Environmental Microbiology and Microbial Ecology Commons^™

Construction And Analysis Of Three Multi-Partite Synthetic Microbial Communities, Alexander J. Lazzara, Jacob K. Fanning

Honors Theses

Microbial Communities are of interest to molecular biologists hoping to understand the nature of metabolic interactions between co-existing, or possibly mutualistic, organisms. These interactions are ubiquitous in nature, but understanding the molecular mechanisms involved remains challenging and not well understood. Here, we design three tri-partite microbial circuits based on possible interactions among involved microbes, which are discussed and may suggest mutualistic interactions. Carbon and nitrogen molecular pathways and the intracellular metabolism of each microbe is discussed. We present minimal growth media that will ensure that organisms utilize available resources, which may originate from metabolic processes in neighboring microbes, simulating a …

How Historic Shipwrecks Influence Dispersal Of Deep-Sea Microbiomes, Rachel Moseley

Master's Theses

This thesis investigates how historic shipwrecks potentially shape dispersal of deep-sea microbiomes. Processes impacting dispersal of microbiomes around artificial structures in the ocean and how they connect to other deep-sea habitats is unknown. Dispersal processes are explained for some macroorganisms by theories in ecology, specifically the Theory of Island Biogeography and the Wooden Stepping Stone hypothesis. These have not been investigated for microorganisms, and thus this work will probe if they are applicable to microbial biogeography in this habitat. Experiments were conducted to establish new “island-like” features in near proximity (25-125 m) to wooden-hulled historic shipwrecks in the northern Gulf …

Resistance Of The Freshwater Microbiome To A Combination Of Pesticides, Gabriel Hooper

Senior Honors Theses

Pesticides are used prevalently throughout the United States and can negatively affect non-target organisms. Rain run-off can move multiple pesticides into freshwater ecosystems and bring them in contact with non-target organisms that have variable tolerances to pollution. This study seeks to improve our understanding of how an acute exposure to a combination of pesticides may restructure microbial communities by examining the microbiome before and after a 48-hour exposure to 2000 ppb of herbicides (glyphosate, atrazine, and 2,4-D). Pesticide exposure did not significantly alter the alpha or beta diversity of the sample types, which demonstrates the ability of freshwater microbiomes to …

A Novel Jumbo Phage Phima05 Inhibits Harmful Microcystis Sp., Ampapan Naknaen, Oramas Suttinun, Komwit Surachat, Eakalak Khan, Rattanaruji Pomwised

Civil and Environmental Engineering and Construction Faculty Research

Microcystis poses a concern because of its potential contribution to eutrophication and production of microcystins (MCs). Phage treatment has been proposed as a novel biocontrol method for Microcystis. Here, we isolated a lytic cyanophage named PhiMa05 with high efficiency against MCs-producing Microcystis strains. Its burst size was large, with approximately 127 phage particles/infected cell, a short latent period (1 day), and high stability to broad salinity, pH and temperature ranges. The PhiMa05 structure was composed of an icosahedral capsid (100 nm) and tail (120 nm), suggesting that the PhiMa05 belongs to the Myoviridae family. PhiMa05 inhibited both planktonic and aggregated …

Microbially-Mediated Carbonate Dissolution And Precipitation; Towards A Protocol For Ex-Situ, Cave-Analogue Cultivation Experiments, Vanessa E. Johnston, Andrea Martín-Pérez, Sara Skok, Janez Mulec

International Journal of Speleology

Subterranean calcite dissolution and precipitation are often considered as strictly geochemical processes. The active involvement of microbes in these processes is commonly underestimated in the literature due to general oligotrophic conditions in caves, except in particular cave conditions, such as sulfidic caves and moonmilk deposits, where the presence of microbes likely plays a key role in mineral deposition. Here, we study the possible involvement of microbes from Postojna Cave, Slovenia, in carbonate dissolution (litholysis) and precipitation (lithogenesis). Microbes were sampled from small pools below hydrologically diverse drip sites and incubated on polished limestone tablets at 10 and 20°C for 2 …

Project Alien, Rebecca Mccallin, Madelyn Hoying, Alex Evans, Matthew Nestler, Karli Rae Sutton, Garett Craig, Lucia Secaia Del Cid, Alexander Guy, Rachel Fernandez, Amanda Trusiak, Paige Aley, Ingabire Gakwerere, Nina Dorfner, Maria Mosbacher, Mary Flavin, Selvin Hernandez, Audrey Steen, Benjamin Kazimer

Undergraduate Research and Scholarship Symposium

Project ALIEN is a comprehensive plan to send humans to Mars to look for life on the Martian surface while exploring the viability and adaptability of terrestrial microbes in Martian atmospheric conditions. ALIEN will use a ballistic capture trajectory to get to Mars and stay in aerostationary orbit for a 30-day surface mission, during which two surface crewmembers will perform a variety of experiments to achieve the mission’s goals of Martian microbial discovery within brines of the Gale Crater and terrestrial microbe adaptability and viability to Martian conditions. Experimentation is based on the presumption that Martian microbes are metabolically similar …

Microplastics: Nacogdoches County’S Hidden Threat, Jordan Stanford, Sydney Matlock, Courtney Sims, Samantha Montes

Undergraduate Research Conference

Microplastics and their threat to marine environments are well known, but studies in freshwater environments are few and far between. Microplastics can be created by the breaking down of plastics or in the process of making plastics. They affect biological lifeforms in a multitude of ways, water temperature, permeability of the sediment. Pollution in Texas waterways have motivated groups like the Environmental Protection Agency, Trash Free Texas, and Environment Texas to get involved. The objectives of this study are two analyze Bonita and La Nana Bayou for microplastic presence and to educate and create awareness for Nacogdoches County on microplastics. …

Seasonal Variation Of E. Coli Abundance And Antibiotic Resistance Patterns In Water And Sediment Samples From Two Creeks With Different Potential Fecal Contamination Sources., James S. Zumhagen, Timothy Gsell

Research Days

Escherichia coli has served as the primary indicator for fecal contamination for the past 30 years, but more recent studies suggest that this bacteria may survive the cold weather in the soil making it difficult to tell whether it is new contamination or old contamination. Studies have found that exposure to various contaminants such as heavy metals, water treatment chemicals, agricultural runoff, fecal contamination, and antibiotics, creates an increase in the resistance of the microbes exposed to it. Wastewater treatment facilities, animal hospitals and wastewater sites increase the bacterial load and the prevalence of antibiotic resistance of bacteria residing bacteria …

Taxonomic Microbiome Profiling And Abundance Patterns In The Cacao (Theobroma Cacao L.) Rhizosphere Treated With Arbuscular Mycorrhizal Fungi And Bamboo Biochar, Angelbert D. Cortes, Nelly S. Aggangan, Rina B. Opulencia

The Philippine Agricultural Scientist

Biochar and arbuscular mycorrhizal fungi (AMF) are agricultural interventions adopted by farmers to improve the growth of crops in nutrient-deficient acidic soil, which relatively influence the biological properties in the rhizosphere. This greenhouse study investigated the changes in prokaryotic diversity in the rhizosphere of cacao plants grown in acidic soil with AMF and bamboo biochar (BB) for 15 months under nursery conditions. Metagenomic analysis of the V3-V4 region of the 16S rRNA gene of the rhizosphere with AMF, 15% BB, and AMF + 15% BB revealed that the addition of AMF and BB reduced the sample's diversity, but the treatments …

Distribution, Diversity, And Biogeography Of Anaerobic Carbon Monoxide Uptake By Microbial Communities In Soils And Sediments, Amber N. Depoy

LSU Master's Theses

Carbon monoxide (CO) is primarily known for being a toxic gas. However, CO is used by microorganisms as an electron or carbon source in a variety of respiratory processes. Different kinds of microorganisms utilize CO aerobically and anaerobically, using two distinct CO dehydrogenases (CODHs). Aerobes oxidize CO using a molybdenum-dependent dehydrogenase (Mo-CODH), while anaerobes utilize a nickel-dependent CO dehydrogenase (Ni-CODH). Studies of the biochemistry and microbiology of aerobic and anaerobic CO oxidation are extensive, but relatively little is known about the ecology of anaerobic CO oxidation. In an effort to test new hypotheses about the ecology of anaerobic CO oxidation, …

A Comparison Of Intertidal Metazoan Biodiversity Between Previously Oiled Sheared And Intact Marsh Margins And Between Multiple Salinity Zones In The Coastal Marshes Of Louisiana, Patrick M. Rayle

LSU Master's Theses

Marshes in Louisiana are under threat from numerous natural and anthropogenic sources. A consequence of these threats are sheared marsh margins, which result from the impact of storm surge on previously oiled, weakened marsh. These conditions occurred in Louisiana marshes after Hurricane Isaac in 2012 followed the Deepwater Horizon oil spill in 2010, particularly in the shorelines surrounding Bay Jimmy. The second and third chapters of this thesis focus on the differences in biodiversity between the sheared and intact marsh margins in impacted sites in Bay Jimmy. Metabarcoding methods were used to determine community composition of the sediment within marsh …

Microbiological Study In A Gneissic Cave From Sri Lanka, With Special Focus On Potential Antimicrobial Activities, Ethige Isuru P. Silva, Pathmakumara Jayasingha, Saman Senanayake, Anura Dandeniya, Dona Helani Munasinghe

International Journal of Speleology

The emergence of antibiotic resistance is a global health crisis, thus the search for novel antimicrobial compounds has become a continuous necessity. Underexplored and extreme environments, such as cave ecosystems, have been identified as a promising potential source for the discovery of novel microorganisms with novel antimicrobial compounds (AMC). This study presents the first cave microbiological investigation in Sri Lanka, with a special preference for bioprospecting of novel AMC. The cave sediment characterization demonstrated the presence of close to strong acidic conditions (pH 3.1 – 3.3) and thus indicates the possibility of isolating acidophilic microorganisms. Eight cave wall/ceiling fungal strains …

The Response Of Marine Synechococcus To A Landscape Of Environmental Stressors: A Proteomic Exploration, Dana E. Michels

Master's Theses

In the field of marine microbial ecology, many questions remain unanswered with regards to the physiological trade-offs made by phytoplankton to maximize growth (e.g., nutrient acquisition) and minimize loss (e.g., predation defenses). These tradeoffs, which occur at the cellular level, have wide reaching impacts on food web dynamics and global biogeochemical cycles. In the first chapter, we explored the use of a non-canonical amino acid (NCAA) technique, bioorthogonal non-canonical amino-acid tagging (BONCAT), in phytoplankton model systems. This technique has potential to work well in natural systems by enabling isolation of only newly synthesized proteins during an incubation period with the …

Japanese Quail (Coturnix Japonica) As A Novel Model To Study The Relationship Between The Avian Microbiome And Microbial Endocrinology-Based Host-Microbe Interactions, James Keane, Joshua M. Lyte, Julia Eckenberger, Nicholas Anthony, Sandip Shrestha, Daya Marasini, Karrie M. Daniels, Valentina Caputi, Annie M. Donoghue, Mark Lyte

Articles

Background

Microbial endocrinology, which is the study of neuroendocrine-based interkingdom signaling, provides a causal mechanistic framework for understanding the bi-directional crosstalk between the host and microbiome, especially as regards the effect of stress on health and disease. The importance of the cecal microbiome in avian health is well-recognized, yet little is understood regarding the mechanisms underpinning the avian host-microbiome relationship. Neuroendocrine plasticity of avian tissues that are focal points of host-microbiome interaction, such as the gut and lung, has likewise received limited attention. Avian in vivo models that enable the study of the neuroendocrine dynamic between host and microbiome are …

Inhibition Of Biofilm Formation By The Synergistic Action Of Egcg-S And Antibiotics, Shrameeta Shinde, Lee Lee, Tinchun Chu

Department of Biology Faculty Scholarship and Creative Works

Biofilm, a stress-induced physiological state, is an established means of antimicrobial tolerance. A perpetual increase in multidrug resistant (MDR) infections associated with high mortality and morbidity have been observed in healthcare settings. Multiple studies have indicated that the use of natural products can prevent bacterial growth. Recent studies in the field have identified that epigallocatechin gallate (EGCG), a green tea polyphenol, could disrupt bacterial biofilms. A modified lipid-soluble EGCG, epigallocatechin-3-gallate-stearate (EGCG-S), has enhanced the beneficial properties of green tea. This study focuses on utilizing EGCG-S as a novel synergistic agent with antibiotics to prevent or control biofilm. Different formulations of …

Metabolomics-Based Analysis Of Miniature Flask Contents Identifies Tobacco Mixture Use Among The Ancient Maya, Mario Zimmermann, Korey J. Brownstein, Luis Pantoja Díaz, Iliana Ancona Aragón, Scott R. Hutson, Barry Kidder, Shannon Tushingham, David R. Gang

Anthropology Faculty Publications

A particular type of miniature ceramic vessel locally known as “veneneras” is occasionally found during archaeological excavations in the Maya Area. To date, only one study of a collection of such containers successfully identified organic residues through coupled chromatography–mass spectrometry methods. That study identified traces of nicotine likely associated with tobacco. Here we present a more complete picture by analyzing a suite of possible complementary ingredients in tobacco mixtures across a collection of 14 miniature vessels. The collection includes four different vessel forms and allows for the comparison of specimens which had previously formed part of museum exhibitions with recently …

Pressure Effects On Sulfur‐Oxidizing Activity Of Thiobacillus Thioparus, Jorge R. Osman, Hervé Cardon, Gilles Montagnac, Aude Picard, Isabelle Daniel

Life Sciences Faculty Research

Carbon capture and storage technologies are crucial for reducing carbon emission from power plants as a response to global climate change. The CarbFix project (Iceland) aims at examining the geochemical response of injected CO2 into subsurface reservoirs. The potential role of the subsurface biosphere has been little investigated up to now. Here, we used Thiobacillus thioparus that became abundant at the CarbFix1 pilot site after injection of CO2 and purified geothermal gases in basaltic aquifer at 400–800 m depth (4–8 MPa). The capacity of T. thioparus to produce sulfate, through oxidation of thiosulfate, was measured by Raman spectroscopy as a …

Complete Genome Sequence Of Strain Ss-5, A Magnetotactic Gammaproteobacterium Isolated From The Salton Sea, A Shallow, Saline, Endorheic Rift Lake Located On The San Andreas Fault In California, Denis Trubitsyn, Caroline L. Monteil, Corey Geurink, Viviana Morillo Lopez, Luiz Gonzaga Paula De Almeida, Ana Tereza Ribeiro De Vasconcelos, Fernanda Abreu, Dennis A. Bazylinski, Christopher T. Lefevre

Life Sciences Faculty Research

© 2021 American Society for Microbiology. All rights reserved. We report the 3.7-Mb genome sequence of strain SS-5, a magnetotactic, sulfur-oxidizing rod and member of the family Chromatiaceae of the class Gammaproteobacteria, which biomineralizes membrane-bound, elongated, prismatic octahedral, magnetite nanocrystals. This genome sequence brings further diversity for understanding the origin and evolution of magnetotaxis and magnetosome biomineralization.

Utilizing Plastic-Degrading Microbes For Plastic Degradation, Brandon Garcia

Global Sustainable Development Projects

Our oceans are full of pollution and a large portion of those are plastics. They resist degradation from the elements and have long half-lives. About 300 million metric tons of plastic are dumped into our oceans every year. Many of these include polyethylene (PE), polypropylene (PP), polystyrene (PS), etc. Much of this is not recycled and so there is a massive accumulation of it present in our oceans. Microbes tend to form biofilms on these plastics and break them down. However, the relationship between plastics and the diversity of biofilm communities are being understood as well as how we can …

The Effect Of An Acidified-Gypsum Mixture On Broiler Litter Urease-Producing Bacteria And Nitrogen Mineralization, Taylor Chapman, Christopher D. Burt, Dave Bachoon, Miguel L. Cabrera, Christopher Horacek

Graduate Research Showcase

Broiler chicken (Gallus gallus domesticus) production is one of the largest agricultural sectors in the state of Georgia. Broiler litter produced by broiler facilities is rich in organic nitrogen (N), specifically urea, which can be mineralized by poultry litter urease-producing bacteria (PLUP) forming ammoniacal-N (NH₃/NH₄⁺). A large portion of NH₃/NH₄⁺ can be lost as ammonia (NH₃) gas, which negatively impacts bird health and profitability. The release of NH₃ from litter is strongly influenced by the pH of the litter. Flue-gas desulfurization gypsum (FGDG) has been suggested …