Randall W. Gentry

Development of Bacteroides 16S rRNA Gene TaqMan-Based Real-Time PCR Assays for Estimation of Total, Human, and Bovine Fecal Pollution in Water

ABSTRACT Bacteroides species are promising indicators for differentiating livestock and human fecal contamination in water because of their high concentration in feces and potential host specificity. In this study, a real-time PCR assay was designed to target Bacteroides species (AllBac) present in human, cattle, and equine feces. Direct PCR amplification (without DNA extraction) using the AllBac assay was tested on feces diluted in water. Fecal concentrations and threshold cycle were linearly correlated, indicating that the AllBac assay can be used to estimate the total amount of fecal contamination in water. Real-time PCR assays were also designed for bovine-associated (BoBac) and human-associated (HuBac) Bacteroides 16S rRNA genes. Assay specificities were tested using human, bovine, swine, canine, and equine fecal samples. The BoBac assay was specific for bovine fecal samples (100% true-positive identification; 0% false-positive identification). The HuBac assay had a 100% true-positive identification, but it also had a 32% false-positive rate with potential for cross-amplification with swine feces. The assays were tested using creek water samples from three different watersheds. Creek water did not inhibit PCR, and results from the AllBac assay were correlated with those from Escherichia coli concentrations (r2 = 0.85). The percentage of feces attributable to bovine and human sources was determined for each sample by comparing the values obtained from the BoBac and HuBac assays with that from the AllBac assay. These results suggest that real-time PCR assays without DNA extraction can be used to quantify fecal concentrations and provide preliminary fecal source identification in watersheds.

Temporal Variation and Persistence of Bacteria in Streams

Better understanding of bacterial fate and transport in watersheds is necessary for improved regulatory management of impaired streams. Novel statistical time series analyses of coliform data can be a useful tool for evaluating the dynamics of temporal variation and persistence of bacteria within a watershed. For this study, daily total coliform data for the Little River in East Tennessee from 1 Oct. 2000 to 31 Dec. 2005 were evaluated using novel time series techniques. The objective of this study was to analyze the total coliform concentration data to: (i) evaluate the temporal variation of the total coliform, and (ii) determine whether the total coliform concentration data demonstrated any long-term or short-term persistence. For robust analysis and comparison, both time domain and frequency domain approaches were used for the analysis. In the time domain, an autoregressive moving average approach was used; whereas in the frequency domain, spectral analysis was applied. As expected, the analyses showed that total coliform concentrations were higher in summer months and lower in winter months. However, the more interesting results showed that the total coliform concentration exhibited short-term as well as long-term persistence ranging from about 4 wk to approximately 1 yr, respectively. Comparison of the total coliform data to hydrologic data indicated both runoff and baseflow are responsible for the persistence.

The geochemistry and mixing of leakage in a semi-confined aquifer at a municipal well field, Memphis, Tennessee, USA

Abstract The Memphis aquifer in southwestern Tennessee is confined to a semi-confined unconsolidated sand aquifer and is the primary municipal water source in the Memphis metropolitan area. Past studies have identified regions in the metropolitan area in which the overlying upper Claiborne confining unit lacks significant clay and provides a hydraulic connection between the shallow aquifer and the Memphis aquifer. In this study, major solute chemistry, 3H, and 3H/3He groundwater dating are used to investigate the extent and chemical effects of leakage through the confining unit to the Memphis aquifer in the vicinity of a municipal well field. The 3H/3He dates and geochemical modeling of the chemical data are used to constrain mixing fractions and the timing of modern recharge. Tritium activities of as much as 2.8 TU are observed in shallow production wells, but deeper production wells have 3H activities that approach the detection limit. Trends in water chemistry indicate vertical mixing in the aquifer of shallow Na–SO4–Cl-rich water and deeper Ca–Mg–HCO3-rich water. Water chemistry does not vary consistently with seasonal pumping, but 3H activity generally decreases during low use periods. Stable O and H isotopes show little variation and are not useful groundwater tracers for this study. The 3H-bearing, Na–SO4–Cl-rich water is interpreted to reflect recharge of modern water through the upper Claiborne confining unit. The 3H/3He dates from 5 production wells indicate modern recharge, that infiltrated 15–20 a ago, is present in the shallow production wells. Geologic data and hydrologic boundary conditions suggest that the most likely source for continued leakage is a nearby stream, Nonconnah Creek. Geochemical reaction modeling using the NETPATH computer code suggests that proportions of shallow aquifer water leaking into the Memphis aquifer range from 6 to 32%. The 3H/3He dating and NETPATH modeling results correlate well, suggesting that these complementary analytical tools provide an effective means to evaluate proportions of modern water leaking into semi-confined aquifers. These results also indicate a need to carefully consider connections between surface water and semi-confined groundwater resources in wellhead protection programs.

Bioenergy Sustainability in China: Potential and Impacts

The sustainability implications of bioenergy development strategies are large and complex. Unlike conventional agriculture, bioenergy production provides an opportunity to design systems for improving eco-environmental services. Different places have different goals and solutions for bioenergy development, but they all should adhere to the sustainability requirements of the environment, economy, and society. This article serves as a brief overview of China’s bioenergy development and as an introduction to this special issue on the impacts of bioenergy development in China. The eleven articles in this special issue present a range of perspectives and scenario analyses on bioenergy production and its impacts as well as potential barriers to its development. Five general themes are covered: status and goals, biomass resources, energy plants, environmental impacts, and economic and social impacts. The potential for bioenergy production in China is huge, particularly in the central north and northwest. China plans to develop a bioenergy capacity of 30GW by 2020. However, realization of this goal will require breakthroughs in bioenergy landscape design, energy plant biotechnology, legislation, incentive policy, and conversion facilities. Our analyses suggest that (1) the linkage between bioenergy, environment, and economy are often circular rather than linear in nature; (2) sustainability is a core concept in bioenergy design and the ultimate goal of bioenergy development; and (3) each bioenergy development scheme must be region-specific and designed to solve local environmental and agricultural problems.

A COMPARISON OF HYDROLOGY AND VEGETATION BETWEEN A CHANNELIZED STREAM AND A NONCHANNELIZED STREAM IN WESTERN TENNESSEE

The purpose of this study was to provide baseline data on floodplain forest structure, composition, and function that would be needed to predict and monitor the consequences of a proposed stream restoration project. This project would involve the “dechannelization” of Stokes Creek, a stream in western Tennessee that was channelized and leveed in the first half of the 1900s. To this end, we collected data on surface hydrology, soil redox potential (Eh), and the structure and composition of the floodplain vegetation of Stokes Creek. To place our findings into a regional context, we also collected comparable vegetation data from plots located along a nonchannelized stream reach of the Wolf River near Moscow, Tennessee. While hydrologic fluctuations of floodplain sites were synchronous with river dynamics for the Wolf River, the hydrology of floodplain sites at Stokes Creek was constrained by the influence of beaver dams, backflooding, and ponding of overland flow behind levees. Consequently, composition of the forest overstory, understory, and herbaceous strata was significantly different between the two sites. For example, Stokes Creek had a noticeable lack of cypress and tupelo sites, and a greater abundance of red maple. Analyses of size-class structure and woody debris quantity reinforced the existing differences between the more natural and human-impacted systems. While the current hydrology apparently has a negative affect on bottomland hardwoods, scattered regeneration stems and soil redox measurements indicate that a dechannelization effort that yielded lower water tables in the Stokes Creek floodplain potentially could increase bottomland hardwood establishment. [Key words: channelization, western Tennessee, bottomland hardwoods, hydrology.]

Effective saturated hydraulic conductivity of two‐dimensional random multifractal fields

0.991, p < 0.0001). Thisrelationship indicates that hKidecreases with increasing long-range spatial correlation among the K values in the field. Furthermore, as hKi decreases it becomes increasingly dominated by flow channeling. This is because high values of K become more and more clustered as p decreases. This approach may prove useful for the prediction of hKi from generalized dimensions estimated by multifractal analysis of field measurements of K. The results may also be applicable to the design of sampling strategies for multiple small-scale slug tests at a given resolution. Citation: Koirala, S. R., E. Perfect, R. W. Gentry, and J. W. Kim (2008), Effective saturated hydraulic conductivity of two-dimensional random multifractal fields, Water Resour. Res., 44, W08410, doi:10.1029/2007WR006199.

China–U.S. workshop on biotechnology of bioenergy plants

The China and U.S. economies are the globally dominantdrivers of fossil fuel consumption and release of green-house gases and are thus strategically linked to the sus-tainable development of sustainable, alternative, andrenewable energy sources. Because of the dynamics andspatial interdependence between human activities andnatural ecosystems, a major challenge arises: how tooperate a renewable-energy economy within the ecologicalconstraints of the biosphere. Renewable energy utilizesbio-based energy technology and other renewable sourcesas a substitute for fossil fuels. Although current levels andtypes of pollution associated with our present energy useswill decline, renewable energy technologies will introducenew environmental challenges that at present are onlypartly understood or defined. Therefore, a strategy is nee-ded to address the uncertainty of these new activities, whileattempting to protect natural ecological processes in orderto sustain biological resources. Thus, we presume that thecombination of more intensive growth of agriculture andthe production of bioenergy plants coupled with moresustainable management practices is an end goal worthy ofscientific pursuit. The biotechnology of bioenergy plantswill be an important component of this strategy as fasterplant growth, pest resistance, and many other plant char-acteristics that will be required to meet these goals, manyof which cannot be achieved in a reasonable time frame viaconventional breeding.China and the U.S. are natural partners for the devel-opment of biofuel technologies. Although there are dif-ferences in some aspects of their agriculture, naturalresources, economy, and society, the two nations sharemany interests with respect to the environment, climatechange, and scientific pursuits. In both the U.S. and China,it is hoped that the emerging bioenergy industry will giverise to a robust new rural economy in which ethanoland other biofuel and bioproduct production will meet

Hurst Analysis of Hydrologic and Water Quality Time Series

A continued important area of research in hydrologic modeling is the issue of spatial and temporal scaling of biogeochemical properties and processes. Hurst analysis, which is a fractal-based scale invariant approach for analyzing long-term time series data, can provide insight into this issue as a quantitative approach for evaluating temporal scale in time series. The objectives of this paper were to compute the Hurst coefficient (H) for hydrologic and water quality variables, to study the effects of seasonality on H, and to determine how the H for the water quality indicators are related to that of the hydrologic parameters (e.g., discharge and rainfall). Two sites were investigated, Little River and Walker Branch, both located in east Tennessee. The water quality indicators include total coliform for Little River data and nitrate, chloride, sulfate, and calcium concentrations for Walker Branch data. H was estimated using spectral analysis. It was found that H for water quality indicators were significa...

Channelization effects on floodplain functions in western Tennessee

We examined six river reaches in western Tennessee over a two-year period to determine how channel alteration affected floodplain hydrology and nutrient pools. Four sites, two depression and two non-depression, were established on the floodplains of each river, and data on vegetation, water table depth, redox potential, and soil and leaf nutrient pools were collected. Chamelized streams had higher mean water tables and lower soil redox potentials than non-channelized or channelized and leveed streams. Leveed systems appeared to have mostly oxidized soil conditions, similar to uplands. Leaf and soil nutrient pools were generally higher in non-depression sites, especially for channelized streams. A drought between the first and second years of sampling rendered very different results between the two sampling occasions. Following the drying of the floodplain, nutrient pools were not significantly different between depression and nondepression sites. These results underscore the need for a better understanding of the relationships among channel modifications, floodplain hydrology, vegetation, and nutrient cycling.

Numerical modeling of the effect of variation of boundary conditions on vadose zone hydraulic properties

A estimativa precisa e acurada de fluxos hidraulicos na zona vadosa e um fator critico para simular o transporte de agua, nutrientes e contaminantes em sistemas naturais. O objetivo deste estudo foi simular o efeito de variacoes nas condicoes de contorno na estimativa de propriedades hidraulicas do solo (isto e, conteudo de agua, condutividade hidraulica efetiva em condicoes nao saturadas e fluxo hidraulico) em um modelo de fluxo nao saturado unidimensional. Fluxo vertical nao saturado unidimensional foi simulado em um perfil de material franco-argiloso puro e em material franco-argiloso intercalado com camadas de material franco-siltoso distribuido seguindo a terceira iteracao de um modelo do objeto fractal Conjunto de Cantor. As simulacoes foram realizadas no modelo numerico Hydrus 1D. Os potenciais totais superiores e inferiores na coluna unidimensional foram variados ao redor do valor medio de -55 cm para a faixa de valores proxima da saturacao. Isso resultou em combinacoes para potenciais constantes nos limites superior e inferior da coluna de -50 e -60 cm; -40 e -70 cm; -30 e -80 cm; -20 e -90 cm; e -10 e -100 cm, para as condicoes de contorno superior e inferior, respectivamente. Para o intervalo de umidade definido como mais seco o valor medio de potencial de agua no solo foi fixado em -550 cm, resultando em combinacoes de -500 e -600 cm; -400 e -700 cm; -300 e -800 cm; -200 e -900 cm; e -100 e -1.000 cm, para as condicoes de contorno superior e inferior, respectivamente. Houve aumento nos conteudos de agua, fluxos e condutividades hidraulicas com o aumento no gradiente entre os valores estipulados nos limites superior e inferior do dominio. Variacao nas condicoes de contorno nos sistemas de fase pura e em camadas resultou em desvios significativos nos fluxos, conteudos de agua e condutividades hidraulicas com relacao ao caso mais simples (uma diferenca de potencial total entre os limites superior e inferior fixada em 10 cm para o intervalo mais umido e 100 cm para o intervalo mais seco).