Kevin Feris | Boise State University (original) (raw)

Papers by Kevin Feris

One goal of interdisciplinarity is to develop a more holistic understanding of a set of interlink... more One goal of interdisciplinarity is to develop a more holistic understanding of a set of interlinked, complex system processes. Studies rarely couple both a mechanistic understanding of individual processes with their coupled influence on the entire system structure, yet the prospects for climate driven changes in western river systems provide justification for such an effort. We apply such a mechanistic and systems approach to understanding the effects of climate on fire frequency, plant-soil infiltration, sediment transport and stream community and ecosystem dynamics in a large wilderness setting that is likely to experience shifts in the timing or intensity of physical forces if projected climate change scenarios are realized. The Middle Fork Salmon River in central Idaho runs through the Frank Church Wilderness area and is the largest roadless area in the conterminous United States. The relatively southern continental position, complex mountain terrain and wealth of long-term landscape and ecological data in this region make it a tractable system to study the multifaceted and potentially non-linear processes of system change. This presents a unique opportunity to study the effects of climate change in the absence of substantial management effects in a system on the cusp of change. This collection of studies investigates the effects of climate-driven changes in hillslope processes on stream geomorphic and ecologic processes. We investigate 1) how wildfire alters the magnitude, timing and size of sediment delivered to stream channels, 2) how climate-driven changes in the proportion of rain vs. snow dominated basins alter stream hydrology, 3) how wildfire and insect disturbances modify aquatic ecosystems through inputs of nutrients and changes to habitat, 4) how paleo-records of drought, fire, and fire-related debris flows compare with recent data, 5) how fire-related inputs of sediment and wood influence the structure and dynamics of aquatic habitats, and their consequences for organisms, and 6) how hypothesized shifts in climate-related forces alter the function and resiliency of the Salmon River ecosystem. Integrated approaches include the application of legacy datasets, the exploration of historic chemical and physical records of ecosystem change, intensive stream, riparian and forest monitoring, the use of paired experimental watershed approaches, and the development of spatial analysis tools. If feedbacks among geomorphic, hydrologic and ecologic systems are positive this suggests a possible state change in response to a changing climate.

Heavy metal contamination in lotic ecosystems is a major health and environmental concern worldwi... more Heavy metal contamination in lotic ecosystems is a major health and environmental concern worldwide. The Resazurin Resorufin (Raz Rru) Smart Tracer system (Haggerty et al., 2008) provides a novel approach to test current models of microbial ecosystem response to chronic stressors such as heavy metals. These models predict that functional redundancy of metabolic capabilities of community members (e.g. respiration rate and enzyme activity) will compensate for decreases in species diversity until a stress threshold is reached. At this point, species diversity and function are expected to decline rapidly. Contrary to this model, microbial communities of the Clark Fork River (CF), Montana, demonstrate high levels of species diversity along the contamination gradient, whereas community function is inversely proportional to the level of contamination. The Raz Rru tool, a metabolically reactive hydrologic tracer, allows for direct quantification of in-situ microbial respiration rates. Therefore, this tool provides an opportunity to build upon studies of ecosystem response to contamination previously limited to extrapolation of point scale measurements to reach scale processes. The Raz Rru tool is used here to quantify the magnitude of metal induced limits on heterotrophic microbial respiration in communities that have evolved to different levels of chronic metal exposure. In this way we propose to be able to test a novel hypothesis concerning the nature of evolution of community processes to chronic stress and persistent environmental pollutants. Specifically, we hypothesize that metal contamination produces a measureable metabolic cost to both tolerant and intolerant communities. To test this hypothesis, rates of respiration associated with hyporheic sediments, supporting intact microbial communities, were quantified in the presence and absence of an acute Cd exposure in column experiments. Hyporheic sediment was collected from differently contaminated locations within the CF and compared to sediment from pristine reference sites. The biological reduction rate of Raz to Rru, K_12 in the Advection Dispersion Equation (ADE) below, represents rates of sediment associated heterotrophic respiration. ∂C_Raz}/{∂t} = {α_Lν}/{R} {∂^2C_Raz}/{∂x^2} - {ν}/{R} {∂C_Raz}/{∂x} - k_1C_Raz -k_12C_Raz [/tex] {∂C_Rru}/{∂t} = {α_Lν}/{R} {∂^2C_Rru}/{∂x^2} -{ν}/{R} {∂C_Rru}/{∂x} - k_2C_Rru + k_12 {M_Rru}/{M_Raz}CRaz [/tex] The Raz-Rru ADE will be optimized through the Markov Chain Monte Carlo method. Preliminary analysis of Cl^- tracer data provides input estimation of physical parameters, populating the hydrological terms of the ADE necessary for elucidation of K_12. It is expected that sediment metal content and K_12 are inversely related and that acute Cd exposure will negatively affect K_12 of both communities, with communities inhabiting metal contaminated sediments demonstrating a smaller reduction in K_12. This project has the potential to contribute to a revised theory of community response to metal induced chronic ecosystem stress, while contributing to the further development and application of the Raz Rru Smart Tracer system.

Environmental Science & Technology, 2008

Ethanol (EtOH) is a commonly used fuel oxygenate in reformulated gasoline and is an alternative f... more Ethanol (EtOH) is a commonly used fuel oxygenate in reformulated gasoline and is an alternative fuel and fuel supplement. Effects of EtOH release on aquifer microbial ecology and geochemistry have not been well characterized in situ. We performed a controlled field release of petroleum constituents (benzene (B), toluene (T), o-xylene (o-X) at ∼1-3 mg/L each) with and without EtOH (∼500 mg/L). Mixed linear modeling (MLM) assessed effects on the microbial ecology of a naturally sulfidic aquifer and how the microbial community affected B, T, and o-X plume lengths and aquifer geochemistry. Changes in microbial community structure were determined by quantitative polymerase chain reaction (qPCR) targeting Bacteria, Archaea, and sulfate reducing bacteria (SRB); SRB were enumerated using a novel qPCR method targeting the adenosine-5′-phosphosulfate reductase gene. Bacterial and SRB densities increased with and without EtOH-amendment (1-8 orders of magnitude). Significant increases in Archaeal species richness; Archaeal cell densities (3-6 orders of magnitude); B, T, and o-X plume lengths; depletion of sulfate; and induction of methanogenic conditions were only observed with EtOHamendment. MLM supported the conclusion that EtOH-amendment altered microbial community structure and function, which in turn lowered the aquifer redox state and led to a reduction in bioattenuation rates of B, T, and o-X.

Ethanol has replaced MTBE in gasoline in California and elsewhere, in part to reduce problems wit... more Ethanol has replaced MTBE in gasoline in California and elsewhere, in part to reduce problems with MTBE contamination of groundwater resulting from fuel spills. We are conducting field studies of the subsurface impacts of releases of ethanol-containing gasoline. In May 2004, we began side-by-side controlled release experiments at an existing fuel spill site (a former gasoline station) at Vandenberg Air Force Base, California. In one side of the paired experiments, we have been releasing benzene, toluene, o-xylene and tracers in a controlled and steady rate into a shallow, extremely well-characterized aquifer. In the other side, we have been releasing benzene, toluene, o-xylene, tracers and ethanol into the aquifer in the same manner. Using an extremely detailed grid of monitoring wells, we are gathering information on the migration and fate of the species in the two sides, and thus on the differences caused by the presence of the ethanol on one of the sides. Results from the first several months of the experiments suggest that the preferential degradation of the ethanol causes a significant reduction in the natural attenuation of the BTX species. We are also gaining insight into the impact that the more reduced conditions caused by ethanol degradation have on the fate of MTBE. Changes in the microbial community are being monitored as a means of understanding as well as generalizing the results.

Environmental Science & Technology, 2007

Side-by-side experiments were conducted in an aquifer contaminated with methyl-tert-butyl ether (... more Side-by-side experiments were conducted in an aquifer contaminated with methyl-tert-butyl ether (MTBE) at a former fuel station to evaluate the effect of ethanol release on the fate of pre-existing MTBE contamination. On one side, for ∼9 months we injected groundwater amended with 1-3 mg/L benzene, toluene, and o-xylene (BToX). On the other side, we injected the same, adding ∼500 mg/ L ethanol. The fates of BToX in both sides ("lanes") were addressed in a prior publication. No MTBE transformation was observed in the "No Ethanol Lane." In the "With Ethanol Lane", MTBE was transformed to tert-butyl alcohol (TBA) under the methanogenic and/or acetogenic conditions induced by the in situ biodegradation of the ethanol downgradient of the injection wells. The lag time before onset of this transformation was less than 2 months and the pseudofirst-order reaction rate estimated after 7-8 months was 0.046 d -1 . Our results imply that rapid subsurface transformation of MTBE to TBA may be expected in situations where strongly anaerobic conditions are sustained and fluxes of requisite nutrients and electron donors allow development of an active acetogenic/methanogenic zone beyond the reach of inhibitory effects such as those caused by high concentrations of ethanol. ES062156Q FIGURE 7. Mass discharge (Md) for MTBE and TBA crossing the EH transect (Figure 1) over time in the "No Ethanol Lane" and the "With Ethanol Lane". The specific wells used for the Md calculations are bracketed in Figure 6 and discussed in the Supporting Information.

Microbial Ecology, 2004

Microbial communities in subsurface environments are poorly characterized and the impacts of anth... more Microbial communities in subsurface environments are poorly characterized and the impacts of anthropogenic contamination on their structure and function have not been adequately addressed. The release of contaminant(s) to a previously unexposed environment is often hypothesized to decrease the diversity of the affected community. We characterized the structure of microbial communities along a gradient of benzene, toluene, ethylbenzene, and xylene (BTEX) and methyl-tert-butyl-ether (MTBE) contamination, resulting from a petroleum spill, within a shallow sandy aquifer at Vandenberg Air Force Base (VAFB) in Lompoc, CA. Differences in microbial community composition along the contaminant plume were assessed via a combinatorial approach utilizing denaturing gradient gel electrophoresis (DGGE), cloning and sequencing, intergenic transcribed spacer analysis (ITS), and comparative phylogenetic analysis of partial 16S rDNA sequences. Substantial bacterial sequence diversity, similar levels of species richness, and similar phylo-groups (including the Cytophaga–Flavobacterium–Bacteroidetes group and numerous members of the α-, β-, γ-, δ-, and ε-groups of the proteobacteria) were observed in both uncontaminated and contaminated regions of the aquifer. High-resolution measures (ITS fingerprinting and phylogenetic inference) readily separated communities impacted by the original petroleum spill (in source zone) from those in other parts of the aquifer and indicated that communities exposed to MTBE only were similar to communities in uncontaminated regions. Collectively, these data suggest that petroleum contamination alters microbial community structure at the species and subspecies level. Further study is required to determine whether these changes have an impact on the functioning of this subsurface ecosystem.

Environmental Science & Technology, 2006

Side-by-side experiments were conducted in a sulfatereducing aquifer at a former fuel station to ... more Side-by-side experiments were conducted in a sulfatereducing aquifer at a former fuel station to evaluate the effect of ethanol on biodegradation of other gasoline constituents. On one side, for ∼9 months we injected groundwater amended with 1-3 mg/L benzene, toluene, and o-xylene (BToX). On the other side, we injected the same, adding ∼500 mg/L ethanol. Initially the BToX plumes on both sides ("lanes") extended approximately the same distance. Thereafter, the plumes in the "No Ethanol Lane" retracted significantly, which we hypothesize to be due to an initial acclimation period followed by improvement in efficiency of biodegradation under sulfate-reducing conditions. In the "With Ethanol Lane", the BToX plumes also retracted, but more slowly and not as far. The preferential biodegradation of ethanol depleted dissolved sulfate, leading to methanogenic/acetogenic conditions. We hypothesize that BToX in the ethanol-impacted lane were biodegraded in part within the methanogenic/acetogenic zone and, in part, within sulfate-reducing zones developing along the plume fringes due to mixing with sulfatecontaining groundwater surrounding the plumes due to dispersion and/or shifts in flow direction. Overall, this research confirms that ethanol may reduce rates of biodegradation of aromatic fuel components in the subsurface, in both transient and near steady-state conditions.

Pedobiologia

We used a combination of sampling and statistical approaches to investigate the relative influenc... more We used a combination of sampling and statistical approaches to investigate the relative influence of metals, soil acidity, and organic matter on a suite of analogous plant and microbial community parameters in floodplain soils contaminated by mine wastes in the early twentieth century. We compared the sensitivity of plant and microbial communities to environmental variables and to one another using constrained ordination analyses. Environmental factors accounted for a larger percentage of the total variance in microbial communities (56.2%) than plant communities (22.0%). We also investigated biological and geochemical changes that occurred along a short transect (64 cm) that spanned a transition from productive grassland to an area of barren wasteland representing a total functional collapse of the grassland/soil ecosystem. Along this small-scale transect we quantified geochemical parameters and biological parameters in two soil layers, an upper layer (0-10 cm) and a lower layer (10-20 cm). Results from the short transect indicated that soil respiration was not a strong indicator of underlying metal concentrations, but soil acidity was correlated in the upper and lower layers. PLFA profiles changed with distance along the gradient in the upper, but not the lower layer. Implications for remediation of contaminated floodplain soils are discussed.

Pedobiologia, 2006

Polyphasic studies that used phospholipid fatty acid analysis (PLFA) in conjunction with communit... more Polyphasic studies that used phospholipid fatty acid analysis (PLFA) in conjunction with community level physiological profiling (CLPP) or PCR-based molecular methods were analyzed in order to evaluate the power of each strategy to detect treatment effects on soil microbial community structure (MCS). We found no studies where CLPP or PCR-based methods differentiated treatments that were not also differentiated by PLFA. In 14 of 32 studies (44%), PLFA differentiated treatments that were not resolved by CLPP analysis. In 5 of 25 studies (20%), PLFA differentiated treatments that were not resolved by PCR-based methods. We discuss PLFA, CLPP, and PCR-based methods with respect to power to discriminate change in MCS versus potential for characterization of underlying population level changes.

Soil Biology & Biochemistry, 2005

Page 1. Mine waste contamination limits soil respiration rates: a case study using quantile regre... more Page 1. Mine waste contamination limits soil respiration rates: a case study using quantile regression Philip W. Ramsey a,*, Matthias C. Rilliga , Kevin P. Feris b , Johnnie N. Moore c , James E. Gannon a aMicrobial Ecology ...

Applied and Environmental Microbiology, 2004

Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this ... more Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed (R 2 ‫؍‬ 0.02, P ‫؍‬ 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and the difference in the heavy metal content of hyporheic sediments throughout the year (R 2 ‫؍‬ 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the ␣, ␤, and ␥-proteobacteria and cyanobacteria) were apparent only during the fall and early winter, when the majority of organic matter is deposited into regional streams. These seasonal data suggest that the abundance of susceptible populations responds to heavy metals primarily during seasons when the potential for growth is highest.

Microbial Ecology, 2003

The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox grad... more The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem.

Ecology Letters, 2005

We used a 93-year-old mine waste contamination gradient in alluvial soil to explore the relations... more We used a 93-year-old mine waste contamination gradient in alluvial soil to explore the relationship between ecosystem level functioning and community structure in a chronically stressed ecosystem. The sensitivity of broad functional parameters (in situ soil respiration, microbial biomass, above and below ground plant biomass) and microbial diversity [phospholipid fatty acid (PLFA) abundance and richness] were compared. Functional responses were linear with respect to contaminants while thresholds were detected in the community structural response to contamination along the gradient. For example, in situ soil respiration was negatively and linearly correlated to contamination concentration (R = −0.783, P < 0.01), but changes in microbial community structure only became evident where contaminant concentrations were greater than 28 times above background levels. Our results suggest that functional redundancy does not prevent depression of ecosystem function in the long-term.

Environmental Science & Technology, 2009

Accurate natural resource damage assessment necessitates monitoring organisms or communities that... more Accurate natural resource damage assessment necessitates monitoring organisms or communities that respond most sensitively to contaminants. Observational studies have demonstrated a correlation between fluvial heavy metal deposition and hyporheic microbial community structure. To establish a causal relationship between sediment metal content and the structure of colonizing bacterial communities, we performed a controlled field experiment. River sediments of 1.75-2.36 mm in diameter with five different contaminant concentrations were collected from an environmental metal contamination gradient. Sediments were sterilized and then recolonized by incubation in the hyporheic zone of an uncontaminated river (i.e., a common garden experiment was performed). A significant correlation between hyporheic microbial community structure and heavy metal contamination (R 2 ) 0.81) was observed. The abundance of two phylogenetic groups was highly correlated with the level of heavy metal contamination (Group I, R 2 ) 0.96; Group III, R 2 ) 0.96, most closely affiliated with the R-and γ-proteobacteria, respectively). Microbial community structural responses were detected at metal concentrations an order of magnitude lower than those previously reported to impact benthic macroinvertebrate communities. We conclude that hyporheic microbial communities could offer the most sensitive method for assessing natural resource damage in lotic ecosystems in response to fluvial heavy metal deposition.

Applied and Environmental Microbiology, 2004

Microbial Ecology, 2003

The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox grad... more The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6–96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pronounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone.

One goal of interdisciplinarity is to develop a more holistic understanding of a set of interlink... more One goal of interdisciplinarity is to develop a more holistic understanding of a set of interlinked, complex system processes. Studies rarely couple both a mechanistic understanding of individual processes with their coupled influence on the entire system structure, yet the prospects for climate driven changes in western river systems provide justification for such an effort. We apply such a mechanistic and systems approach to understanding the effects of climate on fire frequency, plant-soil infiltration, sediment transport and stream community and ecosystem dynamics in a large wilderness setting that is likely to experience shifts in the timing or intensity of physical forces if projected climate change scenarios are realized. The Middle Fork Salmon River in central Idaho runs through the Frank Church Wilderness area and is the largest roadless area in the conterminous United States. The relatively southern continental position, complex mountain terrain and wealth of long-term landscape and ecological data in this region make it a tractable system to study the multifaceted and potentially non-linear processes of system change. This presents a unique opportunity to study the effects of climate change in the absence of substantial management effects in a system on the cusp of change. This collection of studies investigates the effects of climate-driven changes in hillslope processes on stream geomorphic and ecologic processes. We investigate 1) how wildfire alters the magnitude, timing and size of sediment delivered to stream channels, 2) how climate-driven changes in the proportion of rain vs. snow dominated basins alter stream hydrology, 3) how wildfire and insect disturbances modify aquatic ecosystems through inputs of nutrients and changes to habitat, 4) how paleo-records of drought, fire, and fire-related debris flows compare with recent data, 5) how fire-related inputs of sediment and wood influence the structure and dynamics of aquatic habitats, and their consequences for organisms, and 6) how hypothesized shifts in climate-related forces alter the function and resiliency of the Salmon River ecosystem. Integrated approaches include the application of legacy datasets, the exploration of historic chemical and physical records of ecosystem change, intensive stream, riparian and forest monitoring, the use of paired experimental watershed approaches, and the development of spatial analysis tools. If feedbacks among geomorphic, hydrologic and ecologic systems are positive this suggests a possible state change in response to a changing climate.

Heavy metal contamination in lotic ecosystems is a major health and environmental concern worldwi... more Heavy metal contamination in lotic ecosystems is a major health and environmental concern worldwide. The Resazurin Resorufin (Raz Rru) Smart Tracer system (Haggerty et al., 2008) provides a novel approach to test current models of microbial ecosystem response to chronic stressors such as heavy metals. These models predict that functional redundancy of metabolic capabilities of community members (e.g. respiration rate and enzyme activity) will compensate for decreases in species diversity until a stress threshold is reached. At this point, species diversity and function are expected to decline rapidly. Contrary to this model, microbial communities of the Clark Fork River (CF), Montana, demonstrate high levels of species diversity along the contamination gradient, whereas community function is inversely proportional to the level of contamination. The Raz Rru tool, a metabolically reactive hydrologic tracer, allows for direct quantification of in-situ microbial respiration rates. Therefore, this tool provides an opportunity to build upon studies of ecosystem response to contamination previously limited to extrapolation of point scale measurements to reach scale processes. The Raz Rru tool is used here to quantify the magnitude of metal induced limits on heterotrophic microbial respiration in communities that have evolved to different levels of chronic metal exposure. In this way we propose to be able to test a novel hypothesis concerning the nature of evolution of community processes to chronic stress and persistent environmental pollutants. Specifically, we hypothesize that metal contamination produces a measureable metabolic cost to both tolerant and intolerant communities. To test this hypothesis, rates of respiration associated with hyporheic sediments, supporting intact microbial communities, were quantified in the presence and absence of an acute Cd exposure in column experiments. Hyporheic sediment was collected from differently contaminated locations within the CF and compared to sediment from pristine reference sites. The biological reduction rate of Raz to Rru, K_12 in the Advection Dispersion Equation (ADE) below, represents rates of sediment associated heterotrophic respiration. ∂C_Raz}/{∂t} = {α_Lν}/{R} {∂^2C_Raz}/{∂x^2} - {ν}/{R} {∂C_Raz}/{∂x} - k_1C_Raz -k_12C_Raz [/tex] {∂C_Rru}/{∂t} = {α_Lν}/{R} {∂^2C_Rru}/{∂x^2} -{ν}/{R} {∂C_Rru}/{∂x} - k_2C_Rru + k_12 {M_Rru}/{M_Raz}CRaz [/tex] The Raz-Rru ADE will be optimized through the Markov Chain Monte Carlo method. Preliminary analysis of Cl^- tracer data provides input estimation of physical parameters, populating the hydrological terms of the ADE necessary for elucidation of K_12. It is expected that sediment metal content and K_12 are inversely related and that acute Cd exposure will negatively affect K_12 of both communities, with communities inhabiting metal contaminated sediments demonstrating a smaller reduction in K_12. This project has the potential to contribute to a revised theory of community response to metal induced chronic ecosystem stress, while contributing to the further development and application of the Raz Rru Smart Tracer system.

Environmental Science & Technology, 2008

Ethanol (EtOH) is a commonly used fuel oxygenate in reformulated gasoline and is an alternative f... more Ethanol (EtOH) is a commonly used fuel oxygenate in reformulated gasoline and is an alternative fuel and fuel supplement. Effects of EtOH release on aquifer microbial ecology and geochemistry have not been well characterized in situ. We performed a controlled field release of petroleum constituents (benzene (B), toluene (T), o-xylene (o-X) at ∼1-3 mg/L each) with and without EtOH (∼500 mg/L). Mixed linear modeling (MLM) assessed effects on the microbial ecology of a naturally sulfidic aquifer and how the microbial community affected B, T, and o-X plume lengths and aquifer geochemistry. Changes in microbial community structure were determined by quantitative polymerase chain reaction (qPCR) targeting Bacteria, Archaea, and sulfate reducing bacteria (SRB); SRB were enumerated using a novel qPCR method targeting the adenosine-5′-phosphosulfate reductase gene. Bacterial and SRB densities increased with and without EtOH-amendment (1-8 orders of magnitude). Significant increases in Archaeal species richness; Archaeal cell densities (3-6 orders of magnitude); B, T, and o-X plume lengths; depletion of sulfate; and induction of methanogenic conditions were only observed with EtOHamendment. MLM supported the conclusion that EtOH-amendment altered microbial community structure and function, which in turn lowered the aquifer redox state and led to a reduction in bioattenuation rates of B, T, and o-X.

Ethanol has replaced MTBE in gasoline in California and elsewhere, in part to reduce problems wit... more Ethanol has replaced MTBE in gasoline in California and elsewhere, in part to reduce problems with MTBE contamination of groundwater resulting from fuel spills. We are conducting field studies of the subsurface impacts of releases of ethanol-containing gasoline. In May 2004, we began side-by-side controlled release experiments at an existing fuel spill site (a former gasoline station) at Vandenberg Air Force Base, California. In one side of the paired experiments, we have been releasing benzene, toluene, o-xylene and tracers in a controlled and steady rate into a shallow, extremely well-characterized aquifer. In the other side, we have been releasing benzene, toluene, o-xylene, tracers and ethanol into the aquifer in the same manner. Using an extremely detailed grid of monitoring wells, we are gathering information on the migration and fate of the species in the two sides, and thus on the differences caused by the presence of the ethanol on one of the sides. Results from the first several months of the experiments suggest that the preferential degradation of the ethanol causes a significant reduction in the natural attenuation of the BTX species. We are also gaining insight into the impact that the more reduced conditions caused by ethanol degradation have on the fate of MTBE. Changes in the microbial community are being monitored as a means of understanding as well as generalizing the results.

Environmental Science & Technology, 2007

Side-by-side experiments were conducted in an aquifer contaminated with methyl-tert-butyl ether (... more Side-by-side experiments were conducted in an aquifer contaminated with methyl-tert-butyl ether (MTBE) at a former fuel station to evaluate the effect of ethanol release on the fate of pre-existing MTBE contamination. On one side, for ∼9 months we injected groundwater amended with 1-3 mg/L benzene, toluene, and o-xylene (BToX). On the other side, we injected the same, adding ∼500 mg/ L ethanol. The fates of BToX in both sides ("lanes") were addressed in a prior publication. No MTBE transformation was observed in the "No Ethanol Lane." In the "With Ethanol Lane", MTBE was transformed to tert-butyl alcohol (TBA) under the methanogenic and/or acetogenic conditions induced by the in situ biodegradation of the ethanol downgradient of the injection wells. The lag time before onset of this transformation was less than 2 months and the pseudofirst-order reaction rate estimated after 7-8 months was 0.046 d -1 . Our results imply that rapid subsurface transformation of MTBE to TBA may be expected in situations where strongly anaerobic conditions are sustained and fluxes of requisite nutrients and electron donors allow development of an active acetogenic/methanogenic zone beyond the reach of inhibitory effects such as those caused by high concentrations of ethanol. ES062156Q FIGURE 7. Mass discharge (Md) for MTBE and TBA crossing the EH transect (Figure 1) over time in the "No Ethanol Lane" and the "With Ethanol Lane". The specific wells used for the Md calculations are bracketed in Figure 6 and discussed in the Supporting Information.

Microbial Ecology, 2004

Microbial communities in subsurface environments are poorly characterized and the impacts of anth... more Microbial communities in subsurface environments are poorly characterized and the impacts of anthropogenic contamination on their structure and function have not been adequately addressed. The release of contaminant(s) to a previously unexposed environment is often hypothesized to decrease the diversity of the affected community. We characterized the structure of microbial communities along a gradient of benzene, toluene, ethylbenzene, and xylene (BTEX) and methyl-tert-butyl-ether (MTBE) contamination, resulting from a petroleum spill, within a shallow sandy aquifer at Vandenberg Air Force Base (VAFB) in Lompoc, CA. Differences in microbial community composition along the contaminant plume were assessed via a combinatorial approach utilizing denaturing gradient gel electrophoresis (DGGE), cloning and sequencing, intergenic transcribed spacer analysis (ITS), and comparative phylogenetic analysis of partial 16S rDNA sequences. Substantial bacterial sequence diversity, similar levels of species richness, and similar phylo-groups (including the Cytophaga–Flavobacterium–Bacteroidetes group and numerous members of the α-, β-, γ-, δ-, and ε-groups of the proteobacteria) were observed in both uncontaminated and contaminated regions of the aquifer. High-resolution measures (ITS fingerprinting and phylogenetic inference) readily separated communities impacted by the original petroleum spill (in source zone) from those in other parts of the aquifer and indicated that communities exposed to MTBE only were similar to communities in uncontaminated regions. Collectively, these data suggest that petroleum contamination alters microbial community structure at the species and subspecies level. Further study is required to determine whether these changes have an impact on the functioning of this subsurface ecosystem.

Environmental Science & Technology, 2006

Side-by-side experiments were conducted in a sulfatereducing aquifer at a former fuel station to ... more Side-by-side experiments were conducted in a sulfatereducing aquifer at a former fuel station to evaluate the effect of ethanol on biodegradation of other gasoline constituents. On one side, for ∼9 months we injected groundwater amended with 1-3 mg/L benzene, toluene, and o-xylene (BToX). On the other side, we injected the same, adding ∼500 mg/L ethanol. Initially the BToX plumes on both sides ("lanes") extended approximately the same distance. Thereafter, the plumes in the "No Ethanol Lane" retracted significantly, which we hypothesize to be due to an initial acclimation period followed by improvement in efficiency of biodegradation under sulfate-reducing conditions. In the "With Ethanol Lane", the BToX plumes also retracted, but more slowly and not as far. The preferential biodegradation of ethanol depleted dissolved sulfate, leading to methanogenic/acetogenic conditions. We hypothesize that BToX in the ethanol-impacted lane were biodegraded in part within the methanogenic/acetogenic zone and, in part, within sulfate-reducing zones developing along the plume fringes due to mixing with sulfatecontaining groundwater surrounding the plumes due to dispersion and/or shifts in flow direction. Overall, this research confirms that ethanol may reduce rates of biodegradation of aromatic fuel components in the subsurface, in both transient and near steady-state conditions.

Pedobiologia

We used a combination of sampling and statistical approaches to investigate the relative influenc... more We used a combination of sampling and statistical approaches to investigate the relative influence of metals, soil acidity, and organic matter on a suite of analogous plant and microbial community parameters in floodplain soils contaminated by mine wastes in the early twentieth century. We compared the sensitivity of plant and microbial communities to environmental variables and to one another using constrained ordination analyses. Environmental factors accounted for a larger percentage of the total variance in microbial communities (56.2%) than plant communities (22.0%). We also investigated biological and geochemical changes that occurred along a short transect (64 cm) that spanned a transition from productive grassland to an area of barren wasteland representing a total functional collapse of the grassland/soil ecosystem. Along this small-scale transect we quantified geochemical parameters and biological parameters in two soil layers, an upper layer (0-10 cm) and a lower layer (10-20 cm). Results from the short transect indicated that soil respiration was not a strong indicator of underlying metal concentrations, but soil acidity was correlated in the upper and lower layers. PLFA profiles changed with distance along the gradient in the upper, but not the lower layer. Implications for remediation of contaminated floodplain soils are discussed.

Pedobiologia, 2006

Polyphasic studies that used phospholipid fatty acid analysis (PLFA) in conjunction with communit... more Polyphasic studies that used phospholipid fatty acid analysis (PLFA) in conjunction with community level physiological profiling (CLPP) or PCR-based molecular methods were analyzed in order to evaluate the power of each strategy to detect treatment effects on soil microbial community structure (MCS). We found no studies where CLPP or PCR-based methods differentiated treatments that were not also differentiated by PLFA. In 14 of 32 studies (44%), PLFA differentiated treatments that were not resolved by CLPP analysis. In 5 of 25 studies (20%), PLFA differentiated treatments that were not resolved by PCR-based methods. We discuss PLFA, CLPP, and PCR-based methods with respect to power to discriminate change in MCS versus potential for characterization of underlying population level changes.

Soil Biology & Biochemistry, 2005

Page 1. Mine waste contamination limits soil respiration rates: a case study using quantile regre... more Page 1. Mine waste contamination limits soil respiration rates: a case study using quantile regression Philip W. Ramsey a,*, Matthias C. Rilliga , Kevin P. Feris b , Johnnie N. Moore c , James E. Gannon a aMicrobial Ecology ...

Applied and Environmental Microbiology, 2004

Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this ... more Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed (R 2 ‫؍‬ 0.02, P ‫؍‬ 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and the difference in the heavy metal content of hyporheic sediments throughout the year (R 2 ‫؍‬ 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the ␣, ␤, and ␥-proteobacteria and cyanobacteria) were apparent only during the fall and early winter, when the majority of organic matter is deposited into regional streams. These seasonal data suggest that the abundance of susceptible populations responds to heavy metals primarily during seasons when the potential for growth is highest.

Microbial Ecology, 2003

The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox grad... more The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem.

Ecology Letters, 2005

We used a 93-year-old mine waste contamination gradient in alluvial soil to explore the relations... more We used a 93-year-old mine waste contamination gradient in alluvial soil to explore the relationship between ecosystem level functioning and community structure in a chronically stressed ecosystem. The sensitivity of broad functional parameters (in situ soil respiration, microbial biomass, above and below ground plant biomass) and microbial diversity [phospholipid fatty acid (PLFA) abundance and richness] were compared. Functional responses were linear with respect to contaminants while thresholds were detected in the community structural response to contamination along the gradient. For example, in situ soil respiration was negatively and linearly correlated to contamination concentration (R = −0.783, P < 0.01), but changes in microbial community structure only became evident where contaminant concentrations were greater than 28 times above background levels. Our results suggest that functional redundancy does not prevent depression of ecosystem function in the long-term.

Environmental Science & Technology, 2009

Accurate natural resource damage assessment necessitates monitoring organisms or communities that... more Accurate natural resource damage assessment necessitates monitoring organisms or communities that respond most sensitively to contaminants. Observational studies have demonstrated a correlation between fluvial heavy metal deposition and hyporheic microbial community structure. To establish a causal relationship between sediment metal content and the structure of colonizing bacterial communities, we performed a controlled field experiment. River sediments of 1.75-2.36 mm in diameter with five different contaminant concentrations were collected from an environmental metal contamination gradient. Sediments were sterilized and then recolonized by incubation in the hyporheic zone of an uncontaminated river (i.e., a common garden experiment was performed). A significant correlation between hyporheic microbial community structure and heavy metal contamination (R 2 ) 0.81) was observed. The abundance of two phylogenetic groups was highly correlated with the level of heavy metal contamination (Group I, R 2 ) 0.96; Group III, R 2 ) 0.96, most closely affiliated with the R-and γ-proteobacteria, respectively). Microbial community structural responses were detected at metal concentrations an order of magnitude lower than those previously reported to impact benthic macroinvertebrate communities. We conclude that hyporheic microbial communities could offer the most sensitive method for assessing natural resource damage in lotic ecosystems in response to fluvial heavy metal deposition.

Applied and Environmental Microbiology, 2004

Microbial Ecology, 2003

The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox grad... more The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6–96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pronounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone.