Environmental Science & Technology
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Item SURVIVAL OF ESCHERICHIA COLI AND CHANGES IN PHYSICOCHEMICAL PARAMETERS IN AQUAPONIC SYSTEMS DURING BASIL AND LETTUCE PRODUCTION(2023) Quach, Emily; Yonkos, Lance; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Aquaponics (APs), a soilless production system, integrates aquaculture and hydroponics to provide local fresh produce while conserving natural resources. The absence of soil in APs eliminates one potential food safety risk present in typical soil-based production systems, but APs may become contaminated from a variety of sources. Escherichia coli TVS 354 long-term survival was evaluated in bench-scale, deep-water APs units. In addition, pathogen presence on basil and lettuce at the time of harvest and changes in the population density of mesophilic aerobic bacteria in APs were measured. Results showed E. coli populations significantly decreased 24 h post-inoculation in water samples and remained undetectable by day 1 post-inoculation. Lettuce harvested on day 60 had detectable E. coli on lettuce leaves and roots at harvest. These results provide new insight on E. coli survival in harvested plants, indicate potential risks for foodborne illnesses, and unreliability of water testing as a monitoring tool.Item AUGMENTING SEQUENCING TECHNOLOGY FOR BETTER INFERENCE IN SOIL MICROBIOME ANALYSIS(2023) Epp Schmidt, Dietrich; Yarwood, Stephanie A; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The advent of DNA sequencing revolutionized the field of microbiome research. Many organisms, by virtue of their codependence and/or growth rate, are either impossible or extremely challenging to get into pure culture. Sequencing allows important taxonomic and phylogenetic information to be obtained independent of culturing. Development of the sequencing technology itself has allowed for high throughput workflow that has allowed low cost and extensive sampling of microbiomes across environments. The co-development of reference datasets for taxonomy and functional assignments, along with open-source bioinformatics pipelines has further empowered scientists to explore microbiomes in many environments. However, there are limitations to sequence data that have constrained the ecological inferences in microbiome research. One such limitation, the compositional nature of sequence data, has impeded our ability to make accurate inferences about the environmental drivers of taxon abundance and covariance across conditions. In this dissertation I explore the use of quantitative PCR in combination with sequencing techniques to generate “Quantitative Sequencing” data (QSeq) that mitigates the limitations of compositionality on inferences relating to taxon abundance and covariance across environmental gradients. In chapter 1, I reviewed key characteristics of the soil environment and sequencing as a mechanism for sampling. In chapter 2, I leveraged modeling, synthesis, and literature review methods to establish the questions and data characteristics that demand QSeq methodology. I show that even small amounts of variation in total abundance make determining the effects of environment (biotic and abiotic factors) on any given taxon unreliable without QSeq. In Chapter 3, I extend the logic of quantitative sequencing to improve metagenome prediction from PICRUSt2. Using data synthesis methods, accounting for 16S gene abundance consistently improved the accuracy of predicted functional genes. This was confirmed by high correlations between predicted and measured gene abundance (QPCR). There was however a large variation in prediction accuracy, likely due in part to database biases and in part to decoupling of bacterial function from taxonomy. In Chapter 4, I applied QSeq in the context of an experimental, long-term farming system that has large gradients in total abundance with depth, and I used QSeq to identify taxa that changed in abundance due to different farming system management and soil depth. Finally in Chapter 5, I used QSeq to identify putative N-fixing taxa that responded to glyphosate in four experimental farming systems. I show that the abundance of these taxa were decoupled from other effects of glyphosate on N-fixation in soybean across farming systems.Item DYNAMICS OF PHYTOPLANKTON POPULATIONS IN IRRIGATION PONDS(2022) Smith, Jaclyn Elizabeth; Hill, Robert L; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The dynamics of phytoplankton community structure in two agricultural irrigation ponds located in Maryland, USA were evaluated. Stable spatiotemporal patterns and zones of consistently higher and consistently lower phytoplankton functional group concentrations were established for both ponds. Moderate and strong correlations were found between the spatial patterns of several water quality parameters and phytoplankton concentrations. Additionally, zones of consistently higher and lower concentrations were found for the cyanobacteria pigment, phycocyanin. Chlorophyll, colored dissolved organic matter, and turbidity were the most influential predictors for phycocyanin concentrations. The prediction of phytoplankton community structure from water quality measurements with the random forest machine learning algorithm was possible and easily measured physicochemical parameter models offered the best model performance. Results of this work indicate that in-situ water quality measurements may be a cost-effective and faster alternative to time-intensive microscopy analysis of phytoplankton, allowing for more efficient water quality monitoring.Item Anthropogenic disturbance alters plant and microbial communities in tidal freshwater wetlands in the Chesapeake Bay, USA(2019) Gonzalez Mateu, Martina; Yarwood, Stephanie A; Baldwin, Andrew H; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Tidal freshwater wetlands are often found near urban centers, and as a result of human development they are subject to multiple environmental stressors. Increases in nutrient runoff, sedimentation, and hydrologic alterations have had significant impacts on these systems and on the ecosystem services they provide. One of the consequences of these stressors is the expansion of invasive species that can affect native biodiversity and the many biogeochemical processes that are key to wetland ecosystem function. This research looked at how human activities affect microbial communities in tidal freshwater wetlands, and explored various aspects of an invasive plant’s ecology in the Chesapeake Bay. In our first study, we found that microbial community composition differed along a rural to urban gradient and identified microbial taxa that were indicators of either habitat. Rural sites tended to have more methanogens and these were also indicators in these system, whereas in urban systems nitrifying bacteria were the main indicator taxa. This study suggested that urban wetlands have different microbial communities and likely different functions than those in rural areas, particularly concerning nitrogen and contaminant removal. Our second study looked at management of an invasive lineage of Phragmites australis which is commonly found in wetlands impacted by nitrogen enrichment. We evaluated the effects of different C:N ratios on the competitive ability of this lineage and a native North American lineage. Even though carbon addition did not improve the native’s competitive ability, we identified facilitative interactions when both lineages were growing together. This suggests that native and invasive Phragmites might coexist if there are no additional disturbances to the system. Our last study focused on plant-fungal interactions, and found that both Phragmites lineages benefitted from inoculation with fungal endophytes under salt stress. These results suggest that studies of plant-fungal interactions can yield insights into mechanisms of invasion, and could be further investigated in native wetland plants susceptible to increased salt stress following sea-level rise. Our results provide insights into plant and microbial ecology in the Chesapeake Bay’s tidal freshwater wetlands, and improve our understanding of the invasion process and management strategies of Phragmites australis.Item Soil microbial processes and community structure in natural and restored tidal freshwater wetlands of the Chesapeake Bay, Maryland, USA(2017) Maietta, Christine E.; Yarwood, Stephane A.; Baldwin, Andrew H.; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Tidal freshwater wetlands are integral to downstream water quality because they capture, store, and transform nutrients. Unfortunately, anthropogenic stressors are negatively impacting these habitats. While wetland restoration is helping to reinstate their presence in the landscape, restored wetlands frequently differ physically, chemically, and biologically from their natural counterparts. This research examined plant, soil, and microbe relationships and how their interactions affect soil carbon (C) storage and cycling in natural and restored tidal freshwater wetlands of the Chesapeake Bay, MD, USA. This research yielded important findings regarding differences between natural and restored habitats. First, we discovered soil microbial community composition of an urban tidal freshwater wetland retained similar composition as their less disturbed, suburban counterpart, and wetland sites constructed using similar restoration methodology produced similar microbial community structure and soil function. Additional research revealed that a natural and a restored wetland store soil C quite differently: A majority of soil C in the natural site was associated with large macroaggregates (> 2000 μm) whereas most soil C in the restored site was associated with smaller macroaggregates (> 250 to < 2000 μm). The distributions of six chemical compound classes (i.e., carboxylics, cyclics, aliphatics, lignin derivatives, carbohydrates derivatives, N-containing compounds) were relatively similar across the five soil fractions from both sites, however. In the final study, anaerobic laboratory mesocosms were used to evaluate the effects of clay content (%) and leaf litter quality on soil C cycling processes over time. This study found restored soils, regardless of clay content, mineralized more C as carbon dioxide (CO2) and methane (CH4) compared to natural wetland soils. Natural soils respired approximately half the volume of gas as restored soils, suggesting the addition of high- or low-quality C substrates to low C systems elicit a greater response from the heterotrophic microbial community. The results of these three studies suggest site history and edaphic features of restored wetlands are important drivers of microbial communities and their function. We propose that practitioners and researchers work together to identify practices that will enhance soil functions, particularly C storage, in tidal freshwater wetlands of the Chesapeake Bay region.Item The Ecology of Urbanization: A Study of Soil Microbial Community Rosponse(2016) Epp Schmidt, Dietrich Jonathan; Yarwood, Stephanie A; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Urbanization is associated with global biodiversity loss of macrophauna and flora through direct and indirect mechanisms, but to date few studies have examined urban soil microbes. Although there are numerous studies on the influence of agricultural management on soil microbial community composition, there has been no global-scale study of human control over urban soil microbial communities. This thesis extends the literature of urban ecology to include soil microbial communities by analyzing soils that are part of the Global Urban Soil Ecology and Education Network (GLUSEEN). Chapter 1 sets the context for urban ecology; Chapters 2 addresses patterns of community assembly, biodiversity loss, and the phylogenetic relationships among community members; Chapter 3 addresses the metabolic pathways that characterize microbial communities existing under different land-uses across varying geographic scales; and Chapter 4 relates Chapter 2 and 3 to one another and to evolutionary theory, tackling assumptions that are particular to microbial ecology.Item THE DISTRIBUTION AND FUNCTION OF DENITRIFICATION GENES: EXPLORING AGRICULTURAL MANAGEMENT AND SOIL CHEMICAL IMPLICATIONS(2016) Bowen, Holly; Yarwood, Stephanie A; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Denitrification is a microbially-mediated process that converts nitrate (NO3-) to dinitrogen (N2) gas and has implications for soil fertility, climate change, and water quality. Using PCR, qPCR, and T-RFLP, the effects of environmental drivers and land management on the abundance and composition of functional genes were investigated. Environmental variables affecting gene abundance were soil type, soil depth, nitrogen concentrations, soil moisture, and pH, although each gene was unique in its spatial distribution and controlling factors. The inclusion of microbial variables, specifically genotype and gene abundance, improved denitrification models and highlights the benefit of including microbial data in modeling denitrification. Along with some evidence of niche selection, I show that nirS is a good predictor of denitrification enzyme activity (DEA) and N2O:N2 ratio, especially in alkaline and wetland soils. nirK was correlated to N2O production and became a stronger predictor of DEA in acidic soils, indicating that nirK and nirS are not ecologically redundant.Item Back to Earth: Molecular Approaches to Microbial Ecology Must Consider Soil Morphology and Physicochemical Properties(2015) Dlott, Glade; Yarwood, Stephanie A; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This project studied the influence of different long-term agricultural management regimes on soil microbial communities, and compared survival strategies of individual prokaryotic OTUs in diverse soils subjected to long-term incubation. Together these would show whether alterations to microbial communities affect rates of soil carbon cycling. Agricultural soils were sampled at arbitrary depths above and below the plow layer, and relative abundances of microbes were measured using high-throughput sequencing. `Activity' (rRNA:rDNA) ratios were calculated for individual OTUs identified by high-throughput sequencing of tropical rainforest and temperate cornfield soils after incubation for one year with differing water and carbon availabilities. It was found that depth controls microbial communities to a greater degree than agricultural management, and that the characterization of microbial trophic strategies might be complicated by the often-ignored DNA preservation potential of soil. The study highlights the need for holistic approaches to testing hypotheses in modern microbial ecology.Item COUPLING ANAEROBIC DIGESTION TECHNOLOGY AND FORAGE RADISH COVER CROPPING TO OPTIMIZE METHANE PRODUCTION OF DAIRY MANURE-BASED DIGESTION(2015) Belle, Ashley Juanika; Lansing, Stephanie; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Anaerobic digestion technology was coupled with a new forage radish cover cropping system in order to increase biogas production of a dairy manure digester. Specifically, this research investigated forage radish as a renewable source of energy in terms of methane (CH4) production, the effect of radish co-digestion on hydrogen sulfide (H2S) production, and the relationship between H2S production and methanogenesis limitations. Optimal substrate co-digestion ratios and inoculum to substrate ratios (ISR) were determined in the laboratory with biochemical methane potential assays (300 mL) and pilot-scale complete mix batch digesters (850 L) were constructed and operated to determine energy production potential at the farm-scale level. Laboratory results showed that forage radish had 1.5-fold higher CH4 potential than dairy manure on a volatile solids basis, with increasing the radish content of the co-digestion mixture significantly increasing CH4 production. Initial H2S production also increased as the radish content increased, but the sulfur-containing compounds were rapidly utilized, resulting in all treatments having similar H2S concentrations (0.10-0.14%) and higher CH4 content in the biogas (48-70% CH4) over time. The 100% radish digester had the highest specific CH4 yield (372 ± 12 L CH4/kg VS). The co-digestion mixture containing 40% radish had a lower specific CH4 yield (345 ± 2 L CH4/kg VS), but also showed significantly less H2S production at start-up and high quality biogas (58% CH4). Utilizing 40% radish as substrate, decreasing the ISR below 50% (wet weight) resulted in unstable digestion conditions with decreased CH4 production and an accumulation of butyric and valeric acids. Pilot-scale experiments revealed that radish co-digestion increased CH4 production by 39% and lowered the H2S concentration in the biogas (0.20%) beyond that of manure-only digestion (0.34% - 0.40%), although cumulative H2S production in the radish + manure digesters was higher than manure-only. Extrapolated to a farm-scale (200 cows) continuous mixed digester, co-digesting with a 13% radish mixture could generate 3150 m3 CH4/month, providing a farmer additional revenue up to $3125/month in electricity sales. These results suggest that dairy farmers could utilize forage radish, a substrate that does not compete with food production, to increase CH4 production of manure digesters.Item Release and runoff/infiltration removal of Escherichia coli, enterococci, and total coliforms from land-applied dairy cattle manure(2014) Blaustein, Ryan Andrew; Hill, Robert L; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Simulating the rainfall-induced release of indicator bacteria from manure is essential to microbial fate and transport modeling with regard to water quality and food safety. Experiments were conducted to determine the effects of rainfall intensity, surface slope, and scale on the release of Escherichia coli, enterococci, and total coliforms from land-applied dairy manure. Rainfall intensity did not affect bacterial release dependencies on rainfall depth, but it did have a significant effect on the post-rainfall quantities of indicator bacteria in soil. While bacterial concentrations were evenly released into runoff and infiltration, the surface slope controlled the partitioning of total released bacterial loads. The proportion of E. coli released from manure exceeded enterococci, especially with infiltration flow. Scale had strong, inverse effects on the recovery of land-applied bacteria with runoff. These results will be used to improve microbial fate and transport models, critical for risk assessment of microbial contamination in the environment.