Lichens are among the most prominent and successful life forms of metal-rich habitats, including ultramafic rocks and soils; however, research on lichens of ultramafic habitats is limited, especially on the North American continent. A review of the published literature on lichens of ultramafic substrates in North America yielded a total of 437 lichen species reported from ultramafic rocks and soils. Lichen assemblages of ultramafic substrates vary in composition and are dominated by acidophytic (low pH preferring) taxa with a minor, but consistent, basiphytic (high pH preferring) component. Species lists from ultramafic habitats in different geographic regions varied widely, suggesting that factors unrelated to substrate, such as climate, have a large effect on lichen assemblage composition. However, several studies showed clear differentiation between lichen composition on nearby or adjacent ultramafic and nonultramafic habitats, suggesting that ultramafic substrates harbor regionally unique lichen assemblages. In a regional community ecology study, we sampled lichen biotas of eight ultramafic and eight sandstone outcrops along a 70 km maritime influence gradient in order to test three hypotheses: 1) a substrate effect hypothesis that saxicolous lichen communities of ultramafic and sandstone outcrops are compositionally distinct; 2) a maritime gradient hypothesis that coastal and inland communities are compositionally distinct; and 3) a maritime moderation hypothesis that coastal ultramafic and sandstone communities are more similar than those of inland ultramafic and sandstone. Relationships between lichen communities and abiotic variables were analyzed using perMANOVA. Ultramafic communities showed significant differentiation from sandstone communities in the study area. A total of 134 taxa were recorded - 81 taxa from ultramafic outcrops and 100 taxa from sandstone, with 47 taxa found on both rock types. Ultramafic outcrops were characterized by greater similarity between samples, lower lichen cover, larger differences in cover between north and south aspects, and higher abundance and diversity of cyanolichen taxa relative to sandstone. Coastal, intermediate, and inland communities were compositionally distinct from one another, and sandstone and ultramafic assemblages were significantly differentiated in all coastal distance groups. This study is one of few to quantitatively examine lichen communities of two rock types, and is unique in that it does so at a regional scale. These results add to our understanding of the interactive roles of substrate and maritime influence in lichen community assembly.

<p> Chameleon plant (<em>Houttuynia cordata</em> Thunb.) is native to Southern and Southeastern Asia. It can reproduce sexually through seeds and asexually through rhizomes and is invasive in multiple countries including the U.S. There has been much research on <em>H. cordata</em> as a medicinal species, and its potential as an invasive species is well documented. However, its herbicidal resistance has not previously been quantified. The objective of this study is to assess <em>H. cordata’s </em>resistance to herbicides. This study consisted of two rounds of tests to examine the resistance of <em>H. cordata</em> plants to three commonly used herbicides: SpeedZone, Weed-B-Gon, and Roundup. Two concentrations of each herbicide were used during each trial in the study: the recommended concentration and twice the recommended concentration. Herbicide treatments were applied outside the greenhouse. Herbicides were sprayed uniformly on the plants until the herbicide was dripping off the leaves. The growth of the treated plants was then monitored in the greenhouse. The herbicides generally reduced growth of the plants temporarily. However, plant extermination was not achieved. Plant samples from all herbicidal treatments regrew from rhizomes after all herbicide treatments. Results from the study showed that <em>H. cordata </em>could not be controlled by the recommended concentrations of herbicides commercially available for horticultural uses in the U.S. Doubling the recommended herbicide concentration was also ineffective in exterminating <em>H. cordata </em>plants. This research clearly showed that <em>H. cordata</em> has the potential to become a highly invasive species with the potential to negatively affect the ecological integrity of many communities in the U.S.</p>

The relationship of ant community composition to various habitat characteristics is compared across four habitat types and 12 environmental variables in Mississippi. The four habitat types include pasture, prairie, and oak-hickory forests in the Black Belt and forests in the Flatwoods physiographic region. Ants were sampled using pitfall traps, litter sampling, baiting and hand collecting. A total of 20,916 ants representing 68 species were collected. NMS and ANCOVA both revealed three distinct ant communities (pasture, prairie, and ?forests?) based on species composition and mean ant abundance per habitat type between the four habitat types. Principal component analysis (PCA) partitioned the 12 environmental variation into four axes with eigenvalues >1. Axis 1 differentiated open grass-dominated habitats from woodlands. In contrast axis two mainly separated pastures from prairie remnants. Multiple regression models using the four significant PCA axes revealed that total species richness was significantly affected by variation in the first two PCA axes. Forested sites supported approximately nine more species of ants than prairies and 21 more than pastures. Comparisons of the abundance of ant functional groups were also made between the four habitat types with multiple regression models to investigate how the environmental variables affected certain groups of ants. Annotated notes are included for each ant species encountered during this study.

No description available.

No description available.

The Juan de Fuca Ridge, located 400 km off the coast of Washington State, is home to unstable and unpredictable hydrothermal vent sites where chemosynthetic communities flourish. In 2007 the manned submersible ALVIN retrieved a Ridgeia piscesae tubeworm community in its entirety from the side of the Tower sulfide edifice from the Endeavor segment of the Juan de Fuca Ridge (47 55.416720 N, 129 6.487020 W, at a depth of 2269 m) using the Bushmaster Jr. collection device. The collection was analyzed for community structure and the data collected were compared to that from several other hydrothermal vent communities. It was determined that substrate composition is a factor that heavily influences community structure. The data were then compared to the community succession model developed by Sarrazin et. al. in 1997 and 1999 (Sarrazin et. al. 1997, Sarrazin and Juniper 1999). The Tower community was found to expand the model as a new community succession classification; that of community iii low flow. The Tower community was then analyzed for diversity, structure and tubeworm morphology in conjunction with two other communities from differing substrata. The Ridgeia piscesae tubeworms were found to be of the "long skinny" morphotype, one that was previously thought to only reside on basaltic substrate. The Tower community has similar species richness and higher species evenness than those from basaltic substrate, but similar richness and lower evenness that those from sulfide. This community type combines the characteristics of those from both substrata, resulting in a community with diversity and structure that is an intermediary between sulfide and basaltic substrates. / Biology

Water hyacinth (Eichhornia crassipes) is a floating non-native plant that has been reoccurring in Lake Chapala, Jalisco, Mexico for more than 100 years. In this research, I explore the effects of water hyacinth on freshwater ecosystems worldwide and specifically on Lake Chapala. In chapter 1, I reviewed studies conducted on water hyacinth worldwide and found that the effects of water hyacinth on water quality are similar but the magnitude of effects is dependent on the percent cover and potentially the spatial configuration of water hyacinth mats. Water hyacinth's effect on aquatic invertebrates, fish, and waterbirds is less predictable and dependent on conditions prior to invasion. In chapter 2, I tested for relationships between percent water hyacinth cover and waterbird abundance, species diversity, community composition, and habitat use. In general, I found a weak positive relationship or no relationship between these variables. In Chapter 3, I monitored habitat use by American Coots (Fulica americana) in a variety of habitats around Lake Chapala. I found that the time spent in water hyacinth positively corresponded to the percent water hyacinth cover and that the time foraging in water hyacinth was positively related to the time spent in water hyacinth. In Chapter 4, I compared invertebrate assemblages in open water to those within and at the edge of water hyacinth mats, emergent vegetation, and submerged trees. I also examined invertebrate assemblages within the roots of water hyacinth plants and compared assemblages between patch and shoreline water hyacinth plants. I found that density and taxonomic richness of water column invertebrates were generally higher in association with water hyacinth, but that mean percent cover of water hyacinth affected the magnitude of differences among habitats and vegetation types. I did not find significant differences in root invertebrate density and taxonomic richness between patch and shoreline water hyacinth plants. In chapter 5, I discuss how water hyacinth affected dissolved oxygen and water transparency on a small, localized scale, but was not the driving factor for seasonal differences. The overall results suggest that water hyacinth had a minimal ecological effect on Lake Chapala during this study. / Ph. D.

Host-associated microbial communities, also known as microbiomes, are essential to the health of their hosts, and disturbance of these communities can negatively impact host fitness. The honey bee gut microbiome is a relatively simple host-associated community that makes an excellent model system for studying microbiome stability. In addition, honey bees are essential agricultural pollinators, so factors that impact their health are important for food security. The presented research focused on the stability of the honey bee gut microbiome in response to disturbance from the antibiotic tetracycline. Tetracycline was chosen because it is the most commonly used antibiotic in beekeeping, and may have negative effects on bees through the disruption of their gut microbiomes. The first study presents a new fecal sampling method for studying the honey bee gut microbiome of individual bees over time. This method accurately represented bacterial community structure in the gut microbiome as determined with 16S rRNA gene amplicon sequencing, as fecal and whole gut samples did not differ significantly for individual bees. The fecal sampling technique was then used to examine changes to individual honey bee gut bacterial communities before and after tetracycline exposure. Minimal differences in gut community structure were detected prior to and five days after tetracycline treatment. However, there was variability in how individual gut microbiomes were affected by tetracycline treatment, highlighting the importance of intraspecific variation in response to disturbance. The second study investigated whether the timing of disturbance during a host's life impacts microbiome community stability. Newly emerged bees were treated with tetracycline, returned to their hive, and recollected 7 or 14 days later. The gut communities of the bees were then characterized using 16S rRNA gene amplicon sequencing. Gut microbiome structure of bees treated with tetracycline at emergence differed from controls both 7 and 14 days after emergence, with the antibiotic-treated bees having lower community richness overall. This study showed that early life disturbance of host-associated microbial communities can influence microbiome structure later in life. The final study describes the occurrence of antibiotic resistance genes (ARGs) in honey bee gut bacterial symbionts from hives across the US. Honey bee gut metagenomes were sampled from hives at 13 apiaries located in a transect from Virginia to Washington, and ARG presence was assessed across the sites. We also specifically quantified the abundances of two common tetracycline resistance genes (tet(B) and tet(M)) across apiaries. ARGs, both for antibiotics used in beekeeping and unrelated antibiotics, were detected in honey bee gut bacteria from all apiaries. Tetracycline resistance genes were the most common across all apiaries, and the abundance of two tetracycline resistance genes varied by apiary. Members of the honey bee gut microbiome contained different proportions of ARGs, but taxa within a single family contained similar proportions, possibly indicating phylogeny plays a role in ARG accumulation. In particular, Gilliamella and Frischella, both in the family Orbaceae, contained the highest percentages of ARGs. The results from this study suggest honey bee bacteria act as reservoirs of ARGs. Overall, the presented research contributes to the field of biology by highlighting the importance of intraspecific variation in host-associated microbial communities and presenting a new method for studying honey bee gut microbiome variation at the individual-level, showing that early life events in honey bees influence microbiome development, and suggesting that honey bee bacterial symbionts have adapted to deal with antibiotic disturbance through the accumulation of ARGs. / Doctor of Philosophy / Nearly all animals, including honey bees, have communities of bacteria that live on and in them. These communities, called microbiomes, are often essential to the health of their hosts. For instance, communities of gut bacteria can be important for breaking down food for digestion. Honey bees have approximately 10 bacterial species that consistently live in their guts and provide these types of services to their host. As with many bacterial communities, these beneficial bacteria can be impacted by exposure to antibiotics, even though antibiotics can also be important for treating or preventing dangerous bacterial infections. In honey bee hives, the antibiotic tetracycline is used to prevent bacterial disease. However, tetracycline may simultaneously be negatively impacting colony health through disruption of the honey bee gut microbiome. The goal of the presented work was to understand how tetracycline impacts the honey bee gut microbiome. In my first chapter, I demonstrate a new fecal sampling method that will allow us to understand how gut microbiomes from individual bees change over time. I first compared the bacteria found in fecal samples to those in the whole guts of bees and found that the bacterial communities of the fecal samples and guts were very similar, indicating that fecal sampling is a good method for studying the honey bee gut microbiome. I then used my fecal sampling method to determine how individual honey bee gut microbiomes respond to antibiotic disturbance over time. I collected fecal samples from adult bees prior to treatment, treated the bees with tetracycline, and after five days of being maintained in the lab, recollected fecal samples. My results showed few changes to the bacterial communities before and after treatment, suggesting some honey bee gut microbiomes may be resistant to tetracycline. In my second chapter, I addressed whether exposure to antibiotics early in life had long-term impacts on the gut microbiome. I treated bees at the start of adulthood with tetracycline, returned the bees to their hive for 7 or 14 days, and assessed their microbiome. Tetracycline treatment at the beginning of adulthood changed the gut microbiome later in life, as the microbiomes of tetracycline-treated bees and controls differed from one another both 7 and 14 days after exposure. This chapter shows that disturbances to microbiomes during early life can also affect microbiomes later. My third chapter addressed how honey bee bacteria have adapted to antibiotic use by identifying antibiotic resistance genes (ARGs) in honey bee gut bacteria from 13 hives located in a transect across the US from the state of Washington to Virginia. I found a variety of antibiotic resistance genes in honey bee gut bacteria, both associated with beekeeping and likely environmental contamination. The prevalence of antibiotic resistance genes in honey bee bacteria may help us track antibiotic resistance in the environment. Ultimately, my dissertation contributes to our understanding of how antibiotic use affects honey bees by changing their gut microbiome.

Populations of striped cucumber beetles (<i>Acalymma vittatum</i> Fabr.), spotted cucumber beetles (<i>Diabrotica undecimpunctata howardi</i> Barber), western cucumber beetles (<i>Acalymma trivittatum</i> Mann.), Pennsylvania leatherwings (<i>Chauliognathus pennsylvanicus</i> DeGeer), Diptera (Order: Diptera), lady beetles (Order: Coleoptera, Family: Coccinellidae), hymenoptera (Order: Hymenoptera), and spiders (Order: Araneae) in a cucumber field and a bordering field of uncultivated vegetation were assessed using yellow sticky traps to determine: 1) the relative abundances of target insects across the uncultivated vegetation and the crop field, 2) relationships between target insects and plant species. In both years populations striped and spotted cucumber beetles and Pennsylvania leatherwings (only in 1995) increased significantly and Diptera decreased significantly in the direction of the crop. The strength of these relationships increased over the season to a peak in August in 1995 and July in 1996 and then decreased in September in both years. There were significant correlations between Diptera and sweet-vernal grass in 1995. In 1996, cucumber beetles were correlated with wild violet (<i>Viola</i> spp.) and white clover (<i>Trifolium repens</i>); Diptera with wild violets; and the lady beetle <i>Coleomegilla maculata</i> with goldenrod (<i>Solidago</i> spp.), English plantain (<i>Plantago lanceolata</i>), and marjoram (<i>Origanum</i> spp.) in 1996. This study demonstrated the potential value of increasing the diversity of a cucumber field to control insect pests (and thus reduce pesticide useage) as well as suggested specific plants that influenced insect populations. / Master of Science

The carnivores of Madagascar are likely the least studied of the world's carnivores, thus little is known about threats to their persistence. I provide the first long-term assessment of Madagascar's rainforest carnivore community, including: 1) how multiple forms of habitat degradation (i.e., fragmentation, exotic carnivores, human encroachment, and hunting) affect native and exotic carnivore occupancy; 2) how native and exotic carnivore temporal activity overlap and how body size and niche explain these patterns; 3) how native and exotic carnivores spatially co-occur across the landscape and which variables explain these relationships; and 4) how native and exotic carnivores and humans co-occur with lemurs across Madagascar's largest protected landscape: the Masoala-Makira landscape. From 2008 to 2013 I photographically sampled carnivores and conducted line-transect surveys of lemurs at seven study sites with varying degrees of degradation and human encroachment, including repeat surveys of two sites. As degradation increased, exotic carnivores showed increases in activity and occupancy while endemic carnivore, small mammal, and lemur occupancy and/or activity decreased. Wild/feral cats (Felis sp.) and dogs (Canis familiaris) had higher occupancy (0.37 ± SE 0.08 and 0.61 ± SE 0.07, respectively) than half of the endemic carnivore species across the landscape. Additionally, exotic carnivores had both direct and indirect negative effects on native carnivore occupancy. For example, spotted fanaloka (Fossa fossana) occupancy (0.70 ± SE 0.07) was negatively impacted by both wild/feral cat (beta = -2.65) and Indian civets (beta = -1.20). My results revealed intense pressure from hunting (ex. n = 31 fosa Cryptoprocta ferox consumed per year from 2005-2011 across four villages), including evidence that hunters target intact forest where native carnivore and lemur occupancy and/or activity are highest. I found evidence of high temporal overlap between native and exotic carnivores (ex. temporal overlap between brown-tail vontsira Salanoia concolor and dogs is 0.88), including fosa (Cryptoprocta ferox) avoiding dogs and humans across all seasons. However, I found no evidence of body size or correlates of ecological niche explaining temporal overlap among carnivores. Estimates of spatial co-occurrence among native and exotic carnivores in rainforest habitat revealed strong evidence that native and exotic carnivores occur together less often than expected and that exotic carnivores may be replacing native carnivores in forests close to human settlements. For example, falanouc show a strong increase in occupancy when dogs are absent (0.69 ± SE 0.11) compared to when they are present (0.23 ± SE 0.05). Finally, the two-species interaction occupancy models for carnivores and lemurs, revealed a higher number of interactions among species across contiguous forest where carnivore and lemur occupancy were highest. These various anthropogenic pressures and their effects on carnivore and lemur populations, particularly increases in exotic carnivores and hunting, have wide-ranging, global implications and demand effective management plans to target the influx of exotic carnivores and unsustainable hunting affecting carnivore and primate populations across Madagascar and worldwide. / Ph. D.