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Understanding relationships between biodiversity and ecosystem function is a critical challenge, particularly in freshwater ecosystems where species losses are occurring at unprecedented rates. There is a particular need to examine these relationships in natural settings at large spatial scales. Ongoing, disease-driven amphibian declines may influence the structure and function of stream ecosystems, but little is known of the potential roles of stream-dwelling tadpoles in consumer-resource dynamics, ecosystem functions such as decomposition, and ecosystem-level biogeochemical cycling. Tadpoles in tropical streams likely regulate flows and ratios of nitrogen (N), phosphorus (P), and carbon (C), influencing ecosystems by altering nutrient supplies to other animals and their food resources. I used ecological stoichiometry as a framework to assess how the sudden loss of consumer biodiversity in neotropical headwater streams affected ecosystem function. I quantified N and P excretion and C:N:P ratios of tadpoles, macroinvertebrates, and food resources in healthy sites (pre-decline) and sites where disease-driven amphibian declines had occurred (post-decline). I tested the hypothesis of consumer homeostasis (i.e., that organisms maintain consistent body nutrient ratios by altering excretion chemistry) over a range of taxa and size classes. I also used mesocosms in a natural stream setting to quantify the effects of grazing tadpoles, shredding macroinvertebrates and a combination of the two on leaf decomposition and associated microbial activity. Finally, I examined macroinvertebrate community structure and quantified biomass and nutrient storage in tadpoles, macroinvertebrates, and basal resources in pre-decline and post-decline sites. I also measured excretion rates, volumetric excretion, and nutrient turnover for both tadpoles and macroinvertebrates. Patterns of consumer-resource stoichiometry varied with the presence or absence of tadpoles. There were higher concentrations of C, N, and P in basal resources in pre-decline sites compared to post-decline sites, but little variation in elemental ratios among sites. Elemental composition and molar ratios in grazers and shredders varied, with pronounced differences in %N for gatherers and filterers across sites. Macroinvertebrate grazer elemental composition was higher for all elements and had lower C:N, N:P, and C:P molar ratios in pre-decline sites compare to grazers in post-decline sites, while shredders showed the opposite pattern. There were differences in both taxon-specific allometric and stoichiometric relationships in tadpoles and macroinvertebrates between pre- and post-decline sites. Body P content was a good predictor of tadpole P excretion and tadpoles in pre-decline sites excreted more P per unit body P than those in post decline sites. Individuals deviated from strict homeostasis, and the degree of deviation varied among taxa. Tadpoles also affected leaf decomposition by influencing microbial communities and altering shredding macroinvertebrate feeding. Higher respiration rates of leaf discs in chambers with tadpoles suggested that tadpoles enhanced microbial activity by excreting nutrients through feeding and excretion. Shredders alone had little effect on respiration rates, indicating that tadpoles play an important and unique role in enhancing microbial activity and litter decomposition. Leaf area loss was greatest when tadpoles and macroinvertebrates were together, indicating facilitation. Macroinvertebrates are important nutrient recyclers in neotropical headwater streams, but their role is greatly decreased in the absence of larval amphibians. I measured ~80% lower standing stocks and storage of C, N, and P in basal resources in post-decline compared to pre-decline sites. Storage of C, N, and P in both tadpoles and macroinvertebrates also decreased in post-decline sites. I also observed 98% decreases in tadpole nutrient excretion and egestion rates, and an additional decrease in macroinvertebrate excretion rates (~80%) for both N and P in post-decline versus pre-decline sites. These decreases led to >8,000% increase in the distance that it took tadpoles to turn over the ambient N pools in post-decline sites, and a 130% increase for macroinvertebrates. Similar patterns were evident for P turnover, with turnover distance increasing by 6,000% and 400% in post-decline sites for tadpoles and macroinvertebrates, respectively. My results indicate that N and P excretion by both tadpoles and macroinvertebrates constitute significant nutrient fluxes in these headwater streams. Both tadpole and macroinvertebrate communities were excreting nutrients at similar rates in pre-decline sites, suggesting that they were playing equally significant roles in their contribution to ecosystem demand. My results demonstrate that tadpoles are important consumers in Neotropical headwater streams and their loss significantly alters stream food webs and ecosystem functions.

<p dir="ltr">Physical traits and the hydrologic setting of lake and wetland environments strongly affect the biogeochemical signature of aquatic ecosystems and their structure and function in the landscape. Natural freshwater ecosystems have a high propensity for carbon capture and storage through aerobic production, sedimentation, and sequestration, yet differing physical characteristics including water depth, lake surface area, and watershed size likely influence the extent to which these processes occur. Anthropogenically modified ecosystems also demonstrate complex function regarding carbon cycles, where the influence of human disturbance heightens nutrients and carbon loads into aquatic systems and leads to unique biochemical regimes. Across Indiana, agricultural practices currently affect around 65 percent of the state’s landscape, while urban development and population growth are expected to expand throughout the state. This trend is modeled throughout the midwestern United States, where the impacts of urban development on aquatic environments is further heightened by expected changes in climate, as storm intensity strengthens, and rainfall increases during certain times of the year. While understudied, there is good reason to believe that Indiana’s lakes and wetlands have incredible variability in carbon processing and carbon quality within and between systems. This variation is influenced by the wide variety of drivers including hydrology, geomorphology, water chemistry, metabolic processes, and redox conditions. The interactive influence of each of these drivers, however, is poorly understood across wide scale gradients. Predicting ecosystem productivity and its relationship with carbon dynamics is therefore an important tool for understanding freshwater ecosystems’ contributions to global fluxes of carbon. The variability within and across midwestern ecosystems creates a challenging, yet critical paradigm to understand the complexities of carbon dynamics in aquatic ecosystems, emphasizing the importance for direct data collection across a stratified gradient of ecosystems. This research shows that 1) human-assigned classifications of system type, including lake, reservoir, and wetland, are useful tools in classifying the metabolic and nutrient regimes of lentic systems, and 2) morphological features including lake depth and watershed area influence the structure of carbon quality throughout the water column. Findings provide valuable information to watershed and lake managers on the importance of different physical drivers in determining water quality across a range of lentic systems.</p>

Arsenic is a naturally occurring element, which is toxic to aquatic biota especially in disturbed areas where it may be found at high concentrations. A headwater stream adjacent to an 85 year-old abandoned arsenic mine was investigated to determine the influence of arsenic on stream biota and processes using an upstream (reference) and downstream (mine-influenced) comparative approach. Arsenic concentration was measured monthly at 10 sites along the stream length. Benthic macroinvertebrate surveys were conducted in both reaches five times throughout the course of a year. Leaf breakdown assays were conducted in reference and mine-influenced reaches. Leaf biofilm respiration was recorded during leaf breakdown assays and also with experimental arsenic additions to reference reach leaf biofilms. At the field site, arsenic concentrations varied from below detection limit (<2.5µg/L) to more than 12 mg/L. Macroinvertebrate density was greatly reduced down-gradient of the mine with 154 individuals/m2, while upstream there were 7869 individuals/m2. Leaf biofilm respiration rates were comparable to others found in the literature and not significantly different between reference and mine-influenced reaches. Further, experimental additions of arsenic did not alter biofilm respiration under laboratory conditions. However, shredder abundance on leaf packs was eight to twenty times greater upstream than the mine-influenced reach. Leaf breakdown rate varied two to three fold among sites distributed above and below the mine and were significantly lower in reaches of elevated arsenic concentration. Together, these data suggest that the mining operations on this headwater stream have altered organic matter processing primarily by decreasing invertebrate densities and limiting shredder abundance. / Master of Science

<p>Hemp (Cannabis sativa L.) is an annual crop used to produce a wide range of products including foods, beverages, nutritional supplements, fabrics, and textiles. Hemp has long been conflated with marijuana and has not been grown in the United States for decades. Due to recent legislation, the legal restrictions on growing hemp seem likely to be lifted. However, although interest is high, industrial hemp has not been grown in the U.S. for nearly 80 years and research on virtually all aspects of hemp production in the U.S. is in its infancy. We lack fundamental knowledge regarding cultivar performance, interactions with pests, particularly weeds, and nutrient requirements. Research is needed to address this knowledge gap and potential production issues as well as to determine the attitudes, perceptions and concerns of farmers regarding the potential adoption of this “new” crop. Importantly, research should be conducted before the crop becomes widely available so that farmers can make informed decisions and avoid costly mistakes. My dissertation consists of four chapters. In Chapter 1, I examine the literature for weed management in hemp production and identify research gaps. In Chapter 2, I investigate the complex legal framework that surrounds Cannabisand the resulting complications for hemp production. In Chapter 3, I present research conducted to determine the attitudes, perceptions, interests and concerns of organic farmers regarding the reintroduction and potential adoption of hemp was completed through survey research. Finally, in the fourth chapter, I present research conducted to characterize the growth and phenology of industrial hemp cultivars and identify cultivars suitable for growing conditions in the Midwest, and to determine the effect of delayed planting on the phenology and growth of seed and fiber hemp varieties in the Midwest.</p><p>Weed control and weed management in industrial hemp production is a surprisingly understudied field. Few peer-reviewed field studies on hemp exist on any subject and in particular, weed control and weed management is understudied. Specifically, only three studies designed to address a weed management issues exist in the literature dating back to 1900. Most commodity crops have extensive literature discussing weed management, and such an extensive gap in the hemp literature suggests that research needs to be conducted to determine the impacts of weeds on hemp production. Discrepancies among state laws and current federal drug legislation have created a convoluted, confusing, and impractical framework currently surrounds hemp production in the U.S. The building of pesticide regulation and product safety systems that are specific to the many end uses of Cannabis have yet to occur in the U.S. Interactions between producers, state and federal government, and third-party testing laboratories need to be facilitated to build regulation systems along with educational programs to train growers appropriate best management. Organic farmers are generally considered less risk adverse than the general farming population and often considered early adopters of technology. I surveyed organic farmers in seven Midwestern states and found that 98.5% of the respondents were generally open to new technologies, but that demographics variables explained little of the variation for respondents’ level of innovativeness as well as their openness to hemp.The respondents were generally open to hemp production (88.2% agreed with the statement that they were open to trying hemp production on their farm) and found that attributes of hemp production that conferred relative advantage and were compatible with existing systems were important. Delayed planting of hemp generally reduced the onset and duration of female flowering and the time to seed formation but the magnitude of these effects varied among cultivars. Seed, stalk, and total above ground dry weight yields varied across cultivar and planting date which may have been impacted by inconsistent stand densities stemming from heavy rainfall and wet soils. Results from this dissertation suggest that hemp is an understudied crop in the U.S., but that interest in its production among organic farmers exists. Field results support the importance of both planting date and cultivar for hemp phenology discussed in previous literature and so research needs to be conducted to explore best hemp production practices in the U.S.<br></p><p></p>

<p>Human activities have caused acidification of freshwater systems on a large scale resulting in reduced species diversity and ecological functioning in many lakes and streams. However, many naturally acidic freshwater systems have also been found, for instance in northern Sweden. In regions where such naturally acidic aquatic ecosystems have prevailed over evolutionary periods, species diversity and ecological functioning are not automatically impaired due to possible adaptation to the putatively adverse environmental conditions. I studied species diversity patterns and ecological functioning in anthropogenically acidified, naturally acidic, circumneutral, and limed streams to test the adaptation hypothesis and examine the ecological effects of variation in naturally acidic water chemistry. Species diversity was studied using benthic macroinvertebrates, while functioning was modelled using the decomposition rates of leaf litter. In accordance with the evolutionary species pool hypothesis, species richness was reduced more strongly in regions with anthropogenic than natural acidity when compared to circumneutral streams, supporting the adaptation hypothesis. In contrast, the patterns in ecological functioning along the pH-gradients did not differ between regions with anthropogenic and natural acidity, likely resulting from compensation: the biomass of tolerant taxa probably increased which thus rescued the loss in functioning otherwise mediated by the more sensitive taxa. Furthermore, the naturally variable acidic water chemistry clearly supported distinct macroinvertebrate assemblages, as was reflected in differing patterns of species diversity and ecological functioning. Such naturally acidic waters that were rich in dissolved organic carbon supported higher ecosystem process rates and lower species diversity than waters that contained little dissolved organic carbon. Upon liming naturally acidic streams microbial leaf decomposition increased, whereas shredding decreased along with changes in shredder abundances. The abundance of large caddisflies decreased, while the abundance of small stoneflies increased. The results suggest that various types of benthic macroinvertebrates with varying levels of adaptation and tolerance inhabited the hydrochemically variable naturally acidic streams. The distributions of macroinvertebrates in response to different pH levels and differences in acid quality and how these distributions translate into varying patterns of species diversity and ecological functioning are worthy of further investigation. This will likely improve our understanding of how such naturally acidic streams and their biota can be successfully managed.</p>

Climate models forecast lower and less frequent precipitation in the next 50 years. This is especially pronounced in the central United States, where Texas is expected to lose a week’s worth of rain every summer. Water availability is a primary driver of carbon flux in terrestrial ecosystems – controlling photosynthesis and organic matter decomposition. Thus, under proposed rainfall shifts, understanding the potential ecosystem response is key to predicting the future of terrestrial productivity. Terrestrial nutrient cycling is also driven by microbial saprotrophs, which are the chief decomposers of organic matter. Understanding the microbial response to rain shifts is key in predicting the ecosystem response. Research supports both microbial community specialization to local environment, and that the microbial communities may have the ability to rapidly acclimate to environmental change. To address this question of microbial response, we used a steep natural rainfall gradient along the Edwards Plateau in central Texas. The Edwards Plateau is an ideal field site in which to test these ideas because nearly identical grassland habitat and soils are found across its entirety, while mean annual precipitation ranges from 45 cm to 91 cm. To understand how soil microbial communities varied as a result of historical rainfall differences, we divided the gradient into four isoclines based on precipitation (46-56 cm, 56-66 cm, 66-76 cm, and 76-86 cm), and examined soil and soil microbial community characteristics at three sites in each isocline. We further used soils from the same sites for a reciprocal soil moisture experiment, where we asked how soil microbial communities responded to altered moisture conditions. Using a full factorial design, soils from each site in each isocline were exposed to one of four soil moisture treatments: soil moisture from the ‘home’ isocline and the three other ‘away’ isoclines. The moisture treatments were maintained for one year. Microbial respiration was measured at regular intervals throughout the experiment; fungal hyphal abundance and inorganic nitrogen were measured at the final harvest. The soils collected from the gradient decreased in both soil moisture and hyphal abundance from the wet to the dry end of the gradient, but there was no trend in inorganic nitrogen. In the reciprocal moisture experiment, microbial CO2 respiration was affected by both home isocline and soil moisture treatment. Drier sites had a narrower response to wetter treatments and did not achieve the same activity as wetter sites regardless of soil moisture treatment. In contrast, soils from the wettest isocline experienced severe reductions in activity with drying, with activity at the driest moisture treatment below that found in soils that were from the driest isocline. These patterns are consistent with some degree of local specialization, which may constrain the ability of microbial communities to rapidly acclimate to altered precipitation regimes. This experiment did not include immigration, however, and shifts in community composition in the presence of dispersal may be able to counteract local specialization. Given expected future increases in drought intensity microbial decomposition activity is likely to decrease and local specialization may create a lag in acclimation to the new condition. Thus, local specialization of microbial communities should be considered when predicting ecosystem responses to future climate change and their potential feedbacks to ecosystem productivity and carbon storage. / text

Human activities have caused acidification of freshwater systems on a large scale resulting in reduced species diversity and ecological functioning in many lakes and streams. However, many naturally acidic freshwater systems have also been found, for instance in northern Sweden. In regions where such naturally acidic aquatic ecosystems have prevailed over evolutionary periods, species diversity and ecological functioning are not automatically impaired due to possible adaptation to the putatively adverse environmental conditions. I studied species diversity patterns and ecological functioning in anthropogenically acidified, naturally acidic, circumneutral, and limed streams to test the adaptation hypothesis and examine the ecological effects of variation in naturally acidic water chemistry. Species diversity was studied using benthic macroinvertebrates, while functioning was modelled using the decomposition rates of leaf litter. In accordance with the evolutionary species pool hypothesis, species richness was reduced more strongly in regions with anthropogenic than natural acidity when compared to circumneutral streams, supporting the adaptation hypothesis. In contrast, the patterns in ecological functioning along the pH-gradients did not differ between regions with anthropogenic and natural acidity, likely resulting from compensation: the biomass of tolerant taxa probably increased which thus rescued the loss in functioning otherwise mediated by the more sensitive taxa. Furthermore, the naturally variable acidic water chemistry clearly supported distinct macroinvertebrate assemblages, as was reflected in differing patterns of species diversity and ecological functioning. Such naturally acidic waters that were rich in dissolved organic carbon supported higher ecosystem process rates and lower species diversity than waters that contained little dissolved organic carbon. Upon liming naturally acidic streams microbial leaf decomposition increased, whereas shredding decreased along with changes in shredder abundances. The abundance of large caddisflies decreased, while the abundance of small stoneflies increased. The results suggest that various types of benthic macroinvertebrates with varying levels of adaptation and tolerance inhabited the hydrochemically variable naturally acidic streams. The distributions of macroinvertebrates in response to different pH levels and differences in acid quality and how these distributions translate into varying patterns of species diversity and ecological functioning are worthy of further investigation. This will likely improve our understanding of how such naturally acidic streams and their biota can be successfully managed.

Marine ecosystems contain both highly abundant and diverse communities of vertebrates and invertebrates; however anthropogenic activity has drastically altered the species composition and diversity of these ecosystems. Specifically, human activity has targeted high trophic level species and degraded much of the biogenic habitat that faunal communities rely upon. These alterations have resulted in the loss of many marine predators and overall declines of marine biodiversity. To investigate the consequences of marine predator loss and community level species decline, I use a combination of large-scale data synthesis and in situ field observations of marine fish communities. I first use a meta-analysis approach to synthesize the consequences of marine predator loss in benthic marine ecosystems worldwide. From this synthesis, I was able to determine some of the biotic and abiotic factors that regulate the response of marine herbivores and primary producers to predator loss. Specifically, I show that marine predators have the strongest effect on populations of marine herbivores when predators and herbivores were similar in size and when larger herbivores were involved. Conversely the factors that best explained the response of the primary producer populations were related to the abiotic environment. The results show that primary producers respond the most positively to the presence of predators in high nutrient environments. While I found no link between the magnitude of change in the herbivore population and the magnitude of change in the producer population, I was able to demonstrate that primary producers are under the strongest top-down controls when nutrient concentrations are high, sea surface temperatures are low, and when the predator is larger in size than the herbivore. Finally, I use the data related to marine reserves to show that reserves are an effective tool to help reverse the trophic consequences of marine predator loss and that they are most effective when they are older in age. The third chapter examines the links between community diversity and community biomass within fish communities in eelgrass ecosystems in Northern British Columbia. After controlling for environmental variation, I found that it was the dominance of certain species within a community that resulted in the highest ecosystem function. This finding was demonstrated by both the taxonomic and functional metrics of diversity used. While previous work on this topic has shown that richness is positively correlated to function, my results are to the contrary, and suggest that further investigation into which aspects of community diversity drive ecosystem function is required. In conclusion, my results provide a new synthesis of the consequences of marine predator loss across the world and show how species diversity is linked to ecosystem function in local eelgrass fish communities. / Graduate / 2018-12-17

Antibiotic resistance is ubiquitous due to high usage of antibiotics and the capability of bacteria to transfer genes both horizontally and vertically. While this has dire implications for human health, the potential to disturb microbial communities and ecosystem functions they regulate is under appreciated. Antibiotics are commonly used in the livestock sector, accounting for 80% of antibiotic use domestically. This dissertation addresses three facets of this problem. Chapter 2 is a nation-wide survey of antibiotic resistance at dairy operations, aimed at understanding how ecosystem function is affected in situ. Chapter 3 describes a field-experiment, seeking to determine whether antibiotics have effects beyond soil through impacts on plant-microbe-soil feedbacks, thus potentially altering terrestrial ecosystem function. Chapter 4 investigates how rising global temperature interacts with antibiotic exposure through a microcosm-incubation experiment. These multiple stressors (i.e. temperature and antibiotics) could alter microbial community composition or physiology with repercussions on function. Additionally, chapter 4 seeks to determine whether microbes acclimate to continued antibiotic exposure. In chapter 2 I present evidence that increased antibiotic resistant gene (ARG) abundance with exposure to antibiotics and manure, and a correlation between ARGs and microbial stress. This increase in microbial stress results in elevated soil carbon loss. Chapter 3 shows that antibiotic exposure can change plant function – presumably through impacts on rhizospheric microbial community composition. Plants assimilate more nitrogen, but more carbon is lost from the system overall seemingly due to plant-soil-microbe tradeoffs. Chapter 4 shows a temporally dependent temperature–antibiotic interactive effect. Initially, pirlimycin increased microbial respiration at high temperatures, however this diminishes with time. Additional studies of microbial respiration at a range of temperatures show that microbial acclimation to antibiotic exposure may be taking place. However, interactive effects of high temperature and antibiotics appear to inhibit active microbial biomass production. Possible explanations to both of these patterns are the underlying differences in microbial community composition, specifically the fungal:bacterial. My results show that antibiotics not only lead to increased ARG abundance, but also have wide ranging effects on communities and ecosystem processes that are likely to be compounded in the face of global change. / Ph. D. / Antibiotic resistance is becoming ubiquitous. While implications for human health are dire, underappreciated are the potential effects on environmental microbes, given that microbes are drivers of ecosystem function. Antibiotics are commonly used in livestock production, accounting for 80% of antibiotic use domestically, with a substantial proportion of the administered antibiotics passing through livestock while still functional. Therefore understanding how antibiotics may be impacting livestock-associated soils is critical. This dissertation is divided into three data-driven chapters, each addressing a facet of this question. In chapter 2 I show that antibiotic exposure can increase microbial stress and decrease microbial efficiency. This reduction in microbial efficiency results in increased soil carbon loss. In chapter 3 I show that antibiotic exposure can change carbon and nitrogen cycling in plants, presumably through impacts on root-associated microbial composition. Plants assimilated more nitrogen, but more carbon was lost from the system overall, when soil was exposed to manure from cattle administered the antibiotic pirlimycin. Chapter 4 describes an interactive effect between temperature and antibiotic exposure, however, this effect appears to diminish with time. The pirlimycin treatment increased microbial respiration at high temperatures, however this effect was not observed in the second year of v the field portion of this study. Additional experimentation showed some evidence of microbial acclimation to multiple stressors. However other evidence described within this chapter paints a different picture, as interactive effects of high temperature and antibiotics appeared to inhibit active microbial biomass production. Possible explanations to both of these patterns are the underlying differences in microbial community composition, specifically broad differences in the ratio of fungi to bacteria. Therefore antibiotics not only lead to reduced microbial efficiency, but also have wide ranging effects on communities and ecosystem processes that are likely to be compounded in the face of global change.