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Research on insect symbiosis is dominated by insect–bacteria models, however, the role of fungal symbionts in insects is poorly understood. Fungi are de novo synthesizers of many essential nutrients, therefore, insect–fungal pairings can permit specialization on nutritionally deprived diets. Here, I address the costs and benefits of symbiosis using a system of beetle–fungal symbiosis. Specifically, I ask 1) when reared on a low-quality diet, does the beetle increase the number of viable symbionts to compensate for a heightened nutritional demand, and 2) Is the conferred fitness benefit of the symbiont only present in low-quality diets? When reared on low-quality diets, there was no variation in fungal titer in beetles; moreover, there was no cost attributed to hosting symbiont populations when dietary provisions were not required. These findings contrast with many obligate insect–bacterial pairings and suggest that there is no plasticity in resource contribution between partners.

Through photosynthesis microalgae can convert sunlight, water, and CO2 into chemical energy that can be used to generate carbon neutral biofuels and biomass. With an ever-increasing demand and need for petroleum substitutes it is imperative that we improve the output of industrial-relevant crops such as microalgae. One important way of improving output in algae is by understanding the roles that stress and energy conversion is regulated in these organisms. Photosynthetic organisms fundamentally depend on light- and sugar-driven metabolic and signaling networks, which integrate environmental cues to govern and sustain growth and survival. SnRKs (SNF1-related protein kinases) and the photoreceptor neochrome are regulators of energy and stress metabolism, and coordinate energy balance and nutrient metabolism in plants. This work set to elucidate the role that these two sensors play in generating algal biomass. Further, we identified SnRKs in thirty-four algal species and analyzed their SNRK domain motifs and phylogenetic relationships. To determine the importance of the sensors in algal evolution.

Climate change related drought is projected to harm maize production. Water use strategies can help mitigate the impact of drought on crop yield. However, little is known about maize metabolic response to drought at different developmental stages. To shed light on this, drought conditions were applied to maize at the six-leaf stage (V6), twelve leaf stage (V12), and tassel stage (VT). V6 and VT took eight days to achieve a low stomatal conductance threshold, but V12 took 16 days. Differential gene expression analysis of the transcriptome indicates that V6 showed the most response with 53 impacted metabolic pathways, many of which indicated cellular damage and a reduced stress tolerance. V6 showed water conservation. Twelve and ten pathways were modulated under drought conditions at the V12 and VT stages, respectively. V12 had pathway modulation indicating water conservation and improved stress tolerance. VT responses focused on growth and development, not water conservation.

Climate change related drought is projected to harm maize production. Water use strategies can help mitigate the impact of drought on crop yield. However, little is known about maize metabolic response to drought at different developmental stages. To shed light on this, drought conditions were applied to maize at the six-leaf stage (V6), twelve leaf stage (V12), and tassel stage (VT). V6 and VT took eight days to achieve a low stomatal conductance threshold, but V12 took 16 days. Differential gene expression analysis of the transcriptome indicates that V6 showed the most response with 53 impacted metabolic pathways, many of which indicated cellular damage and a reduced stress tolerance. V6 showed water conservation. Twelve and ten pathways were modulated under drought conditions at the V12 and VT stages, respectively. V12 had pathway modulation indicating water conservation and improved stress tolerance. VT responses focused on growth and development, not water conservation.

Through photosynthesis microalgae can convert sunlight, water, and CO2 into chemical energy that can be used to generate carbon neutral biofuels and biomass. With an ever-increasing demand and need for petroleum substitutes it is imperative that we improve the output of industrial-relevant crops such as microalgae. One important way of improving output in algae is by understanding the roles that stress and energy conversion is regulated in these organisms. Photosynthetic organisms fundamentally depend on light- and sugar-driven metabolic and signaling networks, which integrate environmental cues to govern and sustain growth and survival. SnRKs (SNF1-related protein kinases) and the photoreceptor neochrome are regulators of energy and stress metabolism, and coordinate energy balance and nutrient metabolism in plants. This work set to elucidate the role that these two sensors play in generating algal biomass. Further, we identified SnRKs in thirty-four algal species and analyzed their SNRK domain motifs and phylogenetic relationships. To determine the importance of the sensors in algal evolution.

Coccidioidomycosis, caused by soil-dwelling species of Coccidioides, is endemic to the Southwestern United States. It can present as a mild respiratory illness to life-threatening disseminated infections.Multi-gene phylogenetics and tracing patient histories revealed the presence of both Coccidioides species in New Mexico, and Native Americans may represent an unrecognized risk group. A PCR method developed distinguishes Coccidioides species by targeting regions of the mitochondrial genome. Recent advancements in molecular genetics solidifies lungs are not sterile. Illumina community data from 199 small mammals from Arizona, California, and New Mexico demonstrated a great diversity of fungi inhabiting lung tissues. One dominant order, Onygenales, contained a high diversity of animal pathogens including Coccidioides and Blastomyces parvus. Coccidioides sequences were detected in 14 species, in relatively low abundance, and the presence of these sequences did not correlate with shifts in the overall mycobiome. Using both clinical and small mammal lung data, we can determine the distribution of Coccidioides in New Mexico and the greater Southwest.

Coccidioidomycosis, caused by soil-dwelling species of Coccidioides, is endemic to the Southwestern United States. It can present as a mild respiratory illness to life-threatening disseminated infections.Multi-gene phylogenetics and tracing patient histories revealed the presence of both Coccidioides species in New Mexico, and Native Americans may represent an unrecognized risk group. A PCR method developed distinguishes Coccidioides species by targeting regions of the mitochondrial genome. Recent advancements in molecular genetics solidifies lungs are not sterile. Illumina community data from 199 small mammals from Arizona, California, and New Mexico demonstrated a great diversity of fungi inhabiting lung tissues. One dominant order, Onygenales, contained a high diversity of animal pathogens including Coccidioides and Blastomyces parvus. Coccidioides sequences were detected in 14 species, in relatively low abundance, and the presence of these sequences did not correlate with shifts in the overall mycobiome. Using both clinical and small mammal lung data, we can determine the distribution of Coccidioides in New Mexico and the greater Southwest.

Fungi perform several critical functions in the environment. Spatiotemporal distributions of fungal communities will mediate when and where these functions happen and how they vary across the landscape. I first explored tropical tree canopy fungal community variation at small spatial scales and documented near total turnover of fungi across sub-meter distances and among adjacent substrates. The second chapter analyzed fungal turnover over the course of three years, where community stability was driven primarily by abundant fungi. In the third chapter, I tested effects of the environment, including host plant and habitat, on canopy fungal communities and found only small effects, indicating high stochasticity. Finally, I used a greenhouse bioassay to demonstrate that microbial spatial variability impacts plant performance. These results show that fungal communities are spatially variable at small scales, this variability is largely stochastic, and fungi are a source of cryptic environmental heterogeneity with impacts on plant community dynamics.

Fungi perform several critical functions in the environment. Spatiotemporal distributions of fungal communities will mediate when and where these functions happen and how they vary across the landscape. I first explored tropical tree canopy fungal community variation at small spatial scales and documented near total turnover of fungi across sub-meter distances and among adjacent substrates. The second chapter analyzed fungal turnover over the course of three years, where community stability was driven primarily by abundant fungi. In the third chapter, I tested effects of the environment, including host plant and habitat, on canopy fungal communities and found only small effects, indicating high stochasticity. Finally, I used a greenhouse bioassay to demonstrate that microbial spatial variability impacts plant performance. These results show that fungal communities are spatially variable at small scales, this variability is largely stochastic, and fungi are a source of cryptic environmental heterogeneity with impacts on plant community dynamics.

The McMurdo Dry Valleys (MDV) of Antarctica are on the threshold of widespread landscape scale change due to increasing temperature and solar radiation and altered hydrology: buried ice is melting, the soil active layer is thickening, thermokarst features are developing along streams, water tracks are expanding, and lake levels are rising. These changes will impact the microbial communities found in each of the affected habitats. The purpose of this work is to first, understand the spatial distribution of soil bacteria in the MDV, specifically investigating the scale-dependent effects of environmental heterogeneity, and second, to perform surveys and coupled experiments to document and assess the impacts of these changes on the associated microbial communities. Our results suggest that this region harbors highly adapted, endemic communities that are susceptible to changing environmental conditions.

The arrival of white-nose syndrome (WNS), a devastating fungal disease, has highlighted the need to better understand bat microbiota and how bats acquire their microbiota. To address this need, we investigated how bat microbiota compare to microbiota from the cave walls in two El Malpais National Monument caves. The external surfaces of six roosting bats from each cave, representing four different bat species, and their associated microbial mats were sampled. One to three air samples were taken in each cave. Samples were sequenced using Illumina MiSeq sequencing of the 16S rRNA gene for bacterial diversity and the ITS region for fungal diversity. Many bacterial and fungal operational taxonomic units (OTUs) were shared among the sample types. Within the bacterial OTUs, Actinobactria were highest overall in all samples, but were higher in bats than mats. The most prevalent actinobacterial genera recovered were Rhodococcus, Streptomyces, Arthrobacter, and Rubrobacter. SourceTracker suggested bat bacterial communities may originate from mat and air samples. Within the fungal OTUs, Ascomycota were highest overall in all samples, but higher in bats than mats. Prevalent fungal families included Cladosporiaceae, Pleosporaceae, Pseudeurotiaceae, Microascaceae, Leucosporidiaceae, and Mortierellaceae. A top fungal OTU recovered was a close relative of Pseudogymnoascus destructans, the cause of WNS. Our results shed light on a relatively understudied area that could have implications for understanding the source of potential natural defenses of bats, which could be important in predicting which western bats species are most vulnerable to WNS.

My doctoral work focused on understanding the reciprocal relationship between fungi and their environment, namely how fungi respond to environmental flux, as well as how fungi can modify and structure their habitats, especially in the context of climate change. As such, I aimed my research on fungi with distinct adaptations to their environmental niches: endophytic fungi that inhabit plant tissue and thermophilic fungi that are capable of growing at the upper temperature limit for eukaryotic life. My research consisted of three studies. First, I investigated the thermophilic species Myceliophthora heterothallica to demonstrate its use as a model organism for efficient cellulose decomposition by identifying its optimal growth and reproductive conditions, as well as the genes involved in mating. In experiments, M. heterothallica proved to be a tractable organism for genetic manipulation as it was easily grown and successfully mutagenized, and strains could be readily crossed. Sequencing of genomes for several strains of M. heterothallica as well as related species led to the discovery that the structure of the mating-type region of heterothallic (outcrossing) species is atypical when compared to related groups in the same order. Although thermophilic fungi are well understood in applied science, their ecology is still unclear. Therefore, in a second study I surveyed a transect in western North America, spanning from Mexico in Canada, in attempts to define the biogeography of fungal thermophiles. Using culture-based methods, I found that thermophilic fungi can be isolated from a variety of substrates and from diverse habitats. Similar to results from previous studies, there was little specificity to their distribution, but the frequency of recovery showed a reciprocal relationship with latitude. For my final study, I conducted a survey on a more local scale at the Sevilleta National Wildlife Refuge. I collected roots from creosote (Lar

The arrival of white-nose syndrome (WNS), a devastating fungal disease, has highlighted the need to better understand bat microbiota and how bats acquire their microbiota. To address this need, we investigated how bat microbiota compare to microbiota from the cave walls in two El Malpais National Monument caves. The external surfaces of six roosting bats from each cave, representing four different bat species, and their associated microbial mats were sampled. One to three air samples were taken in each cave. Samples were sequenced using Illumina MiSeq sequencing of the 16S rRNA gene for bacterial diversity and the ITS region for fungal diversity. Many bacterial and fungal operational taxonomic units (OTUs) were shared among the sample types. Within the bacterial OTUs, Actinobactria were highest overall in all samples, but were higher in bats than mats. The most prevalent actinobacterial genera recovered were Rhodococcus, Streptomyces, Arthrobacter, and Rubrobacter. SourceTracker suggested bat bacterial communities may originate from mat and air samples. Within the fungal OTUs, Ascomycota were highest overall in all samples, but higher in bats than mats. Prevalent fungal families included Cladosporiaceae, Pleosporaceae, Pseudeurotiaceae, Microascaceae, Leucosporidiaceae, and Mortierellaceae. A top fungal OTU recovered was a close relative of Pseudogymnoascus destructans, the cause of WNS. Our results shed light on a relatively understudied area that could have implications for understanding the source of potential natural defenses of bats, which could be important in predicting which western bats species are most vulnerable to WNS.

The McMurdo Dry Valleys (MDV) of Antarctica are on the threshold of widespread landscape scale change due to increasing temperature and solar radiation and altered hydrology: buried ice is melting, the soil active layer is thickening, thermokarst features are developing along streams, water tracks are expanding, and lake levels are rising. These changes will impact the microbial communities found in each of the affected habitats. The purpose of this work is to first, understand the spatial distribution of soil bacteria in the MDV, specifically investigating the scale-dependent effects of environmental heterogeneity, and second, to perform surveys and coupled experiments to document and assess the impacts of these changes on the associated microbial communities. Our results suggest that this region harbors highly adapted, endemic communities that are susceptible to changing environmental conditions.

My doctoral work focused on understanding the reciprocal relationship between fungi and their environment, namely how fungi respond to environmental flux, as well as how fungi can modify and structure their habitats, especially in the context of climate change. As such, I aimed my research on fungi with distinct adaptations to their environmental niches: endophytic fungi that inhabit plant tissue and thermophilic fungi that are capable of growing at the upper temperature limit for eukaryotic life. My research consisted of three studies. First, I investigated the thermophilic species Myceliophthora heterothallica to demonstrate its use as a model organism for efficient cellulose decomposition by identifying its optimal growth and reproductive conditions, as well as the genes involved in mating. In experiments, M. heterothallica proved to be a tractable organism for genetic manipulation as it was easily grown and successfully mutagenized, and strains could be readily crossed. Sequencing of genomes for several strains of M. heterothallica as well as related species led to the discovery that the structure of the mating-type region of heterothallic (outcrossing) species is atypical when compared to related groups in the same order. Although thermophilic fungi are well understood in applied science, their ecology is still unclear. Therefore, in a second study I surveyed a transect in western North America, spanning from Mexico in Canada, in attempts to define the biogeography of fungal thermophiles. Using culture-based methods, I found that thermophilic fungi can be isolated from a variety of substrates and from diverse habitats. Similar to results from previous studies, there was little specificity to their distribution, but the frequency of recovery showed a reciprocal relationship with latitude. For my final study, I conducted a survey on a more local scale at the Sevilleta National Wildlife Refuge. I collected roots from creosote (Lar

Asymmetric cell division (ACD) is important for cell fate and tissue patterning. Many aspects of ACD in plants, however, are still unclear. The process of ACD can be broadly broken down into three phases: (1) cell polarization, (2) division plane establishment and maintenance, and (3) cell division and cytokinesis. Stomatal development in maize has proven to be a useful model for understanding the ACD mechanism. Previous studies have identified several proteins important for all three phases of ACD. Actin is important in each of the phases of ACD, suggesting an actin motor such as myosin may also be important for ACD. Opaque1 (O1) was previously identified as a gene encoding a maize myosin XI important for protein body localization in seeds (G. Wang et al., 2012). The role of O1 in ACD in maize stomata was investigated. Asymmetric stomata divisions were abnormal in o1 mutants; however asymmetrically dividing cells in o1 mutants polarize normally. This suggests O1 is required for ACD but may not be important for cell polarization. Multiple defects in microtubule-based cell division structures, which are important for division plane establishment and cytokinesis, were observed in the o1 mutant. O1 localizes to a plant-specific cell division structure, the phragmoplast, in asymmetrically and symmetrically dividing cells. Together this data suggest that O1 plays multiple roles in asymmetrically dividing cells.

Asymmetric cell division (ACD) is important for cell fate and tissue patterning. Many aspects of ACD in plants, however, are still unclear. The process of ACD can be broadly broken down into three phases: (1) cell polarization, (2) division plane establishment and maintenance, and (3) cell division and cytokinesis. Stomatal development in maize has proven to be a useful model for understanding the ACD mechanism. Previous studies have identified several proteins important for all three phases of ACD. Actin is important in each of the phases of ACD, suggesting an actin motor such as myosin may also be important for ACD. Opaque1 (O1) was previously identified as a gene encoding a maize myosin XI important for protein body localization in seeds (G. Wang et al., 2012). The role of O1 in ACD in maize stomata was investigated. Asymmetric stomata divisions were abnormal in o1 mutants; however asymmetrically dividing cells in o1 mutants polarize normally. This suggests O1 is required for ACD but may not be important for cell polarization. Multiple defects in microtubule-based cell division structures, which are important for division plane establishment and cytokinesis, were observed in the o1 mutant. O1 localizes to a plant-specific cell division structure, the phragmoplast, in asymmetrically and symmetrically dividing cells. Together this data suggest that O1 plays multiple roles in asymmetrically dividing cells.