Browsing by Author "Barrett, John E."

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    Belowground Fungal Community Change Associated with Ecosystem Development
    Pineda Tuiran, Rosana P. (Virginia Tech, 2017)
    Numerous studies have looked at biotic succession at the aboveground level; however, there are no studies describing fungal community change associated with long-term ecosystem development. To understand ecosystem development, the organisms responsible for shaping and driving these systems and their relationships with the vegetation and soil factors, it is critical to provide insight into aboveground and belowground linkages to ultimately include this new information into ecosystem theory. I hypothesized that fungal communities would change with pedogenesis, that these changes would correlate with vegetation community change, and that they should show change of composition and diversity as the seasons change. Chapter 1 discusses the main topics related to this dissertation. Chapter 2 includes a publication draft that describes a study of sand-dune soil samples from northern Michigan that were analyzed to pinpoint the structural change in the fungal community during the development of the ecosystem. The samples were analyzed by pyrosequencing the soil DNA, targeting the internal transcribed spacer region. Chapter 3 contains a coauthored published paper that describes plant invasion of fields in Virginia to determine how they impact soil bacterial and fungal communities. The bacterial and fungal communities that were invaded by 3 different plant species exhibited similar changes, regardless of plant species, suggesting that some functional traits of invasives may have similar impacts on belowground communities. Chapter 4 remarks the conclusions of this research.
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    Biochar amendment as a tool for improving soil health and carbon sequestration in agro-ecosystems
    Drew, Sophia Eliza (Virginia Tech, 2022-09-14)
    Conventional farming practices and land-use conversions drive carbon out of soil and into the atmosphere, where it contributes to climate change. Biochar, a soil amendment produced by pyrolyzing organic feedstocks under low-oxygen conditions, is a promising tool to restore soil carbon and draw down atmospheric carbon dioxide. Biochar has received considerable attention from scientists, growers, and environmentalists in the last 20 years, but there is still a gap between academic research and practical recommendations on biochar production and application that are relevant to small-scale growers. Here I present the results from two complementary studies that demonstrate the utility of local-scale biochar systems and provide some recommendations for those looking to work with biochar. The first study sought to determine the impact of biochar amendments on soil carbon and nutrient retention on three working farms across a variety of soil types, cropping systems, and climates in the United States. The effect of biochar amendment depended on initial soil characteristics and the properties of the biochar applied. Biochar amendments increased soil carbon in all three sites and increased soil nitrogen at two of the three. In this study pyrolysis conditions appeared to be as important as local soils and climate influences on the efficacy of biochar treatments. The second study was a life cycle assessment using SimaPro software to quantify the carbon balance and global warming potential of biochar produced from three local feedstocks (softwood, hardwood, and hay) applied to pasture soils in Southwest Virginia. Feedstock type, pyrolysis gas yield, and transportation distance significantly contributed to variation in the carbon balance of each agro-ecosystem. Biochar made from softwood lumber scraps performed best, with the highest net carbon storage and lowest global warming potential, followed by biochar made from hardwood scraps. Hay biochar performed worst, with positive carbon emissions (i.e., more carbon released than stored over its life cycle) in most scenarios tested, mainly because of its low biochar yield and the carbon emissions associated with agronomic production and transportation. Together these studies demonstrate the potential of local biochar systems to improve both soil health and carbon sequestration, and reinforce how important it is to know the characteristics of the soil and the production history and properties of the biochar being applied in order to meet soil health and carbon sequestration goals.
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    Biotic interactions are an unexpected yet critical control on the complexity of an abiotically driven polar ecosystem
    Lee, Charles K.; Laughlin, Daniel C.; Bottos, Eric M.; Caruso, Tancredi; Joy, Kurt; Barrett, John E.; Brabyn, Lars; Nielsen, Uffe N.; Adams, Byron J.; Wall, Diana H.; Hopkins, David W.; Pointing, Stephen B.; McDonald, Ian R.; Cowan, Don A.; Banks, Jonathan C.; Stichbury, Glen A.; Jones, Irfon; Zawar-Reza, Peyman; Katurji, Marwan; Hogg, Ian D.; Sparrow, Ashley D.; Storey, Bryan C.; Green, T.G. Allan; Cary, S. Craig (Springer Nature, 2019-02-15)
    Abiotic and biotic factors control ecosystem biodiversity, but their relative contributions remain unclear. The ultraoligotrophic ecosystem of the Antarctic Dry Valleys, a simple yet highly heterogeneous ecosystem, is a natural laboratory well-suited for resolving the abiotic and biotic controls of community structure. We undertook a multidisciplinary investigation to capture ecologically relevant biotic and abiotic attributes of more than 500 sites in the Dry Valleys, encompassing observed landscape heterogeneities across more than 200 km2. Using richness of autotrophic and heterotrophic taxa as a proxy for functional complexity, we linked measured variables in a parsimonious yet comprehensive structural equation model that explained significant variations in biological complexity and identified landscape-scale and fine-scale abiotic factors as the primary drivers of diversity. However, the inclusion of linkages among functional groups was essential for constructing the best-fitting model. Our findings support the notion that biotic interactions make crucial contributions even in an extremely simple ecosystem.
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    The Combined Role of ENSO-driven Sea Surface Temperature Variation and Arctic Sea Ice Extent in Defining Climate Conditions in the Southwestern United States
    Chassot, Amanda M. (Virginia Tech, 2009-05-10)
    Previous research indicates that future reductions in Arctic sea ice cover (SIC) could alter storm tracks and precipitation patterns in western North America and negatively impact water resources in the American southwest. Other research suggests that multiple periods of increased precipitation and/or cooler temperatures in the American southwest during the Little Ice Age (LIA) were due to strong El Niño events; historical records also describe expanded Arctic SIC at this time. We use 16th-19th century Arctic SIC records from the ACSYS Historical Ice Chart Archive as a basis for expanding Arctic SIC from 1870 HadISST data to theoretical LIA extents. Then, in a suite of sensitivity studies, we investigate the relative influences of and interactions between El Niño-Southern Oscillation (ENSO) related sea surface temperature (SST) variation and varying Arctic SIC in controlling storm tracks, precipitation patterns, and overall climate conditions in the American southwest. We find that tropical Pacific SSTs greatly influence climate system response to variability in Arctic SIC, with ENSO-Neutral SSTs permitting the greatest response. Additionally, the degree of expansion and symmetry of Arctic SIC also influence precipitation regime response. These findings suggest that the climate response to future Arctic SIC retreat may not only be highly dependent on the spatial patterns and extent of SIC reductions, but also upon ENSO variability, such that El Nino events may reduce the potential climate impact of ice reductions as compared to Neutral or La Nina events.
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    Connectivity: insights from the US Long Term Ecological Research Network
    Iwaniec, David M.; Gooseff, Michael N.; Suding, Katharine N.; Samuel Johnson, David; Reed, Daniel C.; Peters, Debra P. C.; Adams, Byron J.; Barrett, John E.; Bestelmeyer, Brandon T.; Castorani, Max C. N.; Cook, Elizabeth M.; Davidson, Melissa J.; Groffman, Peter M.; Hanan, Niall P.; Huenneke, Laura F.; Johnson, Pieter T. J.; McKnight, Diane M.; Miller, Robert J.; Okin, Gregory S.; Preston, Daniel L.; Rassweiler, Andrew; Ray, Chris; Sala, Osvaldo E.; Schooley, Robert L.; Seastedt, Timothy; Spasojevic, Marko J.; Vivoni, Enrique R. (2021-05)
    Ecosystems across the United States are changing in complex and surprising ways. Ongoing demand for critical ecosystem services requires an understanding of the populations and communities in these ecosystems in the future. This paper represents a synthesis effort of the U.S. National Science Foundation-funded Long-Term Ecological Research (LTER) network addressing the core research area of "populations and communities." The objective of this effort was to show the importance of long-term data collection and experiments for addressing the hardest questions in scientific ecology that have significant implications for environmental policy and management. Each LTER site developed at least one compelling case study about what their site could look like in 50-100 yr as human and environmental drivers influencing specific ecosystems change. As the case studies were prepared, five themes emerged, and the studies were grouped into papers in this LTER Futures Special Feature addressing state change, connectivity, resilience, time lags, and cascading effects. This paper addresses the "connectivity" theme and has examples from the Phoenix (urban), Niwot Ridge (alpine tundra), McMurdo Dry Valleys (polar desert), Plum Island (coastal), Santa Barbara Coastal (coastal), and Jornada (arid grassland and shrubland) sites. Connectivity has multiple dimensions, ranging from multi-scalar interactions in space to complex interactions over time that govern the transport of materials and the distribution and movement of organisms. The case studies presented here range widely, showing how land-use legacies interact with climate to alter the structure and function of arid ecosystems and flows of resources and organisms in Antarctic polar desert, alpine, urban, and coastal marine ecosystems. Long-term ecological research demonstrates that connectivity can, in some circumstances, sustain valuable ecosystem functions, such as the persistence of foundation species and their associated biodiversity or, it can be an agent of state change, as when it increases wind and water erosion. Increased connectivity due to warming can also lead to species range expansions or contractions and the introduction of undesirable species. Continued long-term studies are essential for addressing the complexities of connectivity. The diversity of ecosystems within the LTER network is a strong platform for these studies.
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    A Continental-Scale Investigation of Factors Controlling the Vulnerability of Soil Organic Matter in Mineral Horizons to Decomposition
    Weiglein, Tyler Lorenz (Virginia Tech, 2019-07-30)
    Soil organic matter (SOM) is the largest terrestrial pool of organic carbon (C), and potential carbon-climate feedbacks involving SOM decomposition could exacerbate anthropogenic climate change. Despite the importance of SOM in the global C cycle, our understanding of the controls on SOM stabilization and decomposition is still developing, and as such, SOM dynamics are a source of major uncertainty in current Earth system models (ESMs), which reduces the effectiveness of these models in predicting the efficacy of climate change mitigation strategies. To improve our understanding of controls on SOM decomposition at scales relevant to such modeling efforts, A and upper B horizon soil samples from 22 National Ecological Observatory Network (NEON) sites spanning the conterminous U.S. were incubated for 52 weeks under conditions representing site-specific mean summer temperature and horizon-specific field capacity (-33 kPa) water potential. Cumulative CO2 respired was periodically measured and normalized by soil organic C content to obtain cumulative specific respiration (CSR). A two-pool decomposition model was fitted to the CSR data to calculate decomposition rates of fast- (kfast) and slow-cycling pools (kslow). Post-LASSO best subsets multiple linear regression was used to construct horizon-specific models of significant predictors for CSR, kfast, and kslow. Significant predictors for all three response variables consisted mostly of proximal factors related to clay-sized fraction mineralogy and SOM composition. Non-crystalline minerals and lower SOM lability negatively affected CSR for both A and B horizons. Significant predictors for decomposition rates varied by horizon and pool. B horizon decomposition rates were positively influenced by nitrogen (N) availability, while an index of pyrogenic C had a negative effect on kfast in both horizons. These results reinforce the recognized need to explicitly represent SOM stabilization via interactions with non-crystalline minerals in ESMs, and they also suggest that increased N inputs could enhance SOM decomposition in the subsoil, highlighting another mechanism beyond shifts in temperature and precipitation regimes that could alter SOM decomposition rates.
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    The Distribution of Surface Soil Moisture over Space and Time in Eastern Taylor Valley, Antarctica
    Salvatore, Mark R.; Barrett, John E.; Fackrell, Laura E.; Sokol, Eric R.; Levy, Joseph S.; Kuentz, Lily C.; Gooseff, Michael N.; Adams, Byron J.; Power, Sarah N.; Knightly, J. Paul; Matul, Haley M.; Szutu, Brian; Doran, Peter T. (MDPI, 2023-06-18)
    Available soil moisture is thought to be the limiting factor for most ecosystem processes in the cold polar desert of the McMurdo Dry Valleys (MDVs) of Antarctica. Previous studies have shown that microfauna throughout the MDVs are capable of biological activity when sufficient soil moisture is available (~2–10% gravimetric water content), but few studies have attempted to quantify the distribution, abundance, and frequency of soil moisture on scales beyond that of traditional field work or local field investigations. In this study, we present our work to quantify the soil moisture content of soils throughout the Fryxell basin using multispectral satellite remote sensing techniques. Our efforts demonstrate that ecologically relevant abundances of liquid water are common across the landscape throughout the austral summer. On average, the Fryxell basin of Taylor Valley is modeled as containing 1.5 ± 0.5% gravimetric water content (GWC) across its non-fluvial landscape with ~23% of the landscape experiencing an average GWC > 2% throughout the study period, which is the observed limit of soil nematode activity. These results indicate that liquid water in the soils of the MDVs may be more abundant than previously thought, and that the distribution and availability of liquid water is dependent on both soil properties and the distribution of water sources. These results can also help to identify ecological hotspots in the harsh polar Antarctic environment and serve as a baseline for detecting future changes in the soil hydrological regime.
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    Disturbance, Functional Diversity and Ecosystem Processes: Does Species Identity Matter?
    Emrick, Verl III (Virginia Tech, 2013-05-24)
    The role of disturbance is widely recognized as a fundamental driver of ecological organization from individual species to entire landscapes. Anthropogenic disturbances from military training provide a unique opportunity to examine effects of disturbance on vegetation dynamics, physicochemical soil properties, and ecosystem processes. Additionally, plant functional diversity has been suggested as the key to ecosystem processes such as productivity and nutrient dynamics. I investigated how disturbance and functional composition both singly and in combination affect vegetation dynamics, soil physicochemical properties, and ecosystem processes. I conducted my research at Fort Pickett, Virginia, USA to take advantage of the spatially and temporally predictable disturbance regime. In order to investigate the effect of plant functional composition on ecosystem properties, I used functional groups comprised of species with similar physiology and effects on ecosystem processes (C4 grasses, C3 grasses, legumes, forbs, woody plants). My study showed that two distinct disturbances associated with military training, vehicle maneuvers, and fire; affect functional group abundance, within functional group richness, and total species richness. I found strong effects of vehicle maneuvers on soil physical properties including an increase in bulk density and reduction in soil porosity. Fire also influenced soil physical properties but more indirectly through the reduction of above ground litter inputs. Though many of the measured physicochemical soil properties at Fort Pickett exhibited statistically significant effects of disturbance, the strength of these relationships appears to be modulated by influences of previous land use. I found statistically significant (P < 0.05) effects of disturbance on chlorophyll fluorescence, and effect of functional composition on available soil N- NH4+. In addition, I detected a significant interactive effect of disturbance class and functional composition on soil CO2 flux. The interactive effects of disturbance and functional composition on soil CO2 flux demonstrated how the loss of functional diversity could lead to instability in ecosystem processes in disturbed ecosystems.    In a dynamic ecosystem, I demonstrated that the abundance and diversity of plant functional groups was significantly influenced by disturbance. By experimentally altering the abundance and diversity of these functional groups in a disturbance-mediated ecosystem, I showed that functional groups and presumably species influence key ecosystem processes.
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    Downstream Dilemma: Navigating Microplastic's Impact on Freshwater Symbiosis in the Anthropocene
    Braswell, Cameron Bryce (Virginia Tech, 2024-06-27)
    Annually, it is estimated that 82 million tons of global plastic waste is either mismanaged or littered, bypassing waste management practices. This mismanagement causes the permeation of plastic debris into the environment, which then undergoes natural degradation processes. These degradation processes result in the proliferation of miniscule plastic particles known as microplastics. Due to the inherent proximity to sources of anthropogenic waste, concerns of microplastic pollution and its impact on freshwater ecosystems have recently increased. Until recently, microplastic research has primarily been focused on the toxicological affects felt by an individual organism rather than the intricate interactions that occur between taxa. Only focusing on the individual toxicological impact turns a blind eye on the communities that maintain ecosystem health and stability. To that end, our experiment was unique as it will be the first study assessing the impact of a freshwater symbiosis, as symbioses in the scope of toxicokinetic studies have primarily been dominated by that of terrestrial and marine relationships. This knowledge gap is a serious concern as its argued freshwater systems are more contaminated, than that of other aquatic habitats. To address this knowledge gap, we conducted mesocosm-based exposure-response assays, exposing the crayfish-branchiobdellidan symbiosis to microplastics of fibrous, microsphere, and tire wear particle morphologies while varying symbiont densities. We used the crayfish-branchiobdellidan model system in our study due to its amenability to laboratory monitoring and manipulation. The crayfish C. appalachiensis, common in the Virginia New River Basin, served as hosts to obligate ectosymbiotic annelids in the order Branchiobdellida. Previous research, using the crayfish-branchiobdellidan symbiosis demonstrated that the interaction is a cleaning symbiosis, where hosts benefit from reduced gill fouling while symbionts benefit from increased resource availability. We observed the physical and behavioral changes of the crayfish-branchiobdellidan symbiosis over a 172-day chronic exposure assay. Our results show, crayfish hosts with higher symbiont densities experienced decreased physical growth when exposed to microplastics compared to the control. This alteration in host growth was the result of increased antagonistic symbiont behavior in the form of gill tissue consumption. Our results suggest microplastics caused a reduction in epibiont abundance, thus decreasing symbiotic resource availability. This reduction in resources resulted in a shift of context dependency, thus increasing parasitic symbiont behavior. This study demonstrates microplastics have the capability to shift symbiotic context from a mutualism to a parasitism.
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    The drivers of freshwater reservoir biogeochemical cycling and greenhouse gas emissions in a changing world
    McClure, Ryan Paul (Virginia Tech, 2020-09-29)
    Freshwater reservoirs store, process, and emit to the atmosphere large quantities of carbon (C). Despite the important role of reservoirs in the global carbon cycle, it remains unknown how human activities are altering their carbon cycling. Climate change and land use are resulting in lower dissolved oxygen (DO) concentrations in freshwater ecosystems, yet more frequent, powerful storms are occurring that temporarily increase DO availability. The net effect of these opposing forces results in anoxia (DO < 0.5 mg L-1) punctuated by short-term increases in DO. The availability of DO controls alternate redox reactions in freshwaters, thereby determining the rate and end products of organic C mineralization, which include two greenhouse gases, carbon dioxide (CO2) and methane (CH4). I performed ecosystem-level DO manipulations and evaluated how changing DO conditions affected redox reactions and the production and emission of CO2 and CH4. I also explored how the magnitude and drivers of CH4 emissions changed spatio-temporarily in a eutrophic reservoir using time series models. Finally, I used a coupled data-modeling approach to forecast future emissions of CH4 from the same reservoir. I found that the depletion of DO results in the rapid onset of alternate redox reactions in freshwater reservoirs for organic C mineralization and greater production of CH4. When the anoxia occurred in the water column (vs. at the sediments), diffusive CO2 and CH4 efflux phenology was affected, and resulted in degassing occurring during storms before fall turnover. I observed that the magnitude of CH4 emissions varied along a longitudinal gradient of a small reservoir and that the environmental drivers of ebullition and diffusion can change substantially both over space (within one hundred meters) and time (within a few weeks). Finally, I developed a forecasting workflow that successfully predicted future CH4 ebullition rates during one summer season. My research provides insight to how changing DO conditions will alter redox reactions in the water column and greenhouse gas emissions, as well as provides a new technique for improving future predictions of CH4 emissions from freshwater reservoirs. Althogether, this work improves our understanding of how freshwater lake and reservoir carbon cycling will change in the future.
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    The Effects of Biochar and Reactive Iron Additions on Soil Carbon and Nitrogen Retention
    Conner, Jared P. (Virginia Tech, 2022-06-02)
    Soil organic matter (SOM) is a critical biogeochemical pool that can be managed as part of global efforts to conserve nutrients and enhance carbon (C) sequestration. But reliably increasing SOM has proven difficult because most of the organic matter that enters soil as plant litter and organic amendments (i.e., compost, manure) is susceptible to decomposition by soil microorganisms and eventually is lost to the environment as greenhouse gases and non-point source pollution. Many soils lack the physical and/or chemical properties that enable some human-modified soils (e.g., terra preta soils in the Amazon Basin) to stabilize and retain C and nutrients in SOM while maintaining relatively high levels of productivity compared to surrounding natural soils that formed under similar conditions. I hypothesized that two of the major stabilizers of organic matter common to terra preta soils of the Amazon basin – black carbon (biochar) and poorly crystalline, reactive iron (Fe) minerals – could be applied to a fine-textured soil from Southwest Virginia to improve the accumulation and retention of C and nitrogen (N). I used a field experiment to compare the effects of three types of locally-produced biochars applied with and without an organic N fertilizer (blood meal) on soil C and N availability. I then used an incubation experiment featuring the soils from the aforementioned field experiment to examine the effects of applying Fe2+ -treated manure effluent on the retention of C and N in unamended and hardwood biochar-amended soils. I found that biochar adsorbed inorganic N in all cases, while providing a reliable, stable increase in SOM due to its recalcitrant nature. However, the manure effluent used in the incubation experiment stimulated the decomposition of mineral-associated organic matter (MAOM), with the addition of Fe2+ to the manure mitigating this apparent positive priming effect and the presence of biochar actually reversing this effect and promoting an increase in MAOM following manure application to biochar-amended soil. Overall, biochar stimulated the retention of N by decreasing the leachable inorganic N in the soil and enhanced soil C stocks. Additionally, biochar applications had the added benefit of promoting the accumulation of manure in soil as stable, microbially-processed MAOM, while co-applying Fe2+ with manure only served to inhibit the priming of native soil C.
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    The Effects of dairy cattle antibiotics on soil microbial community cycling and antibiotic resistance
    Hedin, Matthew Lowell (Virginia Tech, 2018-05-11)
    Antibiotic use in agricultural ecosystems has the potential to increase resistance to antibiotics in soil microbial communities since 40-95% of an antibiotic dose administered to livestock is excreted intact or as metabolites. Exposure to antibiotics is also known to alter microbial community composition, biomass, and physiology, but the potential influences of antibiotic residues on the essential ecosystem processes that microbes regulate, e.g., carbon and nitrogen cycling are not well understood. I investigated the effects of antibiotic residues associated with dairy cattle operations on soil microbial communities and the ecosystem processes they regulate. I examined the effects of antibiotic exposure on the biogeochemical functioning of soil microbial communities by measuring the activity of extracellular enzymes associated with organic matter processing and nutrient mineralization in soils collected from dairy cattle operations across the United States. At each experimental station paired sites were identified by local managers that represented sites with high and low stocking rates of dairy cows who had been treated prophylactically with antibiotics to prevent mastitis. Responses varied among individual enzymes, but I found an overall significant decrease in total hydrolytic enzyme activity under high cattle stocking rates indicating a change in the functioning of the microbial community in soils exposed to antibiotic laden manure. Principle components analysis suggest that while some of the variation in enzyme activities are associated with the abundance of antibiotic resistance genes, soil organic matter (total organic, mineralizable, and particulate organic carbon) was the most significant variable accounting for differences in enzyme activities. This reflects an inherent challenge in studies of antibiotic exposure in agricultural landscapes: the difficulty of distinguishing direct effects of antibiotic residues from the organic matter and nutrient subsidy associated with manure applications. To address this concern I conducted a series of incubation experiments manipulating soils to isolate the influences of antibiotics, manure resource subsidies, and bovine microbiome inoculants into soils. Specifically, I examined soil respiration and antibiotic resistance gene counts using qPCR following treatment with cephapirin, pirilimycin and a positive and negative control. I found that pre-exposure to antibiotics and manure is important in modulating the response of microbial communities (soil respiration, and gene copy numbers of AmpC and TetO) to further antibiotic exposure. I conclude that antibiotics themselves have a direct effect on soil communities and their functioning that is additive to the effect of manure (i.e., as a resource subsidy). This effect is mediated by the history of previous exposure to antibiotics, i.e., cattle stocking density. These results suggest that antibiotic residues from dairy cattle operation may have significant effects on microbial communities and the biogeochemical cycling they regulate in agricultural ecosystems.
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    Effects of experimentally-altered hydrology on ecosystem function in headwater streams
    Northington, Robert M. (Virginia Tech, 2013-05-03)
    Forested headwater stream ecosystems are important integrators of terrestrial and aquatic systems and their function depends greatly on water availability. In the southern Appalachians, models of future climate change predict alterations to the timing and intensity of storms such that most precipitation may be relegated to winter and spring. During the summer and fall, relatively less precipitation will translate to lower stream flows in systems that rarely experience such a lack of water. Given these predicted changes to the hydrologic cycle, I experimentally reduced flow to downstream sections of three streams at the Coweeta Hydrologic Laboratory in NC to assess changes to function in perennial ecosystems. The questions that I addressed included: 1) How is organic matter decomposition regulated by changes to the availability of water? and 2) How does the relationship between nutrient uptake and metabolism change under conditions of varying water availability? The availability of water (as discharge) was shown to be a major control of ecosystem function throughout these studies. Rates of leaf decomposition varied between red maple (Acer rubrum L.) and white oak (Quercus alba L.) with lower discharge in the early autumn regulating the breakdown trajectories of leaves through facilitation of colonization by microbes and macroinvertebrates. The return of water during the winter accelerated decomposition rates in the diverted sites such that mass of leaves remaining were similar to those in upstream sections. Colonization of decomposing organic matter by heterotrophic microbes (especially fungi) increased N immobilization leading to an increase in respiration per unit leaf standing stocks during the fall. Nitrification was detectable during summer low flows when leaf standing stocks were low. Changes in the timing and intensity of precipitation and thus discharge may in turn alter the temporal dynamics of ecosystem function. Leaves may remain in the stream unprocessed which will change the availability of food for macroinvertebrates, the production of which provides nutrition to higher trophic levels. Local-scale differences in organic matter processing and nutrient immobilization may translate to regional differences in food availability over both time and space. Hydrology not only acts as a local control of endogenous processes but acts also regionally through the transport of resources and nutrients to downstream reaches.
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    Effects of land management and climate change on soil microbial communities in Appalachian forest ecosystems
    Osburn, Ernest D. (Virginia Tech, 2021-03-26)
    In terrestrial ecosystems, microorganisms are the dominant drivers of virtually all ecosystem processes, particularly cycling of carbon (C), nitrogen (N), and phosphorus (P). These microbial functions are critical for promoting ecosystem services that support human well-being, such as provisioning of clean drinking water, nitrogen retention, and carbon storage. In forests of the Appalachian region of the eastern US, these ecosystem services are threatened by multiple anthropogenic influences, including present and past land use activities (e.g., logging, conversion to agriculture) and climate change (e.g., intensifying droughts). However, despite the central importance of microbial communities in promoting ecosystem functions, impacts of land management and climate change on soil microorganisms remain poorly understood in the region. This dissertation seeks to address the following questions: 1) How does a new forest management practice, Rhododendron understory removal, influence the ecosystem functions of soil microbial communities? 2) Do historical land management activities have long-term legacy effects on the structure and ecosystem functions of soil microbial communities? And 3) Does historical land use influence responses of soil microbial communities to intensifying drought? In chapter 2, I show that experimental Rhododendron understory removal increased soil C and N availability, thereby promoting increased total microbial biomass. This increased microbial biomass resulted in elevated production of microbial extracellular enzymes, which increased rates of C and N cycling in soils following Rhododendron removal. In chapter 3, I examined soils across several historically disturbed and adjacent undisturbed reference forests and show that historical management activities, e.g., logging, conversion to agriculture, have long-term effects on soil microbial communities 4-8 decades after management activities occurred. These effects included increased bacterial diversity, increased relative abundance of r-selected bacterial taxa, and increased abundance of arbuscular mycorrhizal fungi. In chapter 4, I show that key soil biogeochemical processes, i.e., C mineralization, N mineralization, and nitrification, exhibit generally higher rates in historically disturbed forests relative to adjacent reference forests. Further, I attributed these changes in ecosystem process rates to changes in key aspects of microbial communities, including microbial biomass, extracellular enzyme activities, and bacterial r- vs K-selection. In chapter 5, I conducted a drought-rewetting experiment and show wide-ranging effects of experimental drought on soil microbial communities, including altered diversity, community composition, and shifts in the relative abundances of several specific taxa. Further, drought responses were particularly evident in soils from historically disturbed forests, indicating influences of land management on responses of soil communities to climate change. Finally, in chapter 6, I show that the experimental drought also influenced several ecosystem-scale properties of soils, including increased soil N pools and increased respiratory C loss. Overall, my dissertation reveals wide-ranging effects of anthropogenic activities on soil microorganisms and shows that microbial communities will influence forest responses to global change at the ecosystem scale.
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    Effects of Rhododendron removal on soil bacterial and fungal communities in southern Appalachian forests
    Osburn, Ernest D.; Miniat, Chelcy F.; Elliott, Katherine J.; Barrett, John E. (2021-09-15)
    Rhododendron maximum, a native ericaceous evergreen shrub, is expanding in forests of the southern Appalachian region following eastern hemlock (Tsuga canadensis) mortality due to hemlock woolly adelgid (Adelges tsugae) infestations. The goal of our study was to examine soil microbial community responses to experimental R. maximum removal treatments. The experiment was implemented as a 2 x 2 factorial design, including two R. maximum canopy removal levels (cut vs. not cut) combined with two forest floor removal levels (burned vs. not burned). These treatments were designed as potential management strategies to facilitate hardwood tree establishment in forests that have experienced T. canadensis declines. We sampled soils after removals and characterized bacterial and fungal communities using amplicon sequencing. Shrub removal did not affect bacterial or fungal alpha diversity but did affect both bacterial and fungal community composition. Relative abundances of bacterial phyla and fungal classes exhibited no differences among R. maximum removal treatments. However, specific bacterial and fungal taxa that were responsive to R. maximum removal (i.e., differentially abundant sequences) did exhibit clear patterns at high taxonomic levels. Specifically, taxa that responded negatively to R. maximum removal were found primarily in two bacterial phyla (Proteobacteria and Bacteroidetes) and one fungal class (Archaeorhizomycetes) while positive responders were clustered in several other bacterial phyla (e.g., Actinobacteria, Planctomycetes, Cyanobacteria). Fungal functional guilds also responded to R. maximum removal, including negative responses of ericoid mycorrhizae and positive responses of arbuscular mycorrhizae and wood saprotrophs. Effects of R. maximum removal on soil microbial communities were minor overall, but clear effects on some key functional groups were evident (i.e., mycorrhizal fungi), suggesting that microbial responses to R. maximum removal may influence recovery of forests in the southern Appalachian region.
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    Environmental controls on the abundance, diversity, growth, and activity of  ammonia-oxidizing microorganisms in temperate forest soils
    Norman, Jeffrey Stancill (Virginia Tech, 2014-01-31)
    The goal of my dissertation research was to investigate the structure and function of ammonia-oxidizing microbial communities in temperate forest soils. Accomplishing this goal required a hybrid approach: I used modern molecular biology techniques alongside soil biogeochemical measurements and framed my research using ecological theory largely developed in plant systems. All of my field work was done at Coweeta Hydrologic Laboratory, a Forest Service Station and Long Term Ecological Research Site near Otto, NC. Watershed-level land use manipulations have been performed at Coweeta since the 1930s, including clear-cutting, fertilizing, liming, burning, grazing by cattle, and replanting entire watersheds in white pine. While these treatments were originally imposed to assess the effects of land use on water yield, they have resulted in changes in soil characteristics as well. Working at Coweeta has therefore allowed me to sample ammonia-oxidizer communities across a gradient of soil variables, such as pH and nitrogen (N) availability, within the geographically-constrained area of the Coweeta Basin. First, I used amplicon-based pyrosequencing to independently assess the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) at several sites within Coweeta. I found that AOA and AOB diversity were a function of both resource availability (i.e. N availability) and environmental harshness (i.e. soil pH) in line with general ecological theory developed for plant systems by Tilman and Grime, respectively. Next, I tested whether AOA and AOB were substrate or nutrient limited in this system by adding either N or a nutrient solution containing both potassium and phosphorus to soil incubations and assessing the growth response of AOA and AOB using quantitative polymerase chain reaction (qPCR). I found strong evidence for substrate limitation by AOB and a marginally-significant positive effect of nutrient addition on growth of AOA. Another intriguing finding from this study was that both AOA and AOB grew during unamended soil incubations. Unamended (buried-bag) incubations have been used to estimate in situ rates of nitrification for over 50 years. By measuring the growth of AOA and AOB alongside nitrification during buried-bag incubations, I discovered that AOA are the dominant ammonia-oxidizers in temperate forest soils. However, I found that AOA are much less efficient at using the energy from ammonia oxidation to create biomass than AOB in the forest soils I sampled. Overall, I found that temperate forest soils contain low abundances of AOA and AOB, with relatively low diversity in both groups. This is especially true for the diversity of AOA, where a single taxon dominated the community at every site. Soil pH and N availability seem to be major selective forces for forest soil ammonia oxidizers, though other nutrients such as potassium and phosphorus may regulate the activity of AOA as well. AOA are most-likely the dominant ammonia oxidizers in temperate forest systems, though this may change with increased disturbance. In a broader sense, I found that ecological theory developed for plant communities was applicable to chemoautotrophic microbes despite the large differences in life history between these groups of organisms.
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    Environmental controls over bacterial communities in polar desert soils
    Geyer, Kevin M.; Altrichter, Adam E.; Van Horn, David J.; Takacs-Vesbach, Cristina D.; Gooseff, Michael N.; Barrett, John E. (Ecological Society of America, 2013-10)
    Productivity-diversity theory has proven informative to many investigations seeking to understand drivers of spatial patterns in biotic communities and relationships between resource availability and community structure documented for a wide variety of taxa. For soil bacteria, availability of organic matter is one such resource known to influence diversity and community structure. Here we describe the influence of environmental gradients on soil bacterial communities of the McMurdo Dry Valleys, Antarctica, a model ecosystem that hosts simple, microbially-dominated foodwebs believed to be primarily structured by abiotic drivers such as water, organic matter, pH, and electrical conductivity. We sampled 48 locations exhibiting orders of magnitude ranges in primary production and soil geochemistry (pH and electrical conductivity) over local and regional scales. Our findings show that environmental gradients imposed by cryptogam productivity and regional variation in geochemistry influence the diversity and structure of soil bacterial communities. Responses of soil bacterial richness to carbon content illustrate a productivity-diversity relationship, while bacterial community structure primarily responds to soil pH and electrical conductivity. This diversity response to resource availability and a community structure response to environmental severity suggests a need for careful consideration of how microbial communities and associated functions may respond to shifting environmental conditions resulting from human activity and climate variability.
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    Environmental Controls Over the Distribution and Function of Antarctic Soil Microbial Communities
    Geyer, Kevin M. (Virginia Tech, 2014-07-15)
    Microbial community composition plays a vital role in soil biogeochemical cycling. Information that explains the biogeography of microorganisms is consequently necessary for predicting the timing and magnitude of important ecosystem services mediated by soil biota, such as decomposition and nutrient cycling. Theory developed to explain patterns in plant and animal distributions such as the prevalent relationship between ecosystem productivity and diversity may be successfully extended to microbial systems and accelerate an emerging ecological understanding of the "unseen majority." These considerations suggest a need to define the important mechanisms which affect microbial biogeography as well as the sensitivity of community structure/function to changing climatic or environmental conditions. To this end, my dissertation covers three data chapters in which I have 1) examined patterns in bacterial biogeography using gradients of environmental severity and productivity to identify changes in community diversity (e.g. taxonomic richness) and structure (e.g. similarity); 2) detected potential bacterial ecotypes associated with distinct soil habitats such as those of high alkalinity or electrical conductivity and; 3) measured environmental controls over the function (e.g. primary production, exoenzyme activity) of soil organisms in an environment of severe environmental limitations. Sampling was performed in the polar desert of Antarctica's McMurdo Dry Valleys, a model ecosystem which hosts microbially-dominated soil foodwebs and displays heterogeneously distributed soil properties across the landscape. Results for Chapter 2 indicate differential effects of resource availability and geochemical severity on bacterial communities, with a significant productivity-diversity relationship that plateaus near the highest observed concentrations of the limiting resource organic carbon (0.30mg C/g soil). Geochemical severity (e.g. pH, electrical conductivity) primarily affected bacterial community similarity and successfully explained the divergent structure of a subset of samples. 16S rRNA amplicon pyrosequencing further revealed in Chapter 3 the identity of specific phyla that preferentially exist within certain habitats (i.e. Acidobacteria in alkaline soils, Nitrospira in mesic soils) suggesting the presence of niche specialists and spatial heterogeneity of taxa-specific functions (i.e. nitrite oxidation). Additionally, environmental parameters had different explanatory power towards predicting bacterial richness at varying taxonomic scales, from 57% of phylum-level richness with pH to 91% of order- and genus-level richness with moisture. Finally, Chapter 4 details a simultaneous sampling of soil communities and their associated ecosystem functions (primary productivity, enzymatic decomposition) and indicates that the overall organic substrate diversity may be greater in mesic soils where bacterial diversity is also highest, thus a potentially unforeseen driver of community dynamics. I also quantified annual rates of soil production which range between 0.7 - 18.1g C/m2/yr from the more arid to productive soils, respectively. In conclusion, the extension of biogeographical theory for macroorganisms has proven successful and both environmental severity and resource availability have obvious (although different) effects on the diversity and composition of soil microbial communities.
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    Evaluating Alternative Metacommunity Hypotheses for Diatoms in the McMurdo Dry Valleys Using Simulations and Remote Sensing Data
    Sokol, Eric R.; Barrett, John E.; Kohler, Tyler J.; McKnight, Diane M.; Salvatore, Mark R.; Stanish, Lee F. (2020-09-25)
    Diatoms are diverse and widespread freshwater Eukaryotes that make excellent microbial subjects for addressing questions in metacommunity ecology. In the McMurdo Dry Valleys of Antarctica, the simple trophic structure of glacier-fed streams provides an ideal outdoor laboratory where well-described diatom assemblages are found within two cyanobacterial mat types, which occupy different habitats and vary in coverage within and among streams. Specifically, black mats ofNostocspp. occur in marginal wetted habitats, and orange mats (Oscillatoriaspp. andPhormidiumspp.) occur in areas of consistent stream flow. Despite their importance as bioindicators for changing environmental conditions, the role of dispersal in structuring dry valley diatom metacommunities remains unclear. Here, we use MCSim, a spatially explicit metacommunity simulation package for R, to test alternative hypotheses about the roles of dispersal and species sorting in maintaining the biodiversity of diatom assemblages residing in black and orange mats. The spatial distribution and patchiness of cyanobacterial mat habitats was characterized by remote imagery of the Lake Fryxell sub-catchment in Taylor Valley. The available species pool for diatom metacommunity simulation scenarios was informed by the Antarctic Freshwater Diatoms Database, maintained by the McMurdo Dry Valleys Long Term Ecological Research program. We used simulation outcomes to test the plausibility of alternative community assembly hypotheses to explain empirically observed patterns of freshwater diatom biodiversity in the long-term record. The most plausible simulation scenarios suggest species sorting by environmental filters, alone, was not sufficient to maintain biodiversity in the Fryxell Basin diatom metacommunity. The most plausible scenarios included either (1) neutral models with different immigration rates for diatoms in orange and black mats or (2) species sorting by a relatively weak environmental filter, such that dispersal dynamics also influenced diatom community assembly, but there was not such a strong disparity in immigration rates between mat types. The results point to the importance of dispersal for understanding current and future biodiversity patterns for diatoms in this ecosystem, and more generally, provide further evidence that metacommunity theory is a useful framework for testing hypotheses about microbial community assembly.
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    Evaluating the influence of establishing pine forests and switchgrass fields on local and global climate
    Ahlswede, Benjamin James (Virginia Tech, 2021-05-18)
    Humans have extensively altered terrestrial surfaces through land-use and land-cover change. This change has resulted in increased food, fiber, fuel, and wood that is provisioned by ecosystems to support the human population. Unfortunately, the change has also altered climate through carbon emissions and changes in the surface energy balance. Consequently, maximizing both the provisioning and climate regulation services provided by terrestrial ecosystems is a grand challenge facing a growing global population living in a changing climate. The planting of pine forests for timber and carbon storage and switchgrass fields for bioenergy are two land-cover types that can potentially be used for climate mitigation. Importantly, both are highly productive systems representing contrasts in albedo (grass are brighter than pines) and vegetation height (pines are taller than the grass) along with unknown differences in carbon and water balance that influence local to global climate. Here I use eddy-covariance data to investigate how a transition from a perennial bioenergy crop (switchgrass) to a planted pine plantation alters the local surface temperature, global carbon dioxide concentrations, and global energy balance. First, I found that switchgrass and pine ecosystems have very similar local surface temperatures, especially during the grass growing season. After the switchgrass is harvested, surface temperature in the pine forest is much lower than switchgrass because no vegetation is present to facilitate the evaporation of water. The surface temperature in a bare-ground system (a recent clear-cut) was also high relative to the pine and pre-harvest switchgrass ecosystems. This illustrates the importance of maintaining vegetation cover to reduce local surface temperature. Second, I found that the 30-year mean change in global energy balance (i.e., radiative forcing) from planting a pine ecosystem rather than a switchgrass field was positive (pine warms climate) when considering changes in albedo and carbon measured using eddy-covariance systems. When including harvested carbon, pine and switchgrass can have similar global radiative forcing if all harvested pine carbon is stored, but harvested switchgrass carbon is burned. However, no scenarios I explored resulted in a strong negative radiative forcing by the pine ecosystem relative to the switchgrass field. These results show that afforestation or reforestation in the eastern United States may not result in any climate benefit over planting a switchgrass field. However, the presence of vegetation in both ecosystem types offers a clear benefit by cooling local surface temperatures.