Environmental Microbiology and Microbial Ecology Commons^™

Evaluation Of Organic And Synthetic Herbicides Applications On Indicators Of Soil Health And Weed Suppression In A Conventional Cropping System In Louisiana, Caitlin Denux

LSU Doctoral Dissertations

Synthetic herbicides, with their varying modes of action, are well known for their efficiency in the suppression and control of weed species in U.S. agriculture. However, the consequences of using synthetic herbicides without attention to the surrounding environment can produce chemical run-off, changes in soil health and soil health conditions, and create herbicide-resistant weeds. These consequences have encouraged growers to find alternatives in their weed management programs. In this study, organic and synthetic herbicides were assessed on how well they performed in weed suppression surveys, and their potential effects on soil health indicators. Commonly used indicators include soil pH, β-glucosidase …

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 …

Mechanistic Examination Of Protist-Mediated Plant Growth Through The Comparative Development Of Medicago Truncatula, Shane Connolly

University Scholar Projects

Protists are known to increase plant growth through two main mechanisms: the microbial loop and the alteration of the root microbiome. The microbial loop is a nutrient recycling method in which protists provide inorganic nitrogen ions to the plant. Alteration of root microbiome leads to the removal of plant pathogens and shifting communities towards plant growth-promoting bacteria (PGPB). This study aimed to elicit which mechanism could produce the largest boost in shoot weight for Medicago truncatula. A series of microcosm experiments were explored in which M. truncatula was grown with variable microbiome structures to allow for mechanism differentiation. The …

Comparative Analysis Of Rhizosphere And Endosphere Microbiome Of Different Blueberry Species (Vaccinium Sp.), Niladri Bhowmik

Master's Theses

Blueberries are an important agricultural commodity in all over the United States. Due to its health benefits, there is a huge demand globally, thus expanding the industry. Breeding programs are essential to maintain such industries. Challenges that play a role in contemporary breeding programs are various biotic and abiotic stress factors. Studies have shown that microorganisms are recruited by plants to alleviate them during stressful conditions. Though blueberries have been cultivated for about 100 years, how the microbiome has been affected due to this is poorly understood. We hypothesized that interspecific crosses and artificial selection have significantly changed the microbiome …

Gene Expression Changes Linked To Phenylpropanoid-Based Resistance To Fusarium Head Blight Of Wheat, Shiv Singla

Department of Plant Pathology: Dissertations, Theses, and Student Research

Fusarium graminearum is a devastating pathogen of wheat that causes Fusarium head blight (FHB) and contaminates the grain with the mycotoxin deoxynivalenol (DON). Resistance to FHB is quantitative and it is important to identify additional genes conferring resistance against it. The goal of this thesis was to examine if the constitutive expression of two sorghum phenylpropanoid pathway genes, SbCCoAOMT (encoding caffeoyl-CoA O-methyltransferase) and SbC3’H (encoding p-coumarate 3-hydroxylase), in the moderately-susceptible spring wheat CB037 can provide Type-I and Type-II resistance to F. graminearum and determine the underlying mechanisms of the enhanced resistance. The constitutive expression lines (CCoAOMT413, CCoAOMT421, C3H112, …

Investigating The Impact Of Edaphobacter Aggregans (Wbg-1) On Arabidopsis Thaliana Development, Julia Talbert

Undergraduate Research Symposium

Acidobacteria is a phylum of bacteria that make up 50% of soil microbes. While making up a large proportion of bacteria found in soil, this phylum is largely unexplored with limited information about the bacteria and their impact on plant growth. The selected target of this study is Edaphobacter aggregans, WBG-1, which is a part of a subdivision of acidobacteria. Examining the bacteria’s effects on the development of the model plant Arabidopsis thaliana will provide insight into understanding this unknown phylum of soil-dwelling bacteria. Acidobacteria are an important realm to investigate as they affect agriculture practices. With Missouri being such …

Variation In Synthetic Floral Microbiome Composition Is Largely Ignored By Foraging Bumblebees, Nevin P. Cullen

2023 Midwest Ecology & Evolution Conference

Most flowers are occupied by diverse communities of microbes, which can alter floral attractiveness to key pollinators and floral fitness by interacting with floral traits. Different species of flower often acquire unique communities of microbes. Consequently, pollinators are frequently forced to choose between two flowers with distinct floral microbiomes while foraging. However, it is currently unknown whether pollinators have an inherent preference for flowers containing one floral microbiome over another, and whether microbial preference is modified by variation in floral traits. We investigated this knowledge gap using distinct bacteria and yeasts cultured from a nickel-hyperaccumulating plant and its non-accumulating relative. …

Elevated Co2 Drives Community And Network Structural Change Within Foliar Microbiomes Of Soybean, Connor Morozumi

2023 Midwest Ecology & Evolution Conference

Microbiomes within plants can play large roles in determining responses to stress or perturbation, increasingly common in a rapidly changing world. For example, foliar endophytes are known to increase stress tolerance to drought and decrease herbivory among many other effects. How these microbes are likely to respond to global change themselves is poorly understood. Global changes, such as increased atmospheric CO₂, which can influence host plant physiological processes, have the potential to directly and indirectly alter microbiome community structure. Here, we assessed community and network structure of bacterial and fungal phyllosphere microbiomes within soybean (Glycine max). …

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 …

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 …

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 …

Effect Of Soil Ph And Indigenous Bacterial Populations In Selecting Rhizobial Endophytes Within Soybean Root Nodules, Brianne Danielle Edwards

Graduate Theses/Dissertations

Soybean plants fulfill most of their nitrogen requirement by developing symbiotic associations with four different rhizobial genera, including Bradyrhizobium, Sinorhizobium, Mesorhizobium, and genus Rhizobium. In general, members of Bradyrhizobium and Sinorhizobium have been reported as dominant root nodule endophytes under acidic soils and alkaline soil conditions, respectively. So far, it is unknown whether the selection of rhizobial endophytes is regulated by their ability to survive under different soil pH or driven by host plants regardless of their relative abundance in soil. This study was focused on the assessment of the potential role of soil pH in …

Effect Of Soil Transplantation On Fungal Communities During Restoration, Thomas Luehl

All Master's Theses

Ectomycorrhizal fungi are integral parts of natural ecological systems that provide access to nutrients that would otherwise be unavailable by forming symbiotic relationships with plants. Relationships with ectomycorrhizal fungi are known to improve plant growth rate, increase plant resistance to pathogens, and improve survival. Current revegetation practices often ignore this relationship between fungi and plants. During the revegetation of the Interstate 90 Keechelus Lake wildlife overcrossing (Easton, WA), soil from forest sites adjacent to the restoration area were collected and used to inoculate a set of experimental plots to determine whether ectomycorrhizal fungi would become established in the plots and …

Fine-Scale Genetic Structure In Rhizosphere Microbial Communities Associated With Chamaecrista Fasciculata (Fabaceae), Mahboubeh Hosseinalizadeh Nobarinezhad, Lisa E. Wallace

Biological Sciences Faculty Publications

Soil microbiota of the rhizosphere are an important extension of the plant phenotype because they impact the health and fitness of host plants. The composition of these communities is expected to differ among host plants due to influence by host genotype. Given that many plant populations exhibit fine-scale genetic structure (SGS), associated microbial communities may also exhibit SGS. In this study, we tested this hypothesis using Chamaecrista fasciculata, a legume species that has previously been determined to have significant SGS. We collected genetic data from prokaryotic and fungal rhizosphere communities in association with 70 plants in an area of …

Simple Organic Fertilizer Amendments For Farming In Degraded Soils: Effects On Plant-Microbe Interactions, Andrew Adamski

All NMU Master's Theses

The rapid loss of topsoil, biodiversity, and water quality across agricultural land in the United States and the industrialized world poses some of the most important risks to the future of global and domestic food security. Not only is arable land being lost at an unsustainable pace, but the average age of farmers has also steadily been rising due to a myriad of barriers young, BIPOC (Black, Indigenous, and People of Color), and beginning farmers face. In an attempt to address these issues, worm castings, bokashi tea, fish hydrolysate, and biochar were applied alone and in combination to an extremely …

Nitrogen Availability In Dune Systems And Its Effect On Root Fungal Endophyte Communities., Haley E. Sage

College of Arts & Sciences Senior Theses

As global change persists, changes in resource availability can influence plant-microbe interactions. To understand how resource availability can influence these interactions and species diversity, I focused this research on how varying nitrogen (N) levels affect root endophyte communities in the plant species Ammophila breviligulata, an ecosystem engineer in the dune system. I analyzed the relationship between nitrogen addition and microbial community composition across 60 plots treated with three nitrogen addition levels (control, low, and high) in a long-term experimental field site in the Lake Michigan dunes. I identified Ammophila breviligulata's root endophyte community after creating a culture collection and …

Microbial Diversity And Community Structure In Sediments Associated With The Seagrass (Thallassia Testudinum) In Apalachicola Bay, Florida, Rahma Ahmed, Thomas Mcelroy, Troy Mutchler

Symposium of Student Scholars

Seagrass is an angiosperm which provides many ecosystem services in coastal areas, such as providing food, shelter and nurseries for many species, and decreasing the impact of waves on shorelines. A global assessment reported that 29% of known seagrass meadows are in a state of decline due to the effects of human activity. Seagrass is commonly found in shallow marine waters where they form meadows containing a microbiome that plays an important role in providing nutrients for seagrass growth, though little is known about the microorganisms within the seagrass meadow sediments. Our project collected sediments from seagrass meadows and adjacent …

Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen

Cal Poly Humboldt theses and projects

Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …

Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois, Anna M. Burns

Scripps Senior Theses

This thesis begins with the local history of the Liberty Prairie, the land where I conducted the ecological field-work that I later discuss in my second thesis on soil microbiome diversity (“Examining Soil Microbial Diversity in Transition Zones Between Corn Fields and Restored Prairie in the Upper Midwest"). I examine the Indigenous histories of the land, and the conflicts between the Bodwéwadmi and Euro-American settlers that resulted in the land being farmed for cattle, corn, and soy for over a hundred and fifty years. I then take a step back and analyze the broader historical contexts of Midwestern Corn Belt …

Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest, Anna M. Burns

Scripps Senior Theses

Prairies were once the largest ecosystem in North America, but agriculture and settlement has destroyed up to 99% of their pre-colonization extent. Prairie restorations are a strategy to recover the biodiversity and carbon sequestration functions of these grasslands, but typically occur in isolated strips between agricultural fields. My thesis analyzes how effective prairie restorations in the Liberty Prairie (northeastern Illinois) are at recovering the diversity of the prairie soil microbiome, focusing on verrucomicrobia abundance, alpha diversity, and soil physical characteristics.

Effects Of Traditional And Microbially-Focused Restoration Techniques On Soil Communities In Tallgrass Prairies, Zachary J. Whitacre

Masters Theses

Tallgrass prairies have virtually disappeared in many parts of their former range due to the conversion of this ecosystem to farmland. In more recent years there have been efforts to restore these prairies on reclaimed agricultural land. However, these restored prairies do not resemble their remnant counterparts in many ways, such as in soil microbial community composition and metrics related to carbon storage. In Chapter 1, I show that bacterial communities in a restored prairie and an adjacent remnant prairie in southwest Michigan differ in their immediate and longer-term responses to prescribed fire, a commonly used prairie restoration and maintenance …

Analysis Of Symptom Expressions And Transmission Rates Caused By The Plant Pathogen Phytophthora Ramorum On Native Chaparral Plants From The Genus Arctostaphylos, Bharati Gaonker

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Phytophthora ramorum is the causal agent of Sudden Oak death (SOD), ramorum dieback and ramorum leaf blight which affect both forest environments and nurseries. This oomycete pathogen has had a huge economic impact on the nursery and lumber industry. Forests in California have experienced substantial mortality of oaks affecting the forest dynamics and diversity. Our research investigates four native species and two ornamental cultivars of plants, which belong to the genus Arctostaphylos (manzanita) and are considered to be new hosts for P. ramorum in the chaparral ecosystem of California. Symptom expression and transmission rates were analyzed on Arctostaphylos glauca, …

Identification And Comparison Of Arbuscular Mycorrhizal Fungi And Soil Microbiomes Between American Chestnuts And Surrounding Hardwoods, Sarah Andrews, Geoffrey Eger, Isabella Vahle

Symposium of Student Scholars

Background/Questions/Methods

The introduction of the Chinese chestnut blight in 1904 decimated native American chestnut (Castanea dentata (Marshall) Borkh.) populations. In this study we aim to: 1) document the location of individual chestnuts in our vicinity; 2) document healthy versus blight infected individuals; 3) characterize putative differences in the soil microbiome between infected and non-infected individuals, as well as between chestnuts and hardwood neighbors. With this information we hope to provide new insights into mechanisms that may enhance blight and fungal resistance in American chestnuts through the understanding of the interactions between the trees and their surrounding soil microbiome.

Soil …

Fungi Associated With Herbaceous Plants In Coastal Northern California, Greg Huffman

Natural Sciences and Mathematics | Biological Sciences Master's Theses

The presence of fungal species associated with herbaceous plants was monitored in coastal Marin County, California, USA. The research involved a combination of field sampling surveys and data collection using a stratified random design, pathogen identification through microbiological and molecular analysis, and descriptive analysis and ordination of results. A total of two years of repeated sampling (four times a year) was organized to allow for the detection of seasonal differences in pathogen presence on aerial plant parts. The objective of this study was to identify microbial species present on herbaceous plants using ITS1 sequence analysis. Throughout March of 2018 to …

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 …

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 …

Impact Of Arbuscular Mycorrhizal Fungi On Conyza Canadensis Drought Responses And Possible Mechanisms, Kian G.M. Speck, Ylva Lekberg, Anna Sala

Undergraduate Theses, Professional Papers, and Capstone Artifacts

• Arbuscular mycorrhizal fungi (AMF) are important plant mutualists that can facilitate plant responses to various environmental stressors, such as drought. A plant that may benefit from AMF-induced drought tolerance is Conyza canadensis due to its ability to thrive in dry conditions and its high colonization rate. However, no studies have researched C. canadensis in this context and the exact mechanisms of AMF-induced drought tolerance are still unknown.
• To better understand if and how AMF facilitate drought response in C. canadensis, we conducted a greenhouse experiment comparing the response of mycorrhizal and non-mycorrhizal plants to three watering levels. We measured …

Remnant Assessment And Soil Inoculation To Inform Large-Scale Prairie Restoration At Eastern Washington University, Erik E. Peterson

EWU Masters Thesis Collection

The Palouse Prairie of Eastern Washington and Western Idaho, characterized by rolling hills of deep loess soil, is one of the most endangered ecosystems in the world, with more than 99% converted to tilled farmland. To mitigate this loss, Eastern Washington University has begun prairie restoration on a tilled wheat field adjacent to campus, in the northern extent of the Palouse Prairie Ecoregion. However, effective restoration requires understanding reference conditions, and there are relatively few studies of remnant prairie plant communities or soils, particularly in the Northern Palouse. From north to south in the Palouse Prairie Ecoregion, there are gradients …

Roles Of Non-Frankia Bacteria In Root Nodule Formation And Function In Alnus Sp., Kelsey Christine Mercurio

Honors Theses and Capstones

Plant roots are home to a wide variety of beneficial microbes; understanding and optimizing plant-microbe interactions may be critical to enhance global food security in a sustainable, equitable way. With the help of their nitrogen-fixing bacterial partner, Frankia, actinorhizal plants form symbiotic root nodules and play important roles in agroforestry and land reclamation. However, Frankia does not live alone in nodules, and the other microbial residents may contribute to nodule formation and function. We collected root nodules from alder trees (Alnus sp.) in 2018 and 2019, then isolated DNA and individual bacterial strains to characterize the nodule microbial …

Inaction On Lead Despite The Relevant Knowledge: Predictors, Covariates, And Outreach Implications, Alessandra Rossi, Bernabas Wolde, Pankaj Lal, Melissa Harclerode

Department of Biology Faculty Scholarship and Creative Works

Testing residential soil and paint for lead provides actionable information. By showing where and how much lead exists on the residence, it allows one to quantify risk and determine the best ways to reduce exposure along with the corresponding health and financial costs. For these reasons, several federal and state programs offer outreach to audiences on the benefits of testing residential soil and paint for lead. Not all individuals who know about lead’s adverse health effects, however, test their residence for lead, potentially limiting the actionable information that could have helped to reduce their exposure. Such individuals represent a challenge …