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GENERAL ABSTRACT The Laurentian Great Lake wetlands are highly productive and complex systems. The net loss of wetlands since European settlement has been dramatic. The remaining coastal wetlands continue to be threatened with obliteration or severe environmental degradation. Therefore, the overall objective of this study was to provide information on the ecology of the remaining coastal wetlands within the lower Great Lakes. This study describes a coastal wetland fish community along the north shore of Lake Erie within Long Point Marsh complex over a 24-h period and catch characteristics of three common fishing techniques. The fish community was sampled at two hour intervals over a 24-h period in June, and used three types of gear to determine possible sampling biases from the different collection techniques. A total of 497 fish encompassing 11 taxa were collected. A 2-h interval, four hours prior to sunset, netted the largest number of taxa (including 3 functional feeding groups: ornmvores, planktivores, and piscivores ), as well as highest abundance and biomass values. Seine netting demonstrated a biased towards sampling the smaller planktivores, while fyke nets were biased towards larger omnivorous fish, and boat electrofishing was biased towards the large piscivores. These results will assist scientists and lake managers to develop standardized fish sampling protocol in order to accurately assess differences in wetland fish communities. Seven coastal wetlands within Lake Erie and Ontario along both the Canadian and United States shorelines were studied to verify predicted relationships from the literature and determine the relative influences of various habitat features on zooplankton community structure. Water quality, aquatic macrophyte, zooplankton, and fish community information were collected from the wetlands between July 4th and August 2nd of 2001. The predicted relationships from the literature concerning water quality and macrophyte species richness were verified by the results of this work. Water quality and macrophyte species richness were the most accurate predictors of wetland zooplankton community structure. Identifying the wetland characteristics that play primary roles in structuring zooplankton communities will also assist lake managers to make informed decisions of how to most effectively improve zooplankton habitat, to foster larger-bodied zooplankton populations, making the habitat more suitable for larger populations of larval and juvenile fish. / Thesis / Master of Science (MS)

Soil microbial communities mediate important ecological processes and play essential roles in biogeochemical cycling. Ecosystem disturbances such as surface mining significantly alter soil microbial communities, which could lead to changes or impairment of ecosystem functions. Reforestation procedures were designed to accelerate the reestablishment of plant community and the recovery of the forest ecosystem after reclamation. However, the microbial recovery during reforestation has not been well studied even though this information is essential for evaluating ecosystem restoration success. In addition, the similar starting conditions of mining sites of different ages facilitate a chronosequence approach for studying decades-long microbial community change, which could help generalize theories about ecosystem succession. In this study, the recovery of microbial communities in a chronosequence of reclaimed mine sites spanning 30 years post reforestation along with unmined reference sites was analyzed using next-generation sequencing to characterize soil-microbial abundance, richness, taxonomic composition, interaction patterns and functional genes. Generally, microbial succession followed a trajectory along the chronosequence age, with communities becoming more similar to reference sites with increasing age. However, two major branches of soil microbiota, bacteria and fungi, showed some contrasting dynamics during ecosystem recovery, which are likely related to the difference in their growth rates, tolerance to environmental change and relationships with plants. For example, bacterial communities displayed more intra-annual variability and more complex co-occurrence networks than did fungi. A transition from copiotrophs to oligotrophs during succession, suggested by taxonomic composition shifts, indicated that the nutrient availability is one important factor driving microbial succession. This theory was also supported by metagenomic analysis of the functional genes. For example, the increased abundance of genes involved in virulence, defense and stress response along ages indicated increased competition between microorganisms, which is likely related to a decrease of available nutrients. Metagenomic analysis also revealed that lower relative abundances of methanotrophs and methane monooxygenase at previously-mined sites compared with unmined sites, which supports previous observations that ecological function of methane sink provided by many forest soils has not recovered after 30 years. Because of the difficulty identifying in situ functional mechanisms that link soil microorganisms with environmental change, modeling can be a valuable tool to infer those relationships of microbial communities. However, the extremely high richness of soil microbial communities can result in extremely complicated models that are difficult to interpret. Furthermore, uncertainty about the coherence of ecological function at high microbial taxonomic levels, grouping operational taxonomic units (OTUs) based on phylogenetic linkages can mask trends and relationships of some important OTUs. To investigate other ways to simplify soil microbiome data for modeling, I used co-occurrence patterns of bacterial OTUs to construct functional groups. The resulting groups performed better at characterizing age-related microbial community dynamics and predicted community structures and environmental factors with lower error. / PHD / Disturbances to ecosystems are known to largely impact important ecological functions such as soil carbon loss, decreased nutrient retention and increased greenhouse gas emission. As a result, surface mining, which totally removes the topsoil and original vegetation, has severe negative influences on forest ecosystem function. Reforestation is performed on reclaimed mined sites to accelerate the return of forest vegetation and ecosystem functions. Although considerable research has shown that the plant community can be well developed after 30 years, little is known on whether ecosystem functions are also recovered during a similar time period. As direct mediators of many ecological processes in the environment, soil microorganisms are important for understanding the restoration progress of ecosystems. They could also provide early indications of restoration progress compared to plants. Historically, most soil microorganisms have been difficult to study because they are highly diverse and the majority cannot be cultured in lab, making it difficult to understand changes in the total soil microbiota. However, technological advances such as DNA sequencing have made it feasible to study soil microorganisms in detail. In this work, we studied soil microbial communities from reclaimed mined sites ranging from 5 to 30 years post-reforestation. We found that overall the microbial community was recovering from the disturbances of surface mining, but many differences from unmined soils still remain after 30 years, such as the unrecovered function as methane sink. Two major groups of soil microorganisms, bacteria and fungi, showed different characteristics during recovery, which are likely due to differences between the two groups with regard to growth rates, tolerance to environmental change and relationships with plants. Mathematical modeling is a useful tool for simulating changes and impacts on microbial communities under different conditions, given that actual interactions between microorganisms and their environment can be difficult to measure. However, the high complexity of soil microbial communities becomes an obstacle for modeling that needs to be addressed by simplifying data describing soil microbial community. One approach is grouping organisms based on their natural evolutionary relationships, but this can mask the trends of some microorganisms since all organisms in these groups do not always respond the same to environmental change. Here we used a method of grouping microorganisms based on their co-occurrence patterns, which resulted in better predictions of changes in community structure and environmental factors when applied in modeling.

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. / Master of Science / Ecosystems, including the soils underneath, are the environments that surround us perform a large number of critical human-relevant functions (playing roles in production of food, filtration of water for drinking, sequestration of carbon and nitrogen to build soil organic matter, and buffer against flooding). Yet, how these systems naturally develop over time are still in need of detailed study. One particular area of interest and need is the study of belowground fungal communities. It is not commonly known, but plants and ecosystems are highly dependent on the underground web of fungal hyphae that transform nutrients and provide water to plants. A first step in gaining this understanding utilized a natural ecosystem development gradient known as a chronosequence. It was expected that fungal communities would change as soil and ecosystem development progressed and that they would mimic changes in soil and vegetative properties. Discerning if these linkages occur is the first step to assessing how they work together to create ecosystems and their valuable environmental services. Chapter 1 provides a discussion of the main topics in this dissertation. Chapter 2 is at the heart of the dissertation via a study of fungal communities in a developmental soil ecosystem in northern Michigan in addition, in Chapter 3, I include a coauthored published paper that describes plant invasion of fields in Virginia. Chapter 4 remarks on the major conclusions of this Master thesis, supporting the role that vegetation and fungal community change in soil are associated with one another.

A wetland passive treatment system (PTS) was used to treat mine effluent flowing into East Prong Creek, Virginia. Prior to treatment, copper concentrations in the stream ranged from 8.9 to 32.0 μg/L at the impacted sites and from 0.1 to 7.7 μg/L at the reference site. In kick samples, insect abundance (n) and the number of taxa (#) were reduced at the impacted sites (n = 31, 22, 33, 24 and # = 190, 246, 266, 345, at sites 2 - 5, respectively) relative to the reference site (n = 52, # = 973). Red maple (Acer rubrum) leaves broke down twice as fast at the reference site (k = -0.029) than at sites receiving the untreated effluent (k = -0.016, -0.013, -0.013, -0.013 at sites 2 - 5, respectively). In benthic samples and leaf packs, abundances of all functional groups were reduced at the impacted sites relative to the reference site. In terms of abundance, scrapers and predators were most and least affected by copper, respectively. Following treatment, copper concentrations at the impacted sites in East Prong Creek ranged from 0.1 to 14 μg/L. The wetland PTS was most effective at reducing metal concentrations in the effluent from July to December, when dissolved oxygen concentrations in and flow through the wetland cells were low. Functional recovery preceded recovery of community structure by at least six months. Decomposition rates were similar at all sites in Fall 1994, after six months of treatment (k = -0.012, -0.011, -0.011, -0.012, -0.012) at sites 1 - 5, respectively). Recovery of community structure was not complete after 1 year of treatment. Abundance of collector-filterers and predators recovered quickly following treatment, while recovery of collector-gatherers and shredders was slower. / Master of Science

Headwaters are crucial linkages between upland ecosystems and navigable waterways, serving as important sources of water, sediment, energy, nutrients and invertebrate prey for downstream ecosystems. Surface coal mining in central Appalachia impacts headwaters by burying streams and introducing pollutants to remaining streams including excessive sediments, trace elements, and salinity. Benthic macroinvertebrates are widely used as indicators of biological conditions of streams and are frequently sampled using semi-quantitative methods that preclude calculations of areal densities. Studies of central Appalachian mining impacts in non-acidic streams often focus on biotic effects of salinity, but other types of pollution and habitat alteration can potentially affect benthic macroinvertebrate community (BMC) structure and perhaps related functions of headwater streams. Objectives were: 1) use quantitative sampling and enumeration to determine how density, richness, and composition of BMCs in non-acidic central Appalachian headwaters respond to elevated salinity caused by coal surface mining, and 2) determine if BMC structural differences among study streams may be attributed to habitat and water-quality effects in addition to elevated salinity. I analyzed BMC structure, specific conductance (SC, surrogate measure of salinity), and habitat-feature data collected from 15 streams, each visited multiple times during 2013-2014. BMC structure changed across seasonal samples. Total benthic macroinvertebrate densities did not appear to be impacted by SC during any months, but reduced densities of SC-sensitive taxa were offset by increased densities of SC-tolerant taxa in high-SC streams. Total richness also declined with increasing SC, whereas BMCs in high-SC streams were simplified and dominated by a few SC-tolerant taxa. Taxonomic replacement was detected in high-SC streams for groups of benthic macroinvertebrates that did not exhibit density or richness response, showing that taxonomic replacement could be a valuable tool for detecting BMC changes that are not evident from analyses using conventional metrics. Specific conductance, water-column selenium concentration, large-cobble-to-fines ratio of stream substrate, and relative bed stability were associated with changes in BMC structure. These results suggest multiple stressors are influencing BMCs in mining-influenced Appalachian streams. These findings can inform future management of headwater streams influenced by mining in central Appalachia. / Ph. D. / Humans rely on headwater streams to provide water of sufficient quantity and quality for use in fishing, swimming, and other designated purposes. In central Appalachia USA, surface coal mining impacts headwaters by burying streams and introducing various types of pollutants to remaining streams. Benthic macroinvertebrates, primarily stream insects, are widely used as indicators of stream-water quality because responses by certain groups of benthic macroinvertebrates to types and levels of pollution are known. Studies of central Appalachian coal mining impacts in non-acidic streams often focus on the effects of elevated salinity on benthic macroinvertebrate community (BMC) structure; however, other types of pollution and habitat alteration can also potentially affect BMC structure. Study objectives were to determine how BMCs in central Appalachian headwaters responded to elevated salinity caused by coal surface mining, and to determine if BMC structure differences among study streams may be caused by habitat and water-quality effects other than elevated salinity. I analyzed BMC, salinity, and habitat data collected from 15 streams, each visited up to six times during 2013-2014. I found that BMC structures varied seasonally, likely caused by natural life cycle variation of benthic macroinvertebrates. Streams in watersheds impacted by more areal coal mining disturbance tended to have higher levels of salinity, water selenium concentrations, and fine sediments, and fewer types of benthic macroinvertebrates although total BMC densities were comparable to those in less-disturbed streams. The study revealed that BMCs in mining-influenced streams were less diverse and were likely functioning less effectively than BMCs in forested reference streams. Also, the measurement and analysis methods used to characterize BMC structural responses to pollution influence assessments of stream condition. Understanding the responses of benthic macroinvertebrate structure to changes in habitat and water quality in mining-influenced streams can inform future stream management efforts.