Doctor of Philosophy / Department of Biology / Keith B. Gido / Global climate change could lead to less frequent but more severe precipitation events in the Great Plains, altering the hydrologic regimes of streams. It is important to quantify species roles in these dynamic systems, because changes in stream communities are likely to accompany predicted changes in hydrology. The effects of species on ecosystem processes also are limited by the frequency of disturbance, because prairie streams are harsh, nonequilibrium systems characterized by a wide range of disturbances. In particular, frequent floods that reset the ecosystem to an early successional state can override the influence of consumer populations because the availability of resources is too unpredictable to maintain stable populations of those species or because species are absent following the flood. As flood frequency decreases, potential consumer effects may intensify. Using a combination of field and experimental stream mesocosm experiments, I (1) characterized the ecosystem effects of southern redbelly dace (Phoxinus erythrogaster), a grazing minnow, (2) tested the interactive effects of flood frequency and the presence of water column (red shiner; Cyprinella lutrensis) or grazing minnows (Phoxinus) on ecosystem processes, and (3) tested the effects of species loss from the grazer functional feeding group on stream ecosystem structure and function. I found that dace affected some aspects of ecosystem structure but not function, which suggested that grazer effects in prairie streams may not be consistent across taxa. In the context of flood frequency, both the water column omnivore and dace affected recovery of prairie stream primary producers following flooding disturbance by stimulating production, presumably through nutrient remineralization. However, some of these effects were transient or dependent on flood frequency, and my results indicate that consumer effects depend not only on environmental venue but also on the balance between consumptive losses and nutrient stimulation. In a comparison of the effects of removing different taxa from a grazer assemblage, the loss of crayfish, snails, or dace from a grazer assemblage did not differentially affect ecosystem processes, suggesting overlap in the ecosystem roles of these species in the context of this experiment.

During oil-sands mining all vegetation cover, soil, overburden and oil-sand is removed, leaving pits several kilometres wide and hundreds of metres deep. These pits are reclaimed by a variety of treatments using mineral soil or a mixed peat and mineral soil as the capping layer and planted with trees with natural colonisation from adjacent sites. A number of reclamation treatments covering different age classes were compared with a range of natural forest ecotypes to identify the age at which the treatments become similar to a natural site with respect to vegetation composition and key soil attributes relevant to nutrient cycling. Ecosystem function was estimated from plant community composition, litter decomposition, development of an organic layer and bio-available nutrients. Key response variables including moisture, pH, C:N ratios, bio-available nutrients and ground-cover were analysed by non-metric multidimensional scaling and cluster analysis to discover which reclamation treatments were moving towards or merging with natural forest ecotypes and at what age this occurs. On reclaimed sites, bio-available nutrients including nitrate generally were above the natural range of variability but ammonium, phosphorus, potassium, sodium and manganese were generally very low and limiting to ecosystem development. Plant diversity was similar to natural sites from 5 years to 30 years after reclamation, but declined as reclaimed sites approached canopy closure. Grass and forb leaf litters decomposed faster than aspen or pine in the first year, but decomposition on one reclamation treatment fell below the natural range of variability. Development of an organic layer appeared to be facilitated by the presence of shrubs, while forbs correlated negatively with first-year decomposition of aspen litter. The better restoration amendments for tailings sands involved repeated fertilisation of peat: mineral mixtures in the early years of plant establishment, these became similar to a target ecotype at about 25 years. Good results were also shown by subsoil laid over non-saline overburden and fertilised once, these became similar to a target ecotype at about 15 years. Other treatments receiving a single application of fertiliser remain entrenched in the early reclamation phase for up to 25 years. / Forestry, Faculty of / Graduate

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. / Ph. D.

Genotypic diversity within populations can have important evolutionary consequences, but the ecological effects of intraspecific genetic variation on community and ecosystem function have only been studied in a few systems. I present the results of a three-year study designed to address the ecological impacts of genotypic diversity in quaking aspen (Populus tremuloides Michx.), using aspen genotypes planted across genotypic diversity levels (monoculture and mixture) and watering treatment levels (well-watered and water-limited). First, I demonstrated that significant variation exists among genotypes for a wide range of growth, morphological and physiological traits, and quantified high heritability and coefficient of genetic variation values for those traits. This demonstrates that heritable phenotypic variation exists within an aspen population, which could potentially have community and ecosystem implications. Secondly, I collected ground-dwelling arthropods across experimental treatment levels to determine if there are any community-level implications of genotypic diversity and watering treatment. Ground-dwelling arthropods were significantly affected by the genotypic diversity × watering treatment interaction, such that arthropod taxonomic diversity was lowest in water-limited genotypic mixtures. This result runs counter to the bulk of the plant diversity-arthropod diversity literature, which predicts that plant and arthropod diversity should be positively correlated, and highlights the importance of environmental conditions in mediating the plant-arthropod diversity relationship. Lastly, I show that there are no overall effects of genotypic diversity or watering treatment on tree growth patterns. Instead, there are high levels of variation among genotypes in their responses to treatments (significant genotype × diversity × watering treatment interactions), which are often opposing in direction. I also show that there are significant collection site × diversity × watering treatment interactions, demonstrating that genotypes vary in their response to experimental treatments based in part on their original collection site conditions in the field. This study demonstrates that aspen populations contain high levels of genotypic diversity, but that the ecological effects of genotypic diversity are mediated by the environment (in this case, watering treatment) and can be considerably more complicated than found in most previous studies.

Ecological opportunity—the availability of open niche space to an evolving lineage—has long been thought to modulate the extent of adaptive diversification. Many microbial evolution experiments have confirmed that ecological opportunity drives diversification of initially homogeneous populations into communities of ecologically distinct sub-lineages (ecotypes). Interactions among ecotypes are crucial for both community function and the maintenance of the ecological diversity produced during adaptive diversification, however the factors influencing the evolution of these interactions remain unexplored. We assessed the influence of ecological opportunity on this process by studying communities of the bacterium Pseudomonas aeruginosa that were evolved in either nutritionally complex (COM) or simple (SIM) environments. We measured the net ecological interactions in these communities by comparing the cellular productivity and competitive fitness of whole communities from each environment to that of their component isolates in both complex and simple media. On average, COM communities had both higher productivity and fitness than their component isolates in complex media, indicating that the components of these communities share net positive interactions. The same was not true of SIM communities, which did not differ in either measure from their component isolates. Follow-up experiments revealed that high fitness in two COM communities was driven by rare variants (frequency < 0.1%) that secrete compounds during growth which inhibit PA14, the strain used as a common competitor for fitness assays. Taken together, our results suggest that environments with high levels of ecological opportunity drive diversification into ecotypes that share net positive ecological interactions. The strong effect of diversity on productivity and fitness we found in newly diversified communities has a number of implications for evolutionary ecology as well as the treatment of P. aeruginosa infections.

Despite over four decades of research on deep-sea hydrothermal vent ecosystems, major gaps remain in our understanding of these systems. Knowledge of microeukaryote diversity, abundance, and involvement in ecosystem function lags far behind that of prokaryotes, and contributions of the non-endosymbiotic microbiome in faunal assemblages to ecosystem processes and overall hydrothermal vent microbial diversity are not known. This research addresses these gaps using high-throughput sequencing of 16S/18S rRNA genes and metagenomes from vent and surrounding non-vent habitats encompassing diffuse hydrothermal fluids, plumes, deep seawater, and microbes in assemblages of the foundation tubeworm species Ridgeia piscesae. Co-occurrence/covariance is a central method used, first, between prokaryotes with known extreme habitat preferences and microeukaryotes to infer potential endemism in the latter, and then between microbes and fauna in R. piscesae assemblages to infer interspecies interactions. Microeukaryote distribution and abundance suggest potential vent endemic microeukarya are infrequently encountered, potentially in low abundance, and belong to novel lineages of Rhizaria and Stramenopila. Potential endemism is inferred for relatives of known apusomonads, excavates, and some clades of Syndiniales. R. piscesae assemblages are shown to be hotspots of microbial taxonomic richness and exhibit a robust temperature-driven distinction in assemblage composition above and below ~25°C spanning micro, meio and macro size classes and microbial domains (Bacteria, Archaea, and micro-Eukarya). Likely interacting faunal and microbial taxa among R. piscesae assemblages are identified as ‘core communities’, which included eight macro- and meiofaunal taxa and members of the Bacteroidetes and Epsilonbacteraeota in highT communities (>25°C) and more meiofaunal species in addition to Alpha- and Gammaproteobacteria, and Actinobacteria in lowT communities (<25°C). Core communities were used to guide metagenomic investigations of microbial functional potential. Exploratory metagenomic analysis required development of new methods to deal with compositional data. ‘Enrichment leanings’ were developed to prioritize in-depth functional comparisons between sample types, which revealed clades within core community microbes with differing functional potential between highT and lowT assemblages and between assemblages and fluids. The balance of autotrophy-heterotrophy genes and patterns of genes for different carbon, nitrogen, and sulfur-cycling processes were tested as potential metrics of community-level function but did not distinguish assemblages by highT/lowT designations. This research brings us closer to understanding hydrothermal vent ecosystem function and suggests sizeable continued discovery potential. / Graduate / 2022-06-08

Although it is well documented how introduced species can negatively affect native species, we only poorly understand how they may alter ecosystem functions. We investigated how an invasive fish affected the flux of aquatic insects to terrestrial food webs using mesocosms in a desert spring ecosystem. We compared aquatic insect emergence between alternative community states with monocultures and polycultures of two native species of fish, least chub (Iotichthys phlegethontis) and Utah chub (Gila atraria) plus, introduced western mosquitofish (Gambusia affinis). We tested three hypotheses: (1) aquatic insect biomass will be greater than terrestrial insect biomass and thus, constitute a vital source of energy for terrestrial consumers (2) invasive mosquitofish will negatively impact the biomass of emerging aquatic insects, and (3) terrestrial consumers will negatively respond to decreased emerging aquatic insect biomass. Aquatic insects represented 79% of the flying insect community, and treatments with mosquitofish significantly reduced emergent aquatic insect biomass by 60% relative to the control without mosquitofish. Behavioral traits of invasive species are important, because mosquitofish most heavily affected insects that emerged during the day. Also, spiders that build horizontal webs were negatively correlated with decreasing aquatic insect biomass. Invasive mosquitofish can achieve very dense populations because of their high intrinsic rate of population increase, which can significantly disrupt the flow of energy between aquatic and terrestrial ecosystems, thereby reducing the energy available for terrestrial consumers.

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Terrestrial inputs of organic matter contribute greatly to the functioning of aquatic ecosystems, subsidizing between 30-70% of secondary production. This contribution of terrestrial resources is especially important in boreal lakes that are largely nutrient-poor and thus more responsive to these additions. Yet the mechanisms underlying initial processing of terrestrial resources by microbial communities at the base of lake food webs remain poorly understood. With this in mind, this thesis aims to advance our understanding of lake sediment microbial community assembly and functioning along abiotic gradients, primarily reflecting variation in terrestrial organic matter inputs that are predicted to increase with future environmental change. Chapter 1 reviews current knowledge on the terrestrial support of lake food webs and highlights gaps in understanding the factors influencing the microbial processing of terrestrial resources. It also provides an overview of metagenomics methods for microbial community analysis and their development over the course of the thesis. Chapter 2 tests how much of ecosystem functioning is explained by microbial community structure relative to other ecosystem properties such as the present-day and past environment. Theory predicts that ecosystem functioning, here measured as CO2 production, should increase with diversity, but the individual and interactive effects of other ecosystem properties on ecosystem functioning remain unresolved. Chapter 3 further questions the importance of microbial diversity for ecosystem functioning by asking whether more diverse microbial communities stabilize ubiquitous functions like CO2 production and microbial abundances through time. It also aims to identify the biotic and abiotic mechanisms underlying positive diversity-stability relationships. Chapter 4 then explores how microbial communities assemble and colonize sediments with varying types and amounts of terrestrial organic matter in three different lakes over a two-month period. Understanding how microbial communities change in relation to sediment and lake conditions can help predict downstream ecosystem functions. Finally, Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.