Environmental Microbiology and Microbial Ecology Commons^™

Heavy Metals Implications To Sediment Microbiome And Coral Response To Arsenic Dosing, Dimitrios G. Giarikos, Amy Hirons, Jose V. Lopez, Abigail Renegar, Jason Gershman

SECLER Data

No abstract provided.

Antibiotic Resistance In A Coastal River In Mississippi, Usa – Potential Drivers, Shuo Shen, Wei Wu, Eric A. Saillant, Darrell Jay Grimes

Gulf and Caribbean Research

Wastewater treatment plants (WWTPs) are major sources of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in water bodies. Most studies on the impact of WWTPs on antibiotic resistance have focused on freshwater systems, with little information on coastal and estuarine waters with variable salinity. This study monitored seasonal levels of ARGs at the effluent and downstream of the Pascagoula— Moss Point WWTP in the lower Pascagoula River, a coastal river in southeastern Mississippi, USA. Surface water samples were collected seasonally at upstream, outflow, and 3 downstream sites from February to November 2016. Bacterial resistance to sulfamethazine, tetracycline, and …

A Comparison Of Adenosine Triphosphate With Other Metrics Of Microbial Biomass In A Gradient From The North Atlantic To The Chesapeake Bay, Alexander B. Bochdansky, Amber A. Beecher, Joshua R. Calderon, Alison N. Stouffer, Nyjaee N. Washington

OES Faculty Publications

A new, simplified protocol for determining particulate adenosine triphosphate (ATP) levels allows for the assessment of microbial biomass distribution in aquatic systems at a high temporal and spatial resolution. A comparison of ATP data with related variables, such as particulate carbon, nitrogen, chlorophyll, and turbidity in pelagic samples, yielded significant and strong correlations in a gradient from the tributaries of the Chesapeake Bay (sigma-t = 8) to the open North Atlantic (sigma-t = 29). Correlations varied between ATP and biomass depending on the microscopic method employed. Despite the much greater effort involved, biomass determined by microscopy correlated poorly with other …

Developing Methods For Analysis Of Chiral Small Molecules And D-Amino Acid Containing Peptides, Joshua I. Putman

Chemistry & Biochemistry Dissertations - Archive

This dissertation covers the development of methods to analyze chiral small molecules and d-amino acid containing peptides. The first section covers the development of liquid chromatographic chiral screening approaches for newly synthesized chiral molecules. The next part of the dissertation covers methodologies for the analysis of d-amino acid containing peptides. Lastly the bacterial degradation of three commonly used pesticides by bacteria harvested from Colorado potato beetles (Leptinotarsa decemliniata) is presented.

Twelve new azole compounds and eleven racemic ethanolamine derivatives were synthesized. These twenty-three compounds were evaluated using eight chiral columns, four macrocylic glycopeptides, a cyclodextrin derivative …

Examining The Role Of Microbial Communities In Soil Carbon Cycling Across Levels Of Complexity, Chansotheary Dang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Microorganisms provide the foundation for many ecosystem processes and are important drivers of carbon and nutrient cycling. The advancement of next generation sequencing has allowed researchers to lift open the lid on the ‘black box’ in microbial ecology. While previously unculturable microbes can now be characterized with the 16S rRNA gene, answering ‘who’s there?’ is only part of the challenge. Hidden inside the ‘black box’ remains the question, ‘who’s doing what?’. Recent development in trait-based methods like quantitative stable isotope probing (qSIP) equipped microbial ecologists with the tool to connect taxon-specific traits to ecosystem processes. Despite the growing body of …

Interactions Between Multiple Stressors, Nanomaterials And A Pathogen, In Caenorhabditis Elegans, Jarad Cochran

Theses and Dissertations--Plant and Soil Sciences

Metal and metal oxide nanoparticles (NP), which have received interest for use in agriculture, show in vitro and in vivo toxicity at relatively low concentrations. Silver nanoparticles (Ag NP) and zinc oxide nanoparticles (ZnO NP) cause adverse effects in model soil organisms under environmentally relevant conditions. In most toxicity assessments of nanomaterials, model organisms are exposed to a single stressor. Though single stressor experiments are essential to understanding the fate and effects of released NP, in nature, organisms are affected by multiple stressors, including pathogens, which might exacerbate or mitigate negative effects of NP exposure. There is limited research on …

Dust-Driven Mechanism For Marine Particle Aggregation: Interactions Between Clay Minerals, Heterotrophic Bacteria And Organic Matter Influences Aggregation In Marine Systems, Vignesh Gokuladas Menon

Dartmouth College Master’s Theses

Atmospheric dust deposition plays a crucial role in marine biogeochemical cycles, yet mechanisms underlying its impact on particle dynamics remain unclear. This study investigates the synergistic interactions between marine heterotrophic bacteria and clay minerals in seawater, focusing on their effect on Transparent Exopolymer Particles (TEP) production and organoclay aggregation. Field experiments in the Gulf of Maine and laboratory roller tank studies were conducted using natural microbial communities and model heterotrophic bacterial strains (Alteromonas sp. EZ55, Marinobacter adhaerens HP15, and Sulfitobacter sp. NAS-14.1). Results demonstrate that clay exposure significantly enhances TEP production by bloom-associated heterotrophic bacteria, with increases up to …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Enhancing Urban Water Quality Through Biological-Chemical Treatment: Aquatic Macroinvertebrate Community And Temporal Chlorophyll-A Response, Matthew Chaffee

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

With a growing human population, urbanization is impeding a plethora of natural waterways. Of these, urban ponds play a vital role in nutrient sequestration, flood prevention, and habitat sanctuaries. However, nutrient loading can reduce habitat effectiveness and promote harmful algae blooms. To reduce internal nutrient loads, a biological-chemical treatment strategy consisting of floating treatment wetlands (FTWs) and lanthanum were applied to two urban retention ponds, Densmore and Wilderness Ridge Ponds. To measure effectiveness, chlorophyll-a samples were collected and correlated with Sentinel-2. A novel band algorithm termed 3BR1 produced a strong correlation (R² = 0.72) to physical chlorophyll-a …

Detection Of Dsrab Operon Expression In Desulfotalea Psychrophila Cells Subjected To Simulated Martian Conditions Of Temperature And Regolith's Sulphate Minerals Composition, Sergio Mosquera, Mack Ivey, Vincent F. Chevrier

Biological Sciences Faculty Publications and Presentations

Discoveries of transient liquid water in the Martian polar caps and the presence of liquid lakes and subsurface oceans in icy satellites have increased the interest of scientists in the capabilities of terrestrial extremophiles to grow and remain metabolically active in these extreme environments. The principal goal of this research is to understand the metabolic capacity of the anaerobic psychrophile, Desulfotalea psychrophila, cultured at subfreezing temperatures in media containing various concentrations of sulphate minerals. In this regard, our experiments focused on the detection of D. psychrophila survival and active metabolism, employing a biochamber that can recreate Martian temperatures. Using …

Distinguishing Community Assembly Through Functional Redundancy Models., Sandra A. Tsiorintsoa, Sharon Bewick, Matthew Macauley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Connecting The Nebraska Water Quality Index To The Aquatic Microbial Community Of The North Platte River Basin, Nebraska, Paula R. Guastello

School of Natural Resources: Dissertations, Theses, and Student Research

The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index …

Effect Of Implementing Best Management Practices (Bmps) On Productivity, Water Quality, Soil Health And Economic Return On Louisiana’S Sugarcane Production System, Krizzia L. Guardado

LSU Master's Theses

The constant soil cultivation alongside adverse weather in Louisiana has declined soil and water quality in sugarcane fields. Therefore, the integration of an effective conservation program must be assessed to sustain crop production. Best management practices (BMPs) promote soil health and improve water quality while achieving optimal crop development and cost-effective production system. A study was conducted at two different locations to document the benefits of BMPs (sweeping residue, variable N rate, and cover cropping) implemented collectively and individually compared to the standard farmer’s practices (FP) on sugarcane productivity, nutrient cycling, soil and water quality, and economic return . At …

Symbiotic Ucyn-A Strains Co-Occurred With El Niño, Relaxed Upwelling, And Varied Eukaryotes Over 10 Years Off Southern California, Colette Fletcher-Hoppe, Yi-Chun Yeh, Yubin Raut, J. L. Weissman, Jed A. Fuhrman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Biological nitrogen fixation, the conversion of N₂ gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A’s presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by “universal primers” from monthly samples and resolved into Amplicon …

Ecology Of Viruses In Marine And Coastal Oxygen-Depleted Waters, Sophie Jurgensen

LSU Doctoral Dissertations

Deoxygenation of marine and coastal waters, both caused and exacerbated by a suite of abiotic and biotic factors, has been documented for more than sixty years. The incidence and severity of low-oxygen areas is predicted to expand globally in the coming decades. Despite their colloquial moniker “dead zones,” low-oxygen areas contain thriving and diverse microorganisms that have significant impacts on global biogeochemical cycles including contributing to positive feedback loops that further expand low-oxygen areas. While the diversity and activity of these microorganisms is beginning to be elucidated, the ecology of their viruses is particularly understudied. In this dissertation, I present …

Considerations For The Use Of Mycorrhizal Fungi Inoculants In Coal Mine Reclamation And Reforestation In Appalachia: A Guide Of Best Practices And Management Recommendations, Cole Hansen Reistrup

Master's Projects and Capstones

Nearly all terrestrial plants form symbiotic relationships with mycorrhizal fungi. These beneficial soil microbes support plant health by increasing plants’ access to nutrients and water, protecting them from pathogens, improving soil properties, and more. A challenge to restoring forests on coal mined land in Appalachia is that mine soils are often degraded in a number of ways, including lacking mycorrhizal fungi, which makes mine soils difficult for trees to grow upon. Substantial improvements to coal mine reforestation success have been made since the development of the Forestry Reclamation Approach in 2005 that provides guidelines for how to create a suitable …

Exploring The Dynamics Of Bacterial Populations In The Gut Microbiota, Shaikh Obaidullah

Biology and Medicine Through Mathematics Conference

No abstract provided.

Assessing Functional Biodiversity For The Future Of Plants, Planet, And People, Ali Loker

Doctor of Plant Health Program: Dissertations and Student Research

Biodiversity plays a critical role in supporting life in global ecosystems and its links to ecosystem services and sustainability are recognized by scientific and non-scientific communities. Growing awareness of the importance of biodiversity is accelerated by discussions of its loss, and how to design interventions to conserve and mitigate a biodiversity crisis. Stakeholders are funding and implementing assessment strategies at various scales to help direct conservation efforts. There is also growing interest in measuring and communicating biodiversity outcomes.

Functional biodiversity characterizes the multiplicity of life forms into groups based on their diverse contributions to natural and agro-ecosystems. Assessing functional biodiversity …

Nitrite Cycling In The Primary Nitrite Maxima Of The Eastern Tropical North Pacific, Nicole M. Travis, Colette L. Kelly, Margaret R. Mulholland, Karen L. Casciotti

OES Faculty Publications

The primary nitrite maximum (PNM) is a ubiquitous feature of the upper ocean, where nitrite accumulates in a sharp peak at the base of the euphotic zone. This feature is situated where many chemical and hydrographic properties have strong gradients and the activities of several microbial processes overlap. Near the PNM, four major microbial processes are active in nitrite cycling: ammonia oxidation, nitrite oxidation, nitrate reduction and nitrite uptake. The first two processes are mediated by the nitrifying archaeal/bacterial community, while the second two processes are primarily conducted by phytoplankton. The overlapping spatial habitats and substrate requirements for these microbes …

Implications Of Intraspecific Variation In Soil Microbes On Solidago Performance, Yazeed Alshammari

Masters Theses

This study explored the implications of intraspecific variation in soil microbes on the performance of Solidago altissima, a North American species that has become invasive across several continents. This research explored how different clones of Solidago altissima were associated with bacterial and fungal soil microbial communities, which influenced plant performance. In a common garden of 24 Solidago altissima clones, I analyzed the relationship between soil microbial communities, foliar chemistry, clone genetic relatedness, and plant performance. My methods included analysis of soil microbial communities (bacterial and fungal), genetic distances among clones to assess relatedness, and measures of plant performance (light …

Changes And Relationships Of Soil Aluminum, Organic Matter, And Hydrogen Ion Concentration With Rye Cover Crop, Arron Wilder

Cal Poly Humboldt theses and projects

Soil acidity is a common agricultural problem worldwide, as approximately 50% of all potentially arable soils are affected by pH limitations. At soil pH 3+) is considered to be the chemical form of aluminum in acid soil that hinders plant growth the most. Potentially, soil organic matter (SOM) can ameliorate the toxic effects of Al³⁺ on plants and microbes by binding with Al³⁺, thus preventing Al³⁺ (and other species of aluminum) from interacting in the rhizosphere. Increasing SOM also increases soil health indicators (i.e., microbial activity, soil water holding capacity, aggregate stability, porosity, etc.) while the …

Rapid Bacterial And Fungal Successional Dynamics In First Year After Chaparral Wildfire, M. Fabiola Pulido-Chavez, James W. J. Randolph, Cassandra A. Zalman, Loralee Larios, Peter M. Homyak, Sydney I. Glassman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition …

Application Of A 14c-Assay To Assess Methanotrophic Biodegradation Of Tce In Low Ph Groundwater, Evan Groome

All Theses

Current biological strategies for remediating trichloroethylene (TCE) in low pH aquifers (i.e., pH14C-TCE assay was developed to determine pseudo first-order rate constants for the degradation of TCE in microcosms containing soil and groundwater from the Boeing Michigan Aeronautical Research Center (BOMARC) superfund site, where the pH ranges from 4.1 to 4.9. The ¹⁴C-TCE assay was also adapted to calculate soil-normalized rate constants for data from this site, as well as data that Szwast²¹ collected from the Beltsville Agricultural Research Center (BARC). In addition to natural attenuation, biostimulation through amendments of methane and nutrients were also assessed. This treatment …

Genomic Analysis And Characterization Of Surface Properties Of Naphthalene Degrading Acinetobacter Isolates, Gunn Emilie Berge

Graduate Theses and Dissertations (2019 - present)

No abstract provided.

A Cross-Scale Nexus: Microbial Functional Genes In Tandem With Molecular-Level Nitrogen Fluxes And Implications For Field-Scale Biogeochemical Processes, Srusti Maddala

Graduate Theses and Dissertations

Nitrogen (N) biogeochemical cycling entails close networking between soil nutrients, plant species and resulting microbial communities, and abiotic factors such as temperature, moisture, and pH. To better understand transformations of N in soil microsites, which are known to be rich in N-cycling behavior, the microdialysis technique was employed to generate in situ data on temporal alterations of N during wetting-drying conditions in both the field and laboratory. The objectives were to 1) determine the lifespan of the microdialysis technique in field conditions, 2) evaluate the ability of the method to yield N fluxes that would be differential between the two …

Tissue Decay Tested In Modern Metasequoia Leaves: Implications For Early Diagenesis Of Leaves In Fossil Lagerstätten, Caitlyn R. Witkowski, Qin Leng, Christopher W. Reid, Liang Feng, Hong Yang

Science and Technology Department Faculty Journal Articles

Sedimentary deposits yielding extraordinarily-preserved fossils (known as Lagerstätten) may provide significant insights into the physiology and environments of ancient plants, particularly when the fossils represent their original characteristics with limited diagenetic modifications. To better understand molecular, isotopic, and morphological changes during the early stages of diagenesis, degradation experiments were conducted in two time series: 1) a laboratory decay series using fungi on leaves over the course of a month and 2) a natural decay series with leaves collected from different stages of leaf senescence and early diagenesis. Both experiments used modern leaves of the dawn redwood Metasequoia glyptostroboides …

Biomass Estimation Of Marine Biofilms On Plastic Surfaces, Kian Banihashemi, Fernando Javier Gil

Biological Sciences

Plastics have become a major source of marine pollution, which threatens food safety and quality, human health, and marine ecosystems. Due to the drastic negative effects of plastics in a marine environment, alternative biodegradable plastics are being generated that are more eco-friendly and have less environmental impact. Though some of these plastics are known to biodegrade, the process of degradation for bioplastics has not been heavily studied in a marine environment. This pilot project sought to both quantify the process of biodegradation and compare across different methods for effectiveness of biomass estimation, which serves as an indicator of biodegradation. Plastics …

Assessing The Activity Of Antimicrobial Peptides Against Common Marine Bacteria Located In Rotifer (Brachionus Plicatilis) Cultures, Chelsea Woods, Lindsey Woolley, Gavin Partridge, Mengqi Chen, Evan F. Haney, Robert E.W. Hancock, Nicky Buller, Andrew Currie

Fisheries Research Articles

Rotifers are used as the first feed for marine fish larvae and are grown in large cultures that have high loads of organic matter and heterotrophic bacteria; these bacteria are passed on to the developing fish larvae and can potentially lead to bacterial infections. A modified minimum inhibitory concentration (MIC) protocol for antimicrobial peptides was used to determine the potency of ten antimicrobial peptides (AMPs) in artificial seawater relevant to a rotifer culture (salinity of 25‰) against common marine pathogens. All of the AMPs had antimicrobial activity against the bacterial isolates when the salt concentration was approximately zero. However, in …

Evaluating Soil Health Changes Following Cover Crop And No-Till Integration Into A Soybean (Glycine Max) Cropping System In The Mississippi Alluvial Valley, Alexandra Gwin Firth

Theses and Dissertations

The transition of natural landscapes to intensive agricultural uses has resulted in severe loss of soil organic carbon (SOC), increased CO₂ emissions, river depletion, and groundwater overdraft. Despite negative documented effects of agricultural land use (i.e., soil erosion, nutrient runoff) on critical natural resources (i.e., water, soil), food production must increase to meet the demands of a rising human population. Given the environmental and agricultural productivity concerns of intensely managed soils, it is critical to implement conservation practices that mitigate the negative effects of crop production and enhance environmental integrity. In the Mississippi Alluvial Valley (MAV) region of Mississippi, USA, …

Comparative Transcriptomic Study Between Cyanobacteria That Contain Chlorophyll D And Those That Lack Chlorophyll D, Fernanda Montoya

Honors Capstones

All cyanobacteria, which perform oxygenic photosynthesis on Earth, contain the photosynthetic pigment chlorophyll a (Chl a) that absorbs light in the violet and red region of the visible spectrum. Cyanobacteria of the Acaryochloris species, however, contain the rare photosynthetic pigment chlorophyll d (Chl d) that absorbs light in the far-red region. Chl d’s ability to absorb light in this region allows it to avoid competing with other photosynthetic organisms for light. Creating a photosystem that uses Chl d in plants would be of great use for agricultural land optimization, but requires knowledge of the biosynthetic pathways of …