@article{matteson_graves_hall_kuy_polizzotto_2016, title={Fecal contamination and Microcystis in drinking-water sources of rural Cambodia using PCR and culture-based methods}, volume={6}, ISSN={["2043-9083"]}, DOI={10.2166/washdev.2016.136}, abstractNote={Rural communities within low-income countries frequently rely on a range of drinking-water sources, and each water source varies in its potential for biological contamination. The extent and source of biological contamination in primary drinking sources within Kien Svay, Kandal, Cambodia, were determined by fecal indicator bacteria (FIB) measurements, 16S rDNA genetic markers for human and bovine fecal Bacteroides, presence of the bloom-forming Microcystis species, and the microcystin toxin mcyD gene marker. Thirteen wells, 11 rain barrels, 10 surface-water sites, and five sediment samples were examined during the dry and wet seasons. Surface water was commonly contaminated with FIB, with up to 1.02 × 105Enterococcus sp., 6.13 × 104E. coli, and 2.91 × 104 total coliforms per 100 mL of water. Human and bovine Bacteroides were detected in 100 and 90% of the surface water samples, respectively. Concentrations of FIB in rain-barrels varied by site, however 91% contained human Bacteroides. Microcystis cells were found in 90% of surface water sites, with many also containing microcystin gene mcyD, representing the first report of microcystin-producing cyanobacteria in surface waters of Cambodia. The study results show that many potential drinking-water sources in Cambodia contain harmful bacterial and algal contaminants, and care should be taken when selecting and monitoring water options.}, number={3}, journal={JOURNAL OF WATER SANITATION AND HYGIENE FOR DEVELOPMENT}, author={Matteson, Audrey R. and Graves, Alexandria K. and Hall, Ann M. and Kuy, Dina and Polizzotto, Matthew L.}, year={2016}, month={Sep}, pages={353–361} }
 @article{stall_amoozegar_lindbo_graves_rashash_2014, title={Transport of E. coli in a sandy soil as impacted by depth to water table}, volume={76}, number={6}, journal={Journal of Environmental Health}, author={Stall, C. and Amoozegar, A. and Lindbo, D. and Graves, A. and Rashash, D.}, year={2014}, pages={92–100} }
 @article{ibekwe_leddy_bold_graves_2012, title={Bacterial community composition in low-flowing river water with different sources of pollutants}, volume={79}, ISSN={["1574-6941"]}, DOI={10.1111/j.1574-6941.2011.01205.x}, abstractNote={Pollution of water resources is a major risk to human health and water quality throughout the world. The purpose of this study was to determine the influence of pollutant sources from agricultural activities, urban runoffs, and runoffs from wastewater treatment plants (WWTPs) on bacterial communities in a low-flowing river. Bacterial community structure was monitored using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene clone library. The results were analyzed using nonmetric multidimensional scaling (NMDS) and UniFrac, coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, community structure, and specific functional groups of bacteria in surface water affected by nonpoint sources. From all the sampling points, Bacteria were numerically dominated by three phyla – the Proteobacteria, Bacteroidetes, and Cyanobacteria – accounting for the majority of taxa detected. Overall results, using the b diversity measures UniFrac, coupled with PCoA, showed that bacterial contamination of the low-flowing river was not significantly different between agricultural activities and urban runoff.}, number={1}, journal={FEMS MICROBIOLOGY ECOLOGY}, author={Ibekwe, Abasiofiok Mark and Leddy, Menu B. and Bold, Richard M. and Graves, Alexandria K.}, year={2012}, month={Jan}, pages={155–166} }
 @article{wu_osmond_graves_burchell_duckworth_2012, title={Relationships Between Nitrogen Transformation Rates and Gene Abundance in a Riparian Buffer Soil}, volume={50}, ISSN={0364-152X 1432-1009}, url={http://dx.doi.org/10.1007/s00267-012-9929-z}, DOI={10.1007/s00267-012-9929-z}, abstractNote={Denitrification is a critical biogeochemical process that results in the conversion of nitrate to volatile products, and thus is a major route of nitrogen loss from terrestrial environments. Riparian buffers are an important management tool that is widely utilized to protect water from non-point source pollution. However, riparian buffers vary in their nitrate removal effectiveness, and thus there is a need for mechanistic studies to explore nitrate dynamics in buffer soils. The objectives of this study were to examine the influence of specific types of soluble organic matter on nitrate loss and nitrous oxide production rates, and to elucidate the relationships between these rates and the abundances of functional genes in a riparian buffer soil. Continuous-flow soil column experiments were performed to investigate the effect of three types of soluble organic matter (citric acid, alginic acid, and Suwannee River dissolved organic carbon) on rates of nitrate loss and nitrous oxide production. We found that nitrate loss rates increased as citric acid concentrations increased; however, rates of nitrate loss were weakly affected or not affected by the addition of the other types of organic matter. In all experiments, rates of nitrous oxide production mirrored nitrate loss rates. In addition, quantitative polymerase chain reaction (qPCR) was utilized to quantify the number of genes known to encode enzymes that catalyze nitrite reduction (i.e., nirS and nirK) in soil that was collected at the conclusion of column experiments. Nitrate loss and nitrous oxide production rates trended with copy numbers of both nir and 16s rDNA genes. The results suggest that low-molecular mass organic species are more effective at promoting nitrogen transformations than large biopolymers or humic substances, and also help to link genetic potential to chemical reactivity.}, number={5}, journal={Environmental Management}, publisher={Springer Science and Business Media LLC}, author={Wu, Lin and Osmond, Deanna L. and Graves, Alexandria K. and Burchell, Michael R. and Duckworth, Owen W.}, year={2012}, month={Aug}, pages={861–874} }
 @article{graves_liwimbi_israel_heugten_robinson_cahoon_lubbers_2011, title={Distribution of ten antibiotic resistance genes in E. coli isolates from swine manure, lagoon effluent and soil collected from a lagoon waste application field}, volume={56}, ISSN={["0015-5632"]}, DOI={10.1007/s12223-011-0019-z}, abstractNote={The prevalence of ten antibiotic resistance genes (ARGs) was evaluated in a total of 616 Escherichia coli isolates from swine manure, swine lagoon effluent, and from soils that received lagoon effluent on a commercial swine farm site in Sampson County, North Carolina (USA). Isolates with ARGs coding for streptomycin/spectinomycin (aadA/strA and strB), tetracycline (tetA and tetB), and sulfonamide (sul1) occurred most frequently (60.6-91.3%). The occurrence of E. coli isolates that carried aadA, tetA, tetB, and tetC genes was significantly more frequent in soil samples (34.0-97.2%) than in isolates from lagoon samples (20.9-90.6%). Furthermore, the frequency of isolates that contain genes coding for aadA and tetB was significantly greater in soil samples (82.6-97.2%) when compared to swine manure (16.8-86.1%). Isolates from the lagoon that carried tetA, tetC, and sul3 genes were significantly more prevalent during spring (63.3-96.7%) than during winter (13.1-67.8%). The prevalence of isolates from the lagoon that possessed the strA, strB, and sul1 resistance genes was significantly more frequent during the summer (90.0-100%) than during spring (66.6-80.0%). The data suggest that conditions in the lagoon, soil, and manure may have an impact on the occurrence of E. coli isolates with specific ARGs. Seasonal variables seem to impact the recovery isolates with ARGs; however, ARG distribution may be associated with mobile genetic elements or a reflection of the initial numbers of resistant isolates shed by the animals.}, number={2}, journal={FOLIA MICROBIOLOGICA}, author={Graves, A. K. and Liwimbi, L. and Israel, D. W. and Heugten, E. and Robinson, B. and Cahoon, C. W. and Lubbers, J. F.}, year={2011}, month={Mar}, pages={131–137} }
 @article{hathaway_hunt_graves_bass_caldwell_2011, title={Exploring fecal indicator bacteria in a constructed stormwater wetland}, volume={63}, ISSN={["1996-9732"]}, DOI={10.2166/wst.2011.539}, abstractNote={Microbial pollution in surface waters is a concern throughout the world, with both public health and economic implications. One contributing source to such pollution is stormwater runoff, often treated using various types of stormwater control measures. However, relatively little is known regarding microbe sequestration in constructed stormwater wetlands (CSWs), one type of commonly installed stormwater control measure. In this study, indicator bacteria concentrations in both the water and sediment of a CSW were evaluated at multiple locations. Results suggested that fecal coliform concentrations in stormwater runoff decrease through the system, with relatively consistent concentrations noted throughout the second half of the wetland. This potentially indicates a baseline concentration of fecal coliform is present due to internal processes such as animal activity and microbial persistence. However, wetland sediments showed little E. coli present during most sampling events, with minimal patterns existing with respect to sediment sampling location. CSW designs should promote optimization of hydraulic retention time and minimization of stormwater velocities to promote sedimentation and degradation of microbes by way of wetland treatment functions.}, number={11}, journal={WATER SCIENCE AND TECHNOLOGY}, author={Hathaway, J. M. and Hunt, W. F. and Graves, A. K. and Bass, K. L. and Caldwell, A.}, year={2011}, pages={2707–2712} }
 @article{hathaway_hunt_graves_wright_2011, title={Field Evaluation of Bioretention Indicator Bacteria Sequestration in Wilmington, North Carolina}, volume={137}, ISSN={["1943-7870"]}, DOI={10.1061/(asce)ee.1943-7870.0000444}, abstractNote={Although bioretention has been shown to remove or sequester a wide range of pollutants, relatively little study has been performed to evaluate its ability to sequester indicator bacteria. Two adjacent bioretention areas in Wilmington, North Carolina, were studied. The primary difference in the design of the two systems was soil depth. One bioretention cell was constructed with 25 cm of fill soil (Bioretention-S) and one with 60 cm of fill soil (Bioretention-D). The systems performed differently for indicator bacteria on the basis of multiple performance evaluation metrics. Bioretention-D showed concentration reductions of 70% and 89% for E. coli and enterococci, respectively. Effluent concentrations from Bioretention-D compared well to US EPA target values and other studies in literature. Conversely, Bioretention-S showed concentration “reductions” of -119% and -102% for E. coli and enterococci, respectively. Effluent concentrations from Bioretention-S were substantially higher than USEPA target values an...}, number={12}, journal={JOURNAL OF ENVIRONMENTAL ENGINEERING}, author={Hathaway, J. M. and Hunt, W. F. and Graves, A. K. and Wright, J. D.}, year={2011}, month={Dec}, pages={1103–1113} }
 @article{ibekwe_murinda_graves_2011, title={Genetic Diversity and Antimicrobial Resistance of Escherichia coli from Human and Animal Sources Uncovers Multiple Resistances from Human Sources}, volume={6}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0020819}, abstractNote={Escherichia coli are widely used as indicators of fecal contamination, and in some cases to identify host sources of fecal contamination in surface water. Prevalence, genetic diversity and antimicrobial susceptibility were determined for 600 generic E. coli isolates obtained from surface water and sediment from creeks and channels along the middle Santa Ana River (MSAR) watershed of southern California, USA, after a 12 month study. Evaluation of E. coli populations along the creeks and channels showed that E. coli were more prevalent in sediment compared to surface water. E. coli populations were not significantly different (P = 0.05) between urban runoff sources and agricultural sources, however, E. coli genotypes determined by pulsed-field gel electrophoresis (PFGE) were less diverse in the agricultural sources than in urban runoff sources. PFGE also showed that E. coli populations in surface water were more diverse than in the sediment, suggesting isolates in sediment may be dominated by clonal populations.Twenty four percent (144 isolates) of the 600 isolates exhibited resistance to more than one antimicrobial agent. Most multiple resistances were associated with inputs from urban runoff and involved the antimicrobials rifampicin, tetracycline, and erythromycin. The occurrence of a greater number of E. coli with multiple antibiotic resistances from urban runoff sources than agricultural sources in this watershed provides useful evidence in planning strategies for water quality management and public health protection.}, number={6}, journal={PLOS ONE}, author={Ibekwe, A. Mark and Murinda, Shelton E. and Graves, Alexandria K.}, year={2011}, month={Jun} }
 @article{holt_heugten_graves_see_morrow_2011, title={Growth performance and antibiotic tolerance patterns of nursery and finishing pigs fed growth-promoting levels of antibiotics}, volume={136}, ISSN={["1878-0490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79951956142&partnerID=MN8TOARS}, DOI={10.1016/j.livsci.2010.09.007}, abstractNote={The objective of this study was to evaluate the impact of growth-promoting levels of antibiotics in diets for nursery and finishing pigs on growth performance and antibiotic tolerance patterns. Gilts (n = 200, initial body weight was 6.2 ± 0.003 kg), were allotted based on body weight to one of four treatments in a 2 × 2 factorial randomized complete block design. Nursery treatments consisted of feeding no antibiotics (CON) or an antibiotic diet (ANTI) containing chlortetracycline (CTC; 55 mg/kg). At the end of the nursery phase, one-half of the pigs receiving CON were switched to a diet containing antibiotic (virginiamycin; VIR, 11 mg/kg) and one-half of the pigs receiving ANTI were switched to CON for the remainder of the trial. This created four treatments for the finishing phase, consisting of: control in nursery and finishing (CC), antibiotic in nursery, control in finishing (AC), control in nursery, antibiotic in finishing (CA), or antibiotics throughout (AT). The pigs were weighed at the diet changes during the nursery (weeks 1, 3, and 5) and finishing (weeks 7, 9, 13, 17, and 20) phases. Fecal samples were collected at all diet changes for isolation of fecal coliforms and Enterococcus and subsequently tested for tolerance to CTC and VIR. After 1 week, CON pigs weighed less (7.09 vs. 7.28 kg) and had lower ADG (149 vs. 180 g/day) and ADFI (174 vs. 192 g/day) than ANTI pigs (P < 0.05). No performance differences were observed during the remainder of the study. At the initiation of the study (week 0), the ability of coliforms to grow in the presence of CTC and VIR, respectively, were 68 and 73% and increased to 90 and 96% at week 19 (time effect, P < 0.001). At week 17, tolerance of coliforms to CTC was greater for CA (98%) than AC (86%, time × treatment effect, P < 0.004). Enterococcus tolerance to CTC at week 7 was lower for CC (55%) compared to AT (76%), AC (74%) and CA (83%, time × treatment effect, P < 0.001). At week 9, Enterococcus tolerant to CTC and VIR, respectively, was lower for CC (15 and 18%) than AT (31 and 40%), AC (35 and 35%), and CA (44 and 43%, time × treatment effect, P < 0.001). Antibiotic growth promoters had little impact on growth performance in clean, isolated facilities with high labor inputs. The tolerance of bacteria to antibiotics fluctuated over time and persisted regardless of the use of antibiotic growth promoters.}, number={2-3}, journal={LIVESTOCK SCIENCE}, author={Holt, J. P. and Heugten, E. and Graves, A. K. and See, M. T. and Morrow, W. E. M.}, year={2011}, month={Apr}, pages={184–191} }
 @article{ibekwe_murinda_graves_2011, title={Microbiological Evaluation of Water Quality from Urban Watersheds for Domestic Water Supply Improvement}, volume={8}, ISSN={["1660-4601"]}, DOI={10.3390/ijerph8124460}, abstractNote={Agricultural and urban runoffs may be major sources of pollution of water bodies and major sources of bacteria affecting the quality of drinking water. Of the different pathways by which bacterial pathogens can enter drinking water, this one has received little attention to date; that is, because soils are often considered to be near perfect filters for the transport of bacterial pathogens through the subsoil to groundwater. The goals of this study were to determine the distribution, diversity, and antimicrobial resistance of pathogenic Escherichia coli isolates from low flowing river water and sediment with inputs from different sources before water is discharged into ground water and to compare microbial contamination in water and sediment at different sampling sites. Water and sediment samples were collected from 19 locations throughout the watershed for the isolation of pathogenic E. coli. Heterotrophic plate counts and E. coli were also determined after running tertiary treated water through two tanks containing aquifer sand material. Presumptive pathogenic E. coli isolates were obtained and characterized for virulent factors and antimicrobial resistance. None of the isolates was confirmed as Shiga toxin E. coli (STEC), but as others, such as enterotoxigenic E. coli (ETEC). Pulsed field gel electrophoresis (PFGE) was used to show the diversity E. coli populations from different sources throughout the watershed. Seventy six percent of the isolates from urban sources exhibited resistance to more than one antimicrobial agent. A subsequent filtration experiment after water has gone through filtration tanks containing aquifer sand material showed that there was a 1 to 2 log reduction in E. coli in aquifer sand tank. Our data showed multiple strains of E. coli without virulence attributes, but with high distribution of resistant phenotypes. Therefore, the occurrence of E. coli with multiple resistances in the environment is a matter of great concern due to possible transfer of resistant genes from nonpathogenic to pathogenic strains that may result in increased duration and severity of morbidity.}, number={12}, journal={INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH}, author={Ibekwe, A. Mark and Murinda, Shelton E. and Graves, Alexandria K.}, year={2011}, month={Dec}, pages={4460–4476} }
 @article{ibekwe_lesch_bold_leddy_graves_2011, title={Variations of indicator bacteria in a large urban watershed}, volume={54}, DOI={10.13031/2013.40653}, abstractNote={The contamination of water resources by nonpoint-source fecal pollution is a major concern to human health and water quality throughout the world. The Santa Ana River (SAR) in southern California is an impaired stream with historically high fecal coliform counts. This study evaluated the presence of indicator bacteria at 13 sites in the middle Santa Ana River watershed (MSAR). The objectives of this study were to: (1) examine spatial and temporal characteristics of fecal bacteria loading during dry weather (low or baseline) flow, wet weather (storm) flow, and recessional flow (72 h after storm) along two creeks, at two wastewater treatment plant (WWTP) outlets, and at a control site in the MSAR; and (2) determine how the various sampling locations affected indicator bacteria concentrations in the watershed. Total coliform (TC), fecal coliform (FC), E. coli, enterococci, and total bacterial concentrations were characterized at 13 locations in the watershed over a two-year period. Analysis of covariance (ANOCOVA) was used to test each specific set of bacteria counts, site effects, water flow conditions, and the four water quality covariate effects. Our results showed that the control site (S1) and WWTP estimates always showed significantly lower indicator bacteria than the channels influenced by urban runoff and agricultural activities. The water flow effects indicated that the recessional flow transported significantly lower bacterial counts into the watershed than either the dry weather flow or the storm or wet weather flow. In addition, bacterial count estimates changed far more significantly across different sites in comparison to estimates across seasons or time. These results imply that total TC, FC, E. coli, and enterococci bacterial counts in the MSAR watershed were strongly influenced by spatial location effects, with contamination due to local agricultural and/or urban runoff, in contrast to elevated upstream contamination and/or discharge contamination associated with the two WWTPs. Therefore, this study has provided data for evaluation of the Santa Ana River watershed's total maximum daily load (TMDL) management plans that could also be applicable to other large watersheds with different nonpoint-source pollutants.}, number={6}, journal={Transactions of the ASABE}, author={Ibekwe, A. M. and Lesch, S. M. and Bold, R. M. and Leddy, M. B. and Graves, A. K.}, year={2011}, pages={2227–2236} }
 @article{graves_weaver_2010, title={Characterization of enterococci populations collected from a subsurface flow constructed wetland}, volume={108}, ISSN={["1365-2672"]}, DOI={10.1111/j.1365-2672.2009.04516.x}, abstractNote={Aims:  The aim of this study was to identify and characterize the population of Enterococcus sp. in domestic wastewater as it flows through a constructed wetland.}, number={4}, journal={JOURNAL OF APPLIED MICROBIOLOGY}, author={Graves, A. K. and Weaver, R. W.}, year={2010}, month={Apr}, pages={1226–1234} }
 @article{graves_weaver_entry_2009, title={Characterization of enterococci populations in livestock manure using BIOLOG}, volume={164}, ISSN={["0944-5013"]}, DOI={10.1016/j.micres.2006.11.017}, abstractNote={The BIOLOG system was used to generate knowledge of enterococci populations found in fresh and dry manure of livestock (cattle (Bos taurus), horse (Equus caballus), and sheep (Ovis aires)). Six-hundred and forty Enterococcus isolates from the host sources were observed as a combined fresh manure unit and a combined dry manure unit, E. casseliflavus and E. mundtii were predominant in fresh manure (36% and 35%, respectively) as well as in dry manure (51% and 28%, respectively). The other species were found at a frequency of less than 10%. A chi-square test of the two most predominant Enterococcus sp. indicated that there were some significant differences among the frequency of E. casseliflavus and E. mundtii in cattle and sheep, but not horse. Despite these differences, these two species were overwhelmingly predominant among all three livestock sources.}, number={3}, journal={MICROBIOLOGICAL RESEARCH}, author={Graves, Alexandria and Weaver, R. W. and Entry, James}, year={2009}, pages={260–266} }
 @article{graves_hayedorn_brooks_hagedorn_martin_2007, title={Microbial source tracking in a rural watershed dominated by cattle}, volume={41}, ISSN={["0043-1354"]}, DOI={10.1016/j.watres.2007.04.020}, abstractNote={Antibiotic resistance analysis (ARA), frequency of sampling, and seasonality were evaluated in a rural Virginia watershed dominated by cattle. The selected watershed (Mill Creek) was 3767 ha in size, included two small communities (one sewered and one unsewered), and several farms that when combined contained over 3800 beef and dairy cattle. Monthly monitoring of fecal coliforms at two sampling sites in Mill Creek from January to December, 2001, revealed that the recreational standard (1000 colony forming units, CFUs/100 ml) was exceeded a total of eight times for a 33% violation rate at each site. In addition, stream samples were collected weekly for 4 consecutive weeks during seasonal high flows (March) and seasonal low flows (September–October), plus daily for 7 consecutive days within the weekly schedules for a combined total of 60 stream samples (30 at each of two sites). The recreational standard was exceeded once during seasonal high flow and nine times during seasonal low flow. Microbial source tracking (MST) was performed by ARA to assess the impact of cattle on water quality within the different sampling routines. The resistance patterns of 2880 water isolates and 1158 known source (host-origin) isolates were determined with seven antibiotics at 28 different concentrations. The 1158 isolate database was reduced to 562 unique isolates when clonal ARA patterns were removed. This database of 562 unique isolates had an average rate of correct classification (ARCC) of 95.4%, and several statistical procedures confirmed the library as accurate and representative. Sixty-five percent of 50 challenge-set isolates from sources, but not samples, used in the library were correctly identified. The 562 unique pattern database was used to classify Escherichia coli isolates from water samples into six host source categories. The ARA results showed that cattle were the major source of pollution in the stream and cattle were the dominant source in over 60% of the water samples. Sampling frequency and seasonality had no effect on the MST results, as cattle dominated both seasons and samplings. Deer were a minor contributor in the summer (high water demand), and geese were a minor contributor in the winter when migratory flocks were observed moving through the watershed. An unexpected human allocation was found, especially under seasonal high flow conditions. The exact origin of this human allocation is not known. This project demonstrated that a host-origin library, based on a phenotypic method, could be developed for a well-defined watershed and was both representative of the sources in the watershed and performed reasonably well against a challenge set.}, number={16}, journal={WATER RESEARCH}, author={Graves, A. K. and Hayedorn, C. and Brooks, A. and Hagedorn, R. L. and Martin, E.}, year={2007}, month={Aug}, pages={3729–3739} }