoir, four of 19 sampling sites (21%) were positive for the presence of B. adolescentis under baseflow conditions. The OB fluorescence data suggested that the most likely source for three of these sites was residential, whereas the source of contamination at the remaining site, although of human origin, was probably non-residential. B. adolescentis was present in 83% (19 of 23) of the sampling sites in La Plata. The La Plata sources were more difficult to identify because samples were taken under stormflow conditions, although the presence of OB fluorescence suggested a residential origin in a number of instances. OB fluorescence and traditional bacterial indicators of faecal contamination produced a number of false positive and negative findings for both reservoirs, pointing to the importance of understanding the limitations of these tools for tropical freshwater systems. The results of this study should be useful in developing a weight-of-evidence approach for the identification of potential sources and extent of human faecal contamination in similar tropical reservoirs, a necessary step in the development of management plans to reduce or eliminate these sources.

Research paper thumbnail of Evaluation of microbiological water quality in Point Judith Pond (Rhode Island, USA): Quantitation of fecal pollution and presence of human pathogenic bacteria

Open journal of water pollution and treatment, Mar 31, 2015

Water and sediment samples were collected in the Bluff Hill Cove area of Point Judith Pond from 1... more Water and sediment samples were collected in the Bluff Hill Cove area of Point Judith Pond from 12 stations along three parallel transects, and eelgrass samples were taken at two sites per transect. Fecal enterococci (FE) in the water samples exceeded USEPA regulatory limit of 100 MPN/100 mL for safe recreational and shellfish harvesting use in 24 out of 41 samples. Sediment samples had the lowest FE counts, whereas eelgrass had the highest counts. Using qPCR, H. pylori was detected in 8 out of 41 samples, but E. coli O157:H7 was not detected. Overall, higher levels of H. pylori were detected in 33% of the eelgrass samples and 33% of the sediment samples as compared to 9% in the water column. Microbial source tracking, using the Bacteroides marker HF183, indicated the presence of human fecal bacteria in 7 out of 41 samples, four of which were positive for H. pylori.

Research paper thumbnail of Seasonal shifts in the presence of pathogenic leptospires, Escherichia coli, and physicochemical properties in coastal rivers and streams of Puerto Rico

Journal of Environmental Quality, 2020

Leptospirosis is an emerging zoonotic disease in the Caribbean region and the island of Puerto Ri... more Leptospirosis is an emerging zoonotic disease in the Caribbean region and the island of Puerto Rico. Information on the presence of pathogenic Leptospira in rivers and streams of Puerto Rico is currently lacking. This study aimed to evaluate seasonal shifts in the presence of pathogenic leptospires and the level of Escherichia coli from 32 coastal locations in Puerto Rico's dry and wet seasons. Physicochemical parameters (temperature, salinity, pH, and dissolved oxygen) were determined at each site. The temperature (25.8 °C) and pH (average 7.6) values were all within acceptable USEPA regulatory standards. Thirty‐eight percent of the sites of the dry season and 28% of the wet season sites contained dissolved oxygen levels ≤4 mg L−1, which is relatively low. In the dry season, 19 sites (59%) and 18 (56%) of the wet season sites had E. coli counts >410 most probable number (MPN) 100 ml−1 and would be considered unsafe for recreational use. The lipl32 gene quantitative polymeras...

Research paper thumbnail of Environmental risk assessment for fecal contamination sources in urban and peri-urban estuaries, in Escambia and Santa Rosa counties, FL, USA

Environmental Monitoring and Assessment

Research paper thumbnail of San Juan Bay Estuary

Research paper thumbnail of Detection of Campylobacter jejuni Presence in Trinidad’s Aquatic Environments

Water, Air, & Soil Pollution

Research paper thumbnail of doi:10.1155/2010/595692 Research Article Comparison of Four Polymerase Chain Reaction Methods for the Rapid Detection of Human Fecal Pollution in Marine and

Copyright © 2010 Dave S. Bachoon et al. This is an open access article distributed under the Crea... more Copyright © 2010 Dave S. Bachoon et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We compared the effectiveness of three PCR protocols for the detection of Bifidobacterium adolescentis and one PCR protocol for detecting Bacteroidales as indicators of human fecal pollution in environmental samples. Quantitative PCR indicated that a higher concentration of B. adolescentis DNA was recovered from sewage samples on the 0.2 μm filters compared to the 0.45 μm filters, and there was no evidence of qPCR inhibitors in the DNA extracts. With the Matsuki method (1999), B. adolescentis was detected only in undiluted sewage samples. The King method (2007) performed well and detected B. adolescentis in all of the sewage dilutions (from undiluted to 10 −4). In contrast, the Bonjoch approach(2004) was effective at detecting B. ad...

Research paper thumbnail of Tracking the sources of Leptospira and nutrient flows in two urban watersheds of Puerto Rico

Environmental Monitoring and Assessment

Research paper thumbnail of Environmental risk assessment for fecal contamination sources in urban and peri-urban estuaries, in Escambia and Santa Rosa counties, FL, USA

Environmental Monitoring and Assessment, Jun 21, 2023

Research paper thumbnail of Potential rates of methanogenesis in peat and marl sawgrass wetlands in the Florida Everglades

Research paper thumbnail of Rapid detection of human fecal contamination in estuarine environments by PCR targeting of Bifidobacterium adolescentis

Journal of Microbiological Methods, 2007

Detection of Bifidobacterium adolescentis was used as an effective genetic marker of human fecal ... more Detection of Bifidobacterium adolescentis was used as an effective genetic marker of human fecal contamination in Georgia estuaries. Enterococci enumerations on mEI media indicated that a tributary to the Little Satilla River with 516 CFU/100 ml was the most polluted of all the rivers tested. Extracted DNA from eight river water samples was subjected to a two-step nested PCR protocol using genus and species specific primers for Bifidobacterium spp. and B. adolescentis. B. adolescentis was detected from extracted DNA in Dunbar River, Black Bank Creek, and in a Little Satilla River tributary which demonstrates the presence of human fecal contamination in these three rivers. In the five other estuaries tested including West Point-Federica River and the Altamaha River, which both had less than 16 CFU/100 ml of enterococci, B. adolescentis was not detected.

Research paper thumbnail of Identifying the primary sources of fecal contamination along the beaches and rivers of Trinidad

Journal of Water and Health, Mar 13, 2020

The aim of this study was to identify the main sources of fecal pollution at popular beaches and ... more The aim of this study was to identify the main sources of fecal pollution at popular beaches and rivers in the island of Trinidad. Escherichia coli enumeration and microbial source tracking (MST) were used to identify the primary sources of fecal bacteria contamination at the sites. Nineteen sites exceeded USEPA water quality standards for safe recreational use. Highest levels of fecal contamination were recorded on the central and west coasts of the island and included Brickfield River (4,839 MPN 100 ml À1), Orange Valley Bay (2,406.6 MPN 100 ml À1) and Chaguaramas Bay (1,921.2 MPN 100 ml À1). MST detected human (HF183) fecal pollution at ∼63%, birds at ∼67%, chicken at ∼36% and cattle (BacCow) at ∼34% of the sites. MST is a useful and rapid method for identifying major sources of fecal pollution in rivers and beaches. In Trinidad water bodies, the main sources of fecal pollution were humans and birds. The large number of sites with elevated levels of fecal pollution detected is particularly alarming and represents a serious public health risk.

Research paper thumbnail of RNA recovery and detection of mRNA by RT-PCR from preserved prokaryotic samples

Fems Microbiology Letters, Jul 1, 2001

The effectiveness of maintaining prokaryotic RNA in Synechococcus and Pseudomonas cells, fixed in... more The effectiveness of maintaining prokaryotic RNA in Synechococcus and Pseudomonas cells, fixed in 96% ethanol, 4% paraformaldehyde, or suspended in RNAlater, and held in cold storage for 3 months was compared. Fluorometric determination of the RNA extracted from Synechococcus and Pseudomonas cells indicated that the cell storage treatments tested were equally effective at maintaining their total RNA content. There was not any detectable decrease in the quantity of RNA isolated from the preserved samples during storage. Intact mRNA transcripts of the RuBisCO (rbcL) and nir genes were detected by reverse transcriptase-polymerase chain reaction (RT-PCR) from preserved bacterial cells throughout 3 months of storage. In contrast, RT-PCR failed to amplify the mRNA of the rbcL and nitrite reductase genes in unfixed and/or unpreserved bacterial samples, suggesting that bacterial mRNA can be well maintained during a prolonged storage when cells are preserved properly. In addition, RNAlater is a useful reagent for the storage and maintenance of high quality RNA in unfrozen samples.

Research paper thumbnail of The presence of atrazine and atrazine-degrading bacteria in the residential, cattle farming, forested and golf course regions of Lake Oconee

Journal of Applied Microbiology, Jun 9, 2011

To assess the concentration of atrazine in Lake Oconee and develop a qPCR assay as a potential ma... more To assess the concentration of atrazine in Lake Oconee and develop a qPCR assay as a potential marker for the presence of atrazine-degrading bacteria indicating atrazine contamination. Water and sediment samples were collected from the Oconee Lake at four golf course sites, two residential sites, one cattle farming site and a forested site. Atrazine concentration at the study sites was determined using an ELISA kit and indicated the presence of atrazine from 0·72 ppb at the forested sites to 1·84 ppb at the golf course sites. QPCR results indicate the presence of atzA gene (atrazine chlorohydrolase) from 1·51 × 10(2) gene copies at the residential sites to 3·31 × 10(5) gene copies per 100 ml of water at the golf course regions of the lake and correlated (r = 0·64) with atrazine concentration. Sediment samples had higher atzA gene copies compared with the water samples (P &lt; 0·05). Atrazine concentration and the highest quantity of atzA gene were detected in the golf course regions of the lake. Overall, atrazine concentration monitored in Lake Oconee was below the Environment Protection Agency (EPA) regulatory standards. Quantitative PCR is an efficient technique for assessing the presence of atrazine catabolism gene as a functional marker for atrazine-degrading bacteria and the presence of atrazine contamination.

Research paper thumbnail of Microbial community assessment in oil-impacted salt marsh sediment microcosms by traditional and nucleic acid-based indices

Journal of Microbiological Methods, Jul 1, 2001

The effect of oil amendment in salt marsh sediment microcosms was examined by most probable numbe... more The effect of oil amendment in salt marsh sediment microcosms was examined by most probable number MPN , DNA-hybridization with domain-specific oligonucleotide probes and whole community 16S rDNA-hybridizations. Gas Ž. chromatography GCrMS analysis of oil residues in sediments from microcosms after 3 months of operation showed that the quantity of petroleum hydrocarbons was lower in microcosms amended with oil compared to microcosms amended with Ž. Ž oil q plant detritus. Bacterial numbers total-MPN increased in all experimental microcosms amended with plant detritus,. oil, and oil q plant detritus. In comparison to the intact sediment, the proportions of oil-degrading bacteria increased) 100-fold in the oil amended microcosm and) 10-fold in the plant detritus and the oil q plant detritus amended microcosms. DNA-hybridizations with Bacteria, Archaea and Eukarya oligonucleotide probes indicated few changes in the petroleum contaminated sediment community profile. In contrast, rDNA-hybridizations indicated that the bacterial community profile of the oil-impacted sediments, after 1 month of exposure, was significantly different from the control sediment.

Research paper thumbnail of Detection of <i>Brucella suis</i>, <i>Campylobacter jejuni</i>, and <i>Escherichia coli</i> Strains in Feral Pig (<i>Sus scrofa</i>) Communities of Georgia

Vector-borne and Zoonotic Diseases, Jul 1, 2018

Feral pigs (Sus scrofa) are an environmentally destructive invasive species that act as a reservo... more Feral pigs (Sus scrofa) are an environmentally destructive invasive species that act as a reservoir for zoonotic pathogens. The aim of this study was to determine the presence of Brucella suis, Campylobacter jejuni, and of Escherichia coli in feces of feral pigs from Georgia. Fecal samples were collected from 87 feral pigs from forested and agricultural regions of Georgia. DNA was extracted from the fecal samples and quantitative PCR (qPCR) was used to screen for each of the four pathogens. The qPCR assays indicated that B. suis and eaeA-containing strains of E. coli was present in about 22% and 28% of the samples, respectively. C. jejuni was undetected in any of the feral pig fecal samples. The incidence of B. suis was higher in the pigs from forested region, whereas E. coli strains possessing eaeA gene incidence was higher in the pigs from agricultural regions. In Georgia, feral pigs harbor infectious agents and are a growing threat to the transmission of pathogens to native wildlife, humans, and food crops.

Research paper thumbnail of Quantification of enterococci and bifidobacteria in Georgia estuaries using conventional and molecular methods

Water Research, Aug 1, 2008

Fecal pollution is a serious threat to the estuarine environment along the Georgia coast. Culture... more Fecal pollution is a serious threat to the estuarine environment along the Georgia coast. Culture-dependant and molecular methodologies were utilized to compare and evaluate the abundance of fecal indicator bacteria in four Georgia estuaries (Darien River, Frederica River, Gulley Hole Creek, and St. Marys River). The functionality of enterococci and bifidobacteria as indicator organisms in marine environments was assessed, as well as Bifidobacterium adolescentis densities. At each study site, enterococci were enumerated as colony forming units (CFU) on mEI agar. For quantitative polymerase chain reaction (qPCR), genus-and species-specific primer sets were used to quantify bifidobacteria and B. adolescentis as 16S rRNA gene copies and enterococci as tuf gene copies. A high correlation (r ¼ 0.925) was observed between CFU and qPCR enumeration of enterococci. Enterococci densities in the estuarine rivers ranged from 3-449 CFU/100 ml on mEI plates and 4.58-5.39 Log 10 gene copies/100 ml by qPCR. Bifidobacteria densities ranged from 3.62-4.14 Log 10 gene copies/100 ml and suggested the Frederica River as least affected by fecal bacteria and the Darien River as most affected by fecal pollution. A correlation of 0.46 was observed among qPCR densities of enterococci and bifidobacteria at all sample sites. Quantitative polymerase chain reaction detection of B. adolescentis was a rapid (i.e., less than 2 h) indicator of presumptive human fecal pollution and suggested that Gulley Hole Creek, the Darien River, and the St. Marys River were affected by fecal bacteria derived from a human source. Gulley Hole Creek and the Darien River had the highest levels of fecal pollution detected in the studied estuaries. Molecular quantification of bifidobacteria may be a more accurate method of determining immediate health risks associated with fecal pollution in estuarine water than traditional and contemporary assessments of enterococci.

Research paper thumbnail of Detection of Campylobacter jejuni Presence in Trinidad’s Aquatic Environments

Water Air and Soil Pollution, Jun 1, 2022

Research paper thumbnail of Detection of verotoxin producing Escherichia coli in marine environments of the Caribbean

Marine Pollution Bulletin, Nov 1, 2013

Research paper thumbnail of Remote sensing of the biological dynamics of large-scale salt evaporation ponds

International Symposium on Remote Sensing of Environment, 1992

Optical properties of salt evaporation ponds associated with Exportadora de Sal, a salt productio... more Optical properties of salt evaporation ponds associated with Exportadora de Sal, a salt production company in Baja California Sur, Mexico, were analyzed using a combination of spectroradiometer and extracted pigment data, and Landsat-5 Thematic Mapper imagery. ...

Research paper thumbnail of Tracking human faecal contamination in tropical reservoirs in Puerto Rico

Lakes and Reservoirs: Research and Management, Nov 6, 2008

Using a combination of chemical and microbiological (culture-dependent and-independent) approache... more Using a combination of chemical and microbiological (culture-dependent and-independent) approaches, sources of human faecal contamination were identified in two water reservoirs in Puerto Rico-Guajataca and La Plata. Fluorescence from optical brighteners (OB)-commonly found in laundry detergents-was used as an indicator of contamination from septic systems and other household discharges. Traditional indicators of faecal contamination (e.g. Escherichia coli; faecal enterococci) were enumerated, and human faecal contamination was confirmed through detection of Bifidobacterium adolescentis utilizing polymerase chain reaction (PCR)-based analyses. For Guajataca Reservoir, four of 19 sampling sites (21%) were positive for the presence of B. adolescentis under baseflow conditions. The OB fluorescence data suggested that the most likely source for three of these sites was residential, whereas the source of contamination at the remaining site, although of human origin, was probably non-residential. B. adolescentis was present in 83% (19 of 23) of the sampling sites in La Plata. The La Plata sources were more difficult to identify because samples were taken under stormflow conditions, although the presence of OB fluorescence suggested a residential origin in a number of instances. OB fluorescence and traditional bacterial indicators of faecal contamination produced a number of false positive and negative findings for both reservoirs, pointing to the importance of understanding the limitations of these tools for tropical freshwater systems. The results of this study should be useful in developing a weight-of-evidence approach for the identification of potential sources and extent of human faecal contamination in similar tropical reservoirs, a necessary step in the development of management plans to reduce or eliminate these sources.

Research paper thumbnail of Evaluation of microbiological water quality in Point Judith Pond (Rhode Island, USA): Quantitation of fecal pollution and presence of human pathogenic bacteria

Open journal of water pollution and treatment, Mar 31, 2015

Water and sediment samples were collected in the Bluff Hill Cove area of Point Judith Pond from 1... more Water and sediment samples were collected in the Bluff Hill Cove area of Point Judith Pond from 12 stations along three parallel transects, and eelgrass samples were taken at two sites per transect. Fecal enterococci (FE) in the water samples exceeded USEPA regulatory limit of 100 MPN/100 mL for safe recreational and shellfish harvesting use in 24 out of 41 samples. Sediment samples had the lowest FE counts, whereas eelgrass had the highest counts. Using qPCR, H. pylori was detected in 8 out of 41 samples, but E. coli O157:H7 was not detected. Overall, higher levels of H. pylori were detected in 33% of the eelgrass samples and 33% of the sediment samples as compared to 9% in the water column. Microbial source tracking, using the Bacteroides marker HF183, indicated the presence of human fecal bacteria in 7 out of 41 samples, four of which were positive for H. pylori.

Research paper thumbnail of Seasonal shifts in the presence of pathogenic leptospires, Escherichia coli, and physicochemical properties in coastal rivers and streams of Puerto Rico

Journal of Environmental Quality, 2020

Leptospirosis is an emerging zoonotic disease in the Caribbean region and the island of Puerto Ri... more Leptospirosis is an emerging zoonotic disease in the Caribbean region and the island of Puerto Rico. Information on the presence of pathogenic Leptospira in rivers and streams of Puerto Rico is currently lacking. This study aimed to evaluate seasonal shifts in the presence of pathogenic leptospires and the level of Escherichia coli from 32 coastal locations in Puerto Rico's dry and wet seasons. Physicochemical parameters (temperature, salinity, pH, and dissolved oxygen) were determined at each site. The temperature (25.8 °C) and pH (average 7.6) values were all within acceptable USEPA regulatory standards. Thirty‐eight percent of the sites of the dry season and 28% of the wet season sites contained dissolved oxygen levels ≤4 mg L−1, which is relatively low. In the dry season, 19 sites (59%) and 18 (56%) of the wet season sites had E. coli counts >410 most probable number (MPN) 100 ml−1 and would be considered unsafe for recreational use. The lipl32 gene quantitative polymeras...

Research paper thumbnail of Environmental risk assessment for fecal contamination sources in urban and peri-urban estuaries, in Escambia and Santa Rosa counties, FL, USA

Environmental Monitoring and Assessment

Research paper thumbnail of San Juan Bay Estuary

Research paper thumbnail of Detection of Campylobacter jejuni Presence in Trinidad’s Aquatic Environments

Water, Air, & Soil Pollution

Research paper thumbnail of doi:10.1155/2010/595692 Research Article Comparison of Four Polymerase Chain Reaction Methods for the Rapid Detection of Human Fecal Pollution in Marine and

Copyright © 2010 Dave S. Bachoon et al. This is an open access article distributed under the Crea... more Copyright © 2010 Dave S. Bachoon et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We compared the effectiveness of three PCR protocols for the detection of Bifidobacterium adolescentis and one PCR protocol for detecting Bacteroidales as indicators of human fecal pollution in environmental samples. Quantitative PCR indicated that a higher concentration of B. adolescentis DNA was recovered from sewage samples on the 0.2 μm filters compared to the 0.45 μm filters, and there was no evidence of qPCR inhibitors in the DNA extracts. With the Matsuki method (1999), B. adolescentis was detected only in undiluted sewage samples. The King method (2007) performed well and detected B. adolescentis in all of the sewage dilutions (from undiluted to 10 −4). In contrast, the Bonjoch approach(2004) was effective at detecting B. ad...