MS, Kent State University, 2016, College of Arts and Sciences / Department of Biological Sciences

Through close interactions with biotic and abiotic environments, microbial communities in lakes mediate numerous biogeochemical processes that are essential in regional and global cycles of C, N and P. However, the relationship between bacterial community compositions and environmental conditions is still unclear. Lake Erie's natural gradient of nutrient supply and many other environmental parameters from the Sandusky Bay to the Central Basin provides an ideal experiment to examine how well bacterial community composition tracks environmental changes spatially and temporally. Surface water samples were collected along a transect that ran from the Sandusky Bay (hypereutrophic) via Sandusky Sub-basin (mesoeutrophic) to the Central Basin (oligotrophic) in June, July and August 2012. Zooplankton sample were also collected at each basin in June, July and August to see whether they respond to environmental conditions and to the changing bacterioplankton communities. Physico-chemical parameters were measured in situ. Bacterioplankton was collected on filters and filtrates were used for nutrient analyses, including ammonium, dissolved organic carbon, total dissolved nitrogen, nitrate, nitrite and soluble reactive phosphorus. Chlorophyll a concentration measurements confirmed the expected gradient of primary productivity among sites. Terminal restriction fragment length polymorphism (T-RFLP) analysis was conducted to compare of the microbial community structure and diversity along this natural gradient from the Sandusky Bay to the Central Basin. Additionally, zooplankton community structure and diversity was compared along the transect. Results showed that the free-living bacterioplankton structure differed significantly among sampling time, which was likely contributed by temporal variations in nutrient concentrations. As for the zooplankton community, Cyclopidae, Branchionidae and Synchaetidae were identified as major families (>78.4% of total zooplankton) in all samples. (open full item for complete abstract)

Committee: Xiaozhen Mou (Advisor) Subjects: Aquatic Sciences; Biogeochemistry; Biology; Conservation; Ecology; Environmental Science; Experiments; Freshwater Ecology; Limnology; Microbiology; Molecular Biology; Toxicology

Master of Science in Chemistry, Youngstown State University, 2008, Department of Chemistry

This research was conducted to determine changes in the microbial community in contaminated sediment during fungal remediation of polycyclic aromatic hydrocarbon (PAH) contaminated Mahoning River sediment. The fungus used for remediation was Pleurotus ostreatus, white rot fungi which is capable of degrading a wide range of organic contaminants including PAHs. Microbial community structure was determined using fatty acid profiles from microbial lipids extracted directly from the sediment. Contaminated sediment was collected from Lowellville, OH and was incubated at 25 °C. There were 4 treatments (1 liter of contaminated river sediment) done in duplicate runs as follows: 1) untreated sediment, 2) sediment amended with sawdust, 3) sediment amended with sawdust and augmented with Pleurotus ostreatus and, 4) sediment amended with sawdust, augmented with Pleurotus ostreatus and amended with extra nitrogen after 21 days. At day 0, 21, and 42, lipids were extracted from each treatment (in triplicate). Microbial fatty acids were purified from the lipid extract, methylated and analyzed by GC-MS. The sediment microbial community structure showed great heterogeneity shown as high variability within triplicate samples and as differences between duplicate treatments. Groups of anaerobic bacteria (sulfate reducers and methanogens) persisted throughout the treatments, even though they were exposed to oxygen during mixing and from the surface during the incubation. The abundance of gram negative bacteria, a group of bacteria associated with PAH degradation, showed highest relative abundance on day 42. Even though the microbial structure changed, the microbial biomass (measured as lipid phosphate) remained consistent between triplicate samples and duplicate runs, and changed little during the incubation.

Committee: Carl Johnston PhD (Advisor); Roland Riesen PhD (Committee Member); Daryl Mincey PhD (Committee Member) Subjects: Biology; Chemistry; Environmental Science

Master of Science, The Ohio State University, 2008, Food Agricultural and Biological Engineering

Composting offers the potential to significantly reduce problems associated with manure management including odors, pathogens, ground water pollution, and utilization costs. Two variables that directly affect on-farm composting costs are windrow size and windrow turning frequency. However the size of a windrow is limited by the depth of penetration of oxygen and high temperatures as well as available equipment. In this study three full scale compost sets were set-up at the Ohio Agricultural Research and Developing Center (OARDC) compost pad to evaluate the effects of turning frequency, pile size and seasonal variability on physical (temperature, oxygen, bulk density, moisture and weigh loss), chemical (volatile solid loss, pH, Carbon and Nitrogen concentrations) and biological (plant growth bioassays and microbial community structure) parameters during dairy manure/sawdust composting (DM+S). Based on these data the operational costs for producing and transporting compost were estimated and compared to those for liquid manure and fertilizer. The three treatments consisted of a set of windrows (A) which were turned using a self propelled and tractor drawn windrow turner every three days for a total of 32 turns during 16 weeks, a second set (B) that was turned once every ten days and a third set (C) consisting of much larger piles turned that was also turned every ten days with a loader. All three sets were composted in both winter and summer for 120 days. The hypotheses of the study was that; turning frequency, pile size and season do not significantly affect compost process parameters or the final chemical, physical or biological properties of cured composts. Results showed that neither physical chemical nor biological properties of the final cured composts were significantly affected by turning frequency, season or pile size (p > 0.05). During composting, he the surface area, oxygen concentrations and Total nitrogen losses were significantly affected by pile size ( (open full item for complete abstract)

Committee: Frederick Michel PhD (Advisor); Harold Keener PhD (Committee Member); Brian McSpadden Gardener PhD (Committee Member); Warren Dick PhD (Committee Member) Subjects: Agricultural Engineering

Doctor of Philosophy, The Ohio State University, 2019, Microbiology

The Arctic system has been undergoing a rampant change during the Anthropocene. This anthropogenic change has allowed for additional physical and biological positive feedback processes that in turn accelerate warming in the arctic and subarctic systems. Microbial community/functional dynamics are both (i) dramatically impacted by these rapid changes and (ii) key players in the biological positive feedback process that accelerates the change. Recent technological, analytical, and computational advances have allowed us to ask systems-level questions that encompass microbial and viral community dynamics (along with their potential functional dynamics) and high-resolution environmental measurements. This research took a systems-level approach to look for the first time at (i) the characteristics of Arctic marine viruses in a global context, and (ii) microbial community gene expression in a rapidly changing permafrost thaw gradient. Additionally, novel viral sequences recovered from the marine and terrestrial ecosystems studied here were used to build new resources and tools that accelerate viral discovery in nature. First, studying marine viral macro- and microdiversity from the Arctic Ocean to the Southern Ocean, enabled by the Tara Oceans Expedition, revealed the Arctic Ocean as a hotspot of viral diversity, with ~42% of the recovered viral populations originating from the Arctic Ocean viromes. In total 195,728 viral populations >10 kb were recovered from the global ocean to constitute the Global Ocean Viromes 2.0 (GOV2.0) dataset. Viral communities assorted into five distinct global ecological zones and the arctic viral communities formed their own distinct ecological zone. Additionally, this work revealed unexpected patterns and ecological drivers of viral diversity (at the community, inter-, and intrapopulation levels), within the Arctic Ocean, across latitudes, and across the depth of the global ocean. Second, genome-resolved metaproteomic study of microbial gene (open full item for complete abstract)

Committee: Matthew Sullivan (Advisor); Virginia Rich (Advisor); Kelly Wrighton (Committee Member); Alvaro Montenegro (Committee Member) Subjects: Biogeochemistry; Bioinformatics; Biological Oceanography; Biology; Climate Change; Ecology; Environmental Science; Geobiology; Microbiology; Oceanography; Soil Sciences; Statistics; Virology

Master of Science, The Ohio State University, 2023, Environmental Science

As increases in frequency, duration, intensity, and geographical location of cyanobacterial harmful algal blooms (HABs) have been observed, more timely monitoring and targeted treatment of HABs and their cyanotoxins are crucial for freshwater bodies that are used for drinking water, recreation, and food production sources. To combat this, new management practices with tools that can handle the spatial and temporal variability of HABs are needed for water treatment plants and other sectors to ensure human health and ecosystem health. Unmanned Aerial Vehicles (UAVs), also known as drones, serve as one solution for near real-time monitoring of HABs. Recently, UAVs have gained increasing interest in research and development due to their many applications, efficiency in data collection, and the ability to customize these systems to specific needs. While research has shown that UAVs can accurately estimate chl-a and phycocyanin values -HAB indicators- little research has been conducted analyzing UAV imagery in parallel with microbiome data. In chapter 1, I summarize major relevant topics are summarized related to cyanoHABs, public health, and UAV systems. This provides a holistic view of current knowledge, methods, and limitations in cyanoHAB monitoring and detection. Chapter 2 seeks to explore the microbial community in parallel with environmental data, by analyzing seasonal dynamics, composition, and interactions within the microbial community in a hypereutrophic urban lake. In chapter 3, the feasibility and accuracy of using an UAV system for monitoring a hypereutrophic, urban water body was assessed. Objectives of this chapter include 1) proposing an UAV system and imagery processing framework that can be utilized by non-geospatial experts, 2) assess the accuracy of UAV derived chlorophyll-a values by regressing ground sampled fluorometer values and remotely sensed values, and 3) determine what algorithms and buffer sizes perform the best for cyanobacteria quantific (open full item for complete abstract)

Committee: Jiyoung Lee (Advisor); Joseph Ortiz (Committee Member); Motomu Ibaraki (Committee Member); Rongjun Qin (Committee Member) Subjects: Environmental Science; Microbiology

Doctor of Philosophy, The Ohio State University, 2022, Nutrition Program, The Ohio State University

Branched-chain amino acids (BCAA; valine, isoleucine, and leucine) can be deaminated by many amylolytic bacteria to branched-chain volatile fatty acids (BCVFA, isobutyrate, 2-methylbutyrate, and isovalerate), which are growth factors for some cellulolytic bacteria. Many cellulolytic bacteria cannot uptake BCAA or decarboxylate them, thus depending on cross feeding for BCVFA precursors for carboxylation to BCAA or synthesis of branched-chain fatty acids (BCFA; iso even-chain, iso odd-chain, and anteiso odd-chain) and branched-chain aldehydes (BCALD) found in bacterial phospholipid and plasmalogens, respectively. Supplemental BCVFA and valerate, a straight-chain volatile fatty acid (VFA) that is also a growth factor for some rumen bacteria, have been previously supplemented together in a combination commonly referred to as ‘isoacids'. However, prior in vivo studies have either provided only one BCVFA individually or all BCVFA and valerate but not different combinations of isoacids. Our objective in the first study was to determine an optimal combination of isoacids. Sixty (28 primiparous and 32 multiparous) lactating Jersey cows (106 ± 54 days in milk) were blocked and randomly assigned to either a control (CON) treatment without any isoacids, 2-methylburtyate (MB, 12.3 mmol/kg DM), 2-methylbutyrate and isobutyrate (MB + IB, 7.7 and 12.6 mmol/kg DM of MB and IB), or all 4 isoacids (ISO, 6.2, 7.3, 4.2, and 5.1 mmol/kg DM of MB, IB, isovalerate, and valerate, respectively). The CON diet was fed for 2-wk covariate period, then cattle were fed their assigned treatment for the 8-wk sampling period (n=15). Daily intake and milk yield were recorded and samples from 4 consecutive milkings a week were analyzed for milk components. The milk fatty acid profile was analyzed on wk 5 and wk 9. Treatment tended to interact with parity for both fat and protein concentrations. Primiparous cows did not differ by treatment, whereas multiparous cows supplemented with MB + IB tended to h (open full item for complete abstract)

Committee: Jeffrey Firkins (Advisor); Zhongtang Yu (Committee Member); Robin White (Committee Member); Chanhee Lee (Committee Member) Subjects: Animal Sciences; Microbiology; Nutrition

Doctor of Philosophy, The Ohio State University, 2022, Food, Agricultural and Biological Engineering

The United Nations aims to have sanitation access for all by 2030. Lack of sanitation is a global crisis tied to water availability, environmental pollution, human health, personal dignity, and nutrient loss. This dissertation focuses on a sustainable sanitation solution for coastal areas, namely on-site sanitation with urine diversion and seawater toilet flushing. The main concepts explored are salinity impacts on microbial communities in treatment systems, ability of a septic-tank/intermittent sand bioreactor system to treat seawater-salinity septic-tank effluent and the barriers and facilitators to adoption of urine diversion dry toilets. These three concepts answer fundamental questions about dilution requirements for seawater wastewater and social acceptance of urine diversion systems. Results show that urine diversion seawater toilet flushing with septic tanks and intermittent sand bioreactor treatment systems could feasibly produce discharge-quality effluent and gain social acceptance.

Committee: Karen Mancl (Advisor); Jay Martin (Committee Member); Linda Lobao (Committee Member); Ann Christy (Committee Member) Subjects: Bioinformatics; Ecology; Engineering; Environmental Engineering; Environmental Science; Microbiology; Public Health; Sanitation; Sociology; Sustainability; Water Resource Management

PHD, Kent State University, 2022, College of Arts and Sciences / Department of Biological Sciences

Microplastics are a global concern in aquatic ecology and are readily colonized by bacteria in the environment. There is a lack of information on bacterial colonization of eroded and un-eroded microplastics in freshwater. In this study, six types of microplastics were incubated for 8 weeks in microcosms with water from Lake Erie. Microcosms were inoculated with one of three species: Acinetobacter (A.)calcoaceticus, Burkholderia (B.)cepacia, and Escherichia (E.)coli. These bacterial species are ubiquitous in water bodies associated with human populations. Bacterial surface coverage was determined using electron and fluorescent microscopy. Quantifications of EPS and surface roughness were performed by confocal microscopy and measuring contact angles (θw) of water droplets on microplastics, respectively. Analyses revealed surface coverage differed among bacterial species and plastic types after 8 weeks. As the study progressed, E.coli remained the most abundant while A.calcoaceticus gradually decreased on most surfaces. Analyses of microcosms revealed polypropylene disks had lower bacterial abundance. Conversely, eroded polypropylene disks had highest bacterial abundance, indicating importance of surface roughness (lower θw values) and surface physicochemical properties of microplastics in bacterial colonization. Our results demonstrated that bacterial colonization of microplastics is affected by both the physicochemical properties of microplastics and the physiological properties of colonizing bacteria.

Committee: Laura G. Leff (Advisor); Christopher Blackwood (Committee Member); Daniel Holm (Committee Member); Tara Smith (Committee Member); Xiaozhen Mou (Committee Member) Subjects: Materials Science; Microbiology; Molecular Biology; Plastics

Doctor of Philosophy, University of Akron, 2021, Integrated Bioscience

Caves provide a unique environment for studying microbial ecology, providing a portal to the microbial communities of the terrestrial subsurface. Despite the geologic isolation and nutrient limitation of growth in the subsurface, caves contain remarkably diverse microbial communities, with unique adaptations that allow community subsistence and growth. At Wind Cave National Park, South Dakota, a series of lakes are formed at the intersection of Wind Cave and the regionally important Madison aquifer. These lakes (WCL), provide a rare natural window into the aquifer, and my research has demonstrated that they allow us to examine the microbial community of a karst aquifer without the sources of contamination often associated with surface drilling. Though the isolation (125 m below the surface) and long residence time (~25 years) of water en route to the lakes results in ultraoligotrophic conditions (0.29 mg L-1 TOC), the lakes support a stable and diverse community of microbes, albeit with cell numbers lower than almost any body of water on Earth (~2,300 cells mL-1). This low biomass, combined with a reduced cell size as an adaptive strategy to survival in these nutrient limited conditions, made collecting sufficient cell mass for DNA based analyses problematic. I therefore optimized the standard techniques used to sample aquatic communities, using tangential flow filtration to filter more than 1,000 L of water from the Madison aquifer, through a 45 nm-pore size membrane allowing the capture of even the smallest cells within this microbial ecosystem. Metagenomic sequencing combined with comparative filtration revealed that WCL was enriched in ultrasmall cells, such as those found in the Patescibacteria and Nitrospirota. Evidence of integron-facilitated genetic plasticity suggests that metabolic flexibility is an important mechanism for adaptation and survival in WCL. Finally, our metagenomic and phylogenetic data suggest that manganese plays a central role in primary p (open full item for complete abstract)

Committee: Hazel Barton (Advisor); John Senko (Committee Member); Michael Konopka (Committee Member); Zhong-Hui Duan (Committee Member); R. Joel Duff (Committee Member) Subjects: Biogeochemistry; Biology; Microbiology

Doctor of Philosophy, The Ohio State University, 2020, Earth Sciences

Upland catchments play an outsized role in the processing and export of water, sediments, nutrients, and organic matter, thus strongly influencing downstream water quality. In Chapter 1, an overview of biogeochemical cycling within upland fluvial sediments is presented, focusing on key regional biogeochemical cycling patterns and solute export processes. Additionally, anthropogenic influences on this environment, such as historical mining activities and climate change, are briefly reviewed in this chapter. Chapter 2 explores the relationship between spatial hydrologic heterogeneity and microbial community assembly and functional potential within the hyporheic zone. The region of groundwater and river water mixing, known as the hyporheic zone, is a hotspot of microbial activity that influences solute export and cycling in rivers. Hyporheic mixing patterns can vary over small spatial scales, leading to heterogeneity in fluid chemistry and microbial community composition and function. Here, we integrate new mass-spectrometry data, metagenomic insights, and ecological models with previous analyses of microbial community composition and dissolved organic matter (DOM) quality to understand spatial relationships between hyporheic flow and microbial community assembly, metabolism, and DOM processing at high-resolution (100 locations) along a 200 m meander of East River, Colorado (USA). Ecological modeling revealed a strong linkage between community assembly patterns and underlying hydrologic and geochemical drivers, including the impact of physical heterogeneity (riverbed grain size) on microbial community structure. Geochemical profiles associated with upwelling groundwater suggest the influence of underlying geology, specifically Mancos-derived solutes, in driving community assembly. Distinct microbial community profiles and functional potential in zones of upwelling groundwater suggest that groundwater chemistry may have a greater influence on biogeochemical cycling wi (open full item for complete abstract)

Committee: Michael Wilkins (Advisor); Steven Lower (Advisor); Audrey Sawyer (Committee Member); Elizabeth Griffith (Committee Member) Subjects: Biogeochemistry; Earth; Ecology; Environmental Geology; Environmental Science; Geobiology; Geochemistry; Geology; Hydrology; Limnology; Microbiology; Mineralogy

Master of Science, Miami University, 2019, Microbiology

Communities of microorganisms play an important role in nutrient cycling within aquatic environments as they transform nutrients from organic and dissolved forms to inorganic forms. In wastewater treatment plants, this role is utilized to remove excess nutrients and clean the wastewater. In eutrophic freshwater lakes, microorganisms support the higher food web through the microbial loop. In this study, the microbial communities in the aeration tank of seven wastewater treatment plants as well as in the water column and sediment of two eutrophic lakes are determined and compared using next generation sequencing techniques. The microbial communities in the wastewater treatment plants are very similar, indicating the same microorganisms are carrying out the same processes. The microbial communities in the sediments and water column of both lakes are different from each other while overlap could be detected between the communities in the water columns and sediments of the different lakes. While the wastewater treatment plants and eutrophic lakes are high nutrient aquatic environments, the environmental factors in each are different and result in different microbial communities adapted to the conditions in each environment.

Committee: Annette Bollmann (Advisor); Rachael Morgan-Kiss (Committee Member); Xin Wang (Committee Member) Subjects: Microbiology

PHD, Kent State University, 2018, College of Arts and Sciences / Department of Biological Sciences

This project investigated the effects of cyanobacterial biomass on the community composition of heterotrophic bacteria and the effects of selected isolates from heterotrophic bacterial communities on the morphology of bloom-forming cyanobacteria. First, samples were collected from cyanobacterial blooms in three eutrophic lakes. High-throughput sequencing was used to characterize free-living (FL) bacterial communities and those bacterial communities that were directly associated with cyanobacterial biomass, designated as cyanobacteria-associated (CA) communities. The composition and diversity of FL and CA communities were compared within lakes and across lakes. Though diversity estimates did not vary, composition differed significantly by lake, sampling date, and whether the community was free-living or cyanobacteria-associated. The next stage of the project explored how the morphology of the common bloom-forming cyanobacterium Microcystis aeruginosa could change in response to heterotrophic bacterial neighbors. Bacteria isolated from the CA community during a Microcystis bloom in one of the lakes were co-cultured with predominantly unicellular strains of toxic and non-toxic strains of M. aeruginosa to determine whether isolates could promote colony formation in M. aeruginosa. Isolates which exhibited colony-promoting abilities were selected for further testing to investigate the mechanism by which they could influence Microcystis morphology. Toxic and non-toxic M. aeruginosa were treated with cell-free exudates of bacterial isolates. The morphology, polysaccharide content, and reflectance spectra of M. aeruginosa in each treatment group were compared to those of M. aeruginosa control cultures. Six bacterial isolates belonging to the families Pseudomonadaceae and Bacillaceae enhanced the frequency or size of M. aeruginosa colonies in cultures where a dialysis barrier prevented physical contact between heterotrophic cells and cyanobacterial cells. Toxic and non-to (open full item for complete abstract)

Committee: Laura Leff Ph.D. (Advisor) Subjects: Aquatic Sciences; Biology; Ecology; Environmental Science; Microbiology

Master of Science (MS), Ohio University, 2018, Plant Biology (Arts and Sciences)

Nitrogen deposition has increased the nitrogen content in soils in the unglaciated Allegheny plateau maybe to the point of saturation, which can limit the availability of phosphorus in the acidic, low-phosphorus soils of this region. The soil microbial community plays a critical role in increasing phosphorus availability through the secretion of phosphorus-acquiring extracellular enzymes to “mine” for organic phosphorus. However, there is a lack of fine-scale data on the community members that are directly involved in the mining of phosphorus, e.g. the microbial bioindicators of low-phosphorus soils. In this study, I used data generated in 2014 from the pyrosequencing of the soil microbial community present in an Eastern deciduous forest to determine if there are any observable microbial bioindicators of low-phosphorus availability. Conversely, if there are no candidate bioindicators, I hypothesized that phosphorus mining is a common trait among the soil microbial community. To test these hypotheses, fungal and bacterial DNA was extracted from a long-term research site in the unglaciated Allegheny Plateau. Since 2009, naturally acidic, low-phosphorus soils were fertilized with a phosphate fertilizer to directly increase phosphorus availability and lime to raise pH and indirectly increase phosphorus availability. Metagenomic community analysis revealed several candidate bioindicators of low-phosphorus availability and potential miners of recalcitrant phosphorus, as well as candidate bioindicators of phosphorus abundance.

Committee: Jared DeForest (Advisor); Sarah Wyatt (Committee Member); Erin Murphy (Committee Member) Subjects: Microbiology; Soil Sciences

Master of Science, The Ohio State University, 2018, Environment and Natural Resources

The herbicide glyphosate (N-(phosphonomethyl) glycine) was first introduced in 1974 as a non-selective, broad spectrum, post-emergent agrochemical, branded under the trade name Roundup® and intended to control weed competition in agricultural farming. It gained large popularity and increased usage in 1996 with the introduction of glyphosate resistant soybean (Glycine max) cultivars and again in 1998 with resistant corn (Zea mays) cultivars. Its widespread usage has increased the concern of unknown long-term effects on the soil rhizosphere microbial community. In the same long-term context there is also increased concern over glyphosate's toxicity and accumulation of degradation products, notably aminomethylphosphponic acid (AMPA), which accounts for the majority of detected metabolites in the soil. Chapter one of this thesis will review the current literature on the toxicity and degradability of glyphosate and AMPA in the soil. In chapter two of this thesis a long-term glyphosate greenhouse experiment was designed with two main objectives, (1) determine the effects of long-term glyphosate application for three different glyphosate formulations on glyphosate resistant (GR) soybean rhizosphere microbial communities of two different soil managements, one with and one without a history of glyphosate exposure, and (2) use stable isotope probing (SIP) to identify possible glyphosate degrading microbial functional groups in these two soil managements. The objective of chapter three was to expand on chapter two by investigating the accumulation of glyphosate and AMPA in both the rhizosphere and bulk soil of the same long-term glyphosate greenhouse experiment. Research from a greenhouse study showed that repeated application of glyphosate increased the abundance of gram-negative microorganisms relative to a single application as detected by FAMEs. Likewise a field study also showed that repeated application of glyphosate increased Fusarium fungal colonization on both corn an (open full item for complete abstract)

Committee: Richard Dick (Advisor) Subjects: Agricultural Chemicals; Agriculture; Microbiology; Soil Sciences

Master of Science, The Ohio State University, 2017, Environmental Science

In the face of widespread food insecurity and extreme population growth in sub-Saharan Africa, sustainable, resilient systems are needed to increase agricultural yields that can remediate degraded soils. Agroforestry is one of the suggested strategies and shows some promise. Piliostigma reticulatum and Guiera senegalensis are two indigenous woody species that currently grow interspersed in farmers' fields in Senegal and throughout the Sahel. Shrub management consists of coppicing and burning the above ground biomass before planting. Previous research has shown that decomposition of above ground biomass contributes to soil organic matter and carbon, nitrogen content and phosphorus availability in soils. Hydraulic lift from the long tap roots redistributes moisture to upper soil horizon. In addition, root exudates and root turnover also create ideal habitats for soil microbes. The collective benefits of shrubs on soils results in `resource islands' across the Sahalien landscape. Optimized intercropping with Piliostigma reticulatum and Guiera senegalensis have been shown to increase yields in groundnut (Arachis hypogaea) and pearl millet (Pennisetum glaucum) (Dossa et al., 2012, 20132; Bright et al., 2017). Research has shown that shrubs can promote microbial diversity and activity beneath the canopy of these shrubs over soil outside the influence of shrubs (Deidhou et al., 2009). However, little is known on whether this shift also occurs in the rooting zone of crops growing adjacent to shrubs. Therefore, the first objective of this research was to characterize the effect G. senegalensis and P. reticulatum have on soil microbial communities in a shrub-millet intercropping systems in farmers' fields spanning across a rainfall gradient. A fatty acid methyl ester (FAME) extraction and MIDI microbial biomarker library were used to create a community profile on samples from shrub root zones, millet root zones within shrub influence and millet root zones outside of shrub (open full item for complete abstract)

Committee: richard dick (Advisor); nick basta (Committee Member); olli tuovinen (Committee Member) Subjects: Agriculture; Microbiology; Soil Sciences

Master of Science, The Ohio State University, 2017, Microbiology

Permafrost, which stores approximately 50% of global soil carbon, is thawing rapidly due to climate change, and resident microbes are contributing to changing greenhouse gas emissions. Predictions of the fate of carbon in these regions is poorly constrained. However, improved, careful mapping of microbial community members influencing carbon dioxide and methane emissions will help clarify the system response to continued change. In order to more fully understand connections between the microbial communities, major geochemical transformations, and carbon dioxide and methane emissions, peat cores were collected from the active layers of three permafrost habitats spanning a thaw gradient (collapsed palsa, bog, and fen) at Stordalen Mire, Abisko, Sweden. Anaerobic incubations of shallow and deep subsamples from these sites were performed, with time-course characterization of the changes in microbial communities, peat geochemistry, and carbon dioxide and methane production. The former were profiled with 16S rRNA amplicon sequencing, and select metagenomes. The communities within each habitat and depth were statistically distinct, and changed significantly over the course of the incubations. Overall, Acidobacteria was consistently the dominant microbial phylum in incubations from all three habitat types. With increased thaw, the relative abundance of Actinobacteria tended to decrease, while Chloroflexi and Bacteroidetes increased with thaw; these phyla trends are consistent with microbial communities in the field. The relative abundance of methanogens increased with thaw, and with depth in collapsed palsa and bog samples; this is consistent with the later, more inundated thaw stages and deeper depths being more anoxic and providing conditions favorable to methanogens. Additionally, the microbial biodiversity in the incubations decreased over incubation time. Next, we focused on a polyphyletic group of microbes known as homoacetogens. Homoacetogenesis (CO2 + H2 -> CH3COOH) (open full item for complete abstract)

Committee: Virginia Rich (Advisor); Mike Wilkins (Committee Member); Kelly Wrighton (Committee Member) Subjects: Microbiology

Doctor of Philosophy, The Ohio State University, 2017, Food, Agricultural and Biological Engineering

Lignocellulosic biomass is an abundant source of renewable energy, but its high recalcitrance to biodegradation needs to be overcome to allow its conversion into biofuels. Thus, pretreatment of the lignocellulosic feedstock is usually required. Fungal pretreatment using white rot fungi is an alternative process to traditional thermo-chemical pretreatments that degrades lignin and enhances the enzymatic digestibility of the lignocellulosic biomass. Fungal pretreatment can be performed in solid-state at low temperature, without added chemicals such as strong acids or bases, and no wastewater is generated. However, in comparison with traditional pretreatments, disadvantages such as long residence times, low yields, and feedstock sterilization requirements make it challenging to implement. This work investigates the fungal pretreatment of non-sterile biomass with the white rot fungus, Ceriporiopsis subvermispora, for the production of biofuels using the dedicated energy crop Miscanthus × giganteus. For this purpose, solid-state fungal pretreatment of non-sterile Miscanthus was performed in batch using Miscanthus previously colonized with the fungus as inoculum. The process enhanced the enzymatic digestibility of Miscanthus by 3- to 4-fold over that of untreated Miscanthus after 21 days of incubation time. The finished material from this non-sterile pretreatment was used as inoculum for two more generations in a sequential fungal pretreatment process. A propagation of indigenous fungi that outcolonized C. subvermispora was observed through the generations, showing that sterilization is a required step for the stability and reproducibility of fungal pretreatment. The changes in composition and structure of Miscanthus after fungal pretreatment were compared with those in corn stover, hardwood, and softwood. Fungal pretreatment increased the enzymatic digestibility of hardwood, softwood, and Miscanthus by 2 to 4.5-fold; however, it was not effective for corn stover. Als (open full item for complete abstract)

Committee: Ajay Shah (Advisor); Thomas Mitchell (Committee Member); Thaddeus Ezeji (Committee Member); Fred Michel (Committee Member) Subjects: Agricultural Engineering; Engineering; Environmental Engineering

Doctor of Philosophy, The Ohio State University, 2017, Environmental Science

Yard trimmings (leaves, grass, wood chips, etc.) are abundant lignocellulosic biomass wastes, which need to be treated and/or utilized properly. Composting is a conventional approach to divert yard trimmings from the landfill. Alternatively, solid-state anaerobic digestion (SS-AD) can convert yard trimmings to biogas and digestate. It is promising to develop thermophilic SS-AD that can both produce energy and reduce waste to treat yard trimmings. This research included five inter-related projects: 1) examination of performance of thermophilic SS-AD and composting of yard trimmings with liquid anaerobic effluent as inoculum; 2) evaluation of the effect of yard trimmings on thermophilic SS-AD and prediction of methane yield based on feedstock component ratios; 3) development of a sequential batch thermophilic SS-AD with recirculated digestate as inoculum; 4) investigation of microbial community dynamics in the sequential batch thermophilic SS-AD; and 5) techno-economic comparison of thermophilic SS-AD and composting of yard trimmings. The first project showed that composting had higher degradation than SS-AD, while over half of the degraded carbon was converted to methane in SS-AD. Both SS-AD and composting generated nutrient-rich (N, P, K) end products with different dominant nitrogen forms, which may require different land application methods. The second project showed that digesting yard trimmings mixture alleviated inhibitors and increased methane yield compared to digesting single components. The favorable performance was obtained with equal fractions of the three components. Concentrations of volatile fatty acids (VFA) and ammonia varied with component ratios and correlated with system performance. A mixture design model was established to predict methane yield with good agreement. A sequential batch thermophilic SS-AD of yard trimmings was successfully developed with recirculated digestate as the inoculum in the third project. At substrate-to-inoculum rati (open full item for complete abstract)

Committee: Zhongtang Yu (Advisor); Harold Keener (Advisor); Frederick Michel (Committee Member); Ajay Shah (Committee Member) Subjects: Agricultural Engineering; Environmental Engineering; Environmental Science

Master of Science, The Ohio State University, 2017, Environmental Science

Black shale formations are being increasingly relied upon for energy extractions through the engineered processes of hydraulic fracturing and horizontal drilling. Although some deep terrestrial environments are known to harbor microbial life, little is know of the diversity and function of microbial communities in black shale formations. Our understanding of microbial life in black shale has been hampered by the need to drill into the subsurface with fluids and media containing surface microbial contaminants (e.g. drilling muds), the sample chemistry (i.e. high salt and organics) of the rock, and low expected densities of indigenous microbial cells. This thesis first examined the efficacy of seven extraction methods on PLFA yield, profile quality, and reproducibility from black shale. In all, three lipid extraction methods (modified Bligh and Dyer, modified Folch, and Microwave-assisted) and four variations (Citrate Buffer and Escherichia coli, Mg2+, and POPC spikes) of the modified Bligh and Dyer method were investigated and results demonstrated that adding an intact phospholipid spike (POPC) to the modified Bligh and Dyer extraction mixture provided a 6-fold increase in PLFA yield and better reproducibility among methods tested. This method was subsequently applied to sidewall cores collected from a borehole drilled into the Marcellus shale in an effort to investigate the presence of biomass across the interface of the Marcellus and Mahantango formations. Two drilling mud samples as ii well as paired samples from brine washes collected during core cleaning were also analyzed. PLFA biomass, richness, and profiles of the drilling muds were distinct from those of the brine wash and subsurface cores and were marked with significant amounts of Pseudomonas and Fungal lipid biomarkers. Drilling muds were ~7-fold higher in PLFA biomass than that of the three core samples. Core samples yielded two to six-fold higher biomass than previous PLFA studies of deep subsurface (open full item for complete abstract)

Committee: Paula Mouser Dr. (Advisor); Kelly Wrighton Dr. (Committee Member); Michael Wilkins Dr. (Committee Member) Subjects: Environmental Engineering; Environmental Science; Geology; Microbiology

Master of Science (MS), Ohio University, 2016, Plant Biology (Arts and Sciences)

Landscape studies of separate aquatic and terrestrial ecosystems have been less prevalent to the detriment of scientific understanding of large-scale ecological questions. Under nutrient limited conditions, microorganisms increase the production of extracellular enzymes to breakdown organically bound resources. Nutrients and carbon can become biologically unavailable in acid stressed environments, such as those in southeastern Ohio, that have been affected by more than a century of acidic deposition. In this leaf litter decomposition study, total fatty acid and extracellular enzyme laboratory analyses were utilized to compare forest and benthic stream microbial structure and enzymatic function in response to chronic acid stress. Based on phosphorus acquiring enzyme activity, forests of southeastern Ohio may be phosphorus limited; however, proximal freshwater streams did not exhibit the same functional response. The dynamic nature of lotic freshwater systems may partially explain the unexpected insensitivity to phosphorus enrichment. Microbial structure was also not found to shift under acid stressed conditions.

Committee: Jared DeForest (Advisor) Subjects: Biogeochemistry; Ecology