Summer Research and Extension Experience for Undergraduates at the Interface of Plant, Microbial and Bioenvironmental Sciences

Week 1

• Orientation and administrative training
• Tour and introduction to PLPM laboratories
• Individual student-mentor meetings and REEU plan

Week 2-9

• Individual student-mentor REEU projects discussion
• Laboratory or field research and extension activities
• Weekly brunch/lunch seminar by faculty mentors, featuring critical feedback from students
• Participate in scheduled LAUNCH and College professional development activites

Week 10

• Conclusion of student research projects
• Presentation of research mini symposium
• Focus group feedback discussion

Three items should be sent by applicants in one e-mail with subject “IPMB REEU APPLICATION” to Thomas Chappell ([email protected]) by the deadline, as attachments (not as links to file-sharing services):

1. An internship application form, written by you, developed with feedback from your desired internship host or members of the host’s research team.
   • The statement should describe your interest in research and/or extension topics.  The topic(s) you describe should align with the research and/or extension focuses of you desired host laboratory group.  For information about research being conducted in potential host laboratories, please see the table and descriptions below.
2. An academic transcript (can be unofficial)
3. A resume or CV reflecting experience relevant to research

The fourth item is a recommendation letter (at least one; additional letters may be sent if desired), which you should arrange to be sent directly to Thomas Chappell ([email protected]) by someone at your home institution familiar with your academic and research experience.  Note, no previous research experience is required for this program.  Please request that letter writers use e-mail subject “IPMB REEU REFERENCE” to expedite application processing.

Dr. Sanjay Antony-Babu

Topic: Plant and soil microbiomes

The Antony-Babu Lab focuses on understanding the dynamics of inter-kingdom microbiome-interactions and how it affects the crop production. The lab uses cutting-edge culture-independent (metagenomics, metatranscriptomics and metabolomics) and culture-dependent (culturomics) methods combined with computational biology. The research has several direct biotechnological applications, and the research in the lab focuses on the following key topics. 1) Biofertilizer/biopesticide development: By disentangling the microbial functions that are essential for different growth stages of crop plants, the lab intends to develop “soil probiotics” to improve crop health; and 2) Pathobiomes of plants: Deciphering the interaction between a plant pathogen and its associated microbiomes is necessary to understand pathogenesis and also to design control measures.

Dr. Thomas Chappell

Topic: Plant disease epidemiology and its environmental drivers

The Chappell lab studies plant diseases through modeling and develops software-based forecasting tools useful for a variety of purposes in agriculture and beyond. Undergraduates have pursued diverse projects related to plant disease epidemiology: laboratory studies of moisture and spore mobility in soils, experimental evolution of virulence in a pathogenic/saprophytic-lifestyle fungus, phenology of insect vectors of plant viruses, and programming/robotics to create dataloggers and experimental manipulation to provide data for empirical modeling of environment-disease relationships. These results are used in predictive models, particularly for management of agricultural diseases under varying environmental conditions. Historically, undergraduates have begun projects with experimental design anticipating thorough analysis, commenced research involving purpose-build electronic environmental data recorders, engaged in data science activities of merging and processing multiple sources of data, and concluded with the analysis and modeling.

Dr. Baoye He

Topic: Plant-fungal interactions and signaling

The He lab explores the fascinating world of plant-microbe interactions, focusing on how extracellular vesicles (EVs) mediate communication between plants and fungal pathogens. EVs are nano-sized lipid bilayer vesicles secreted by cells, functioning as carriers of proteins, RNAs, and other bioactive molecules to mediate intercellular communication. A combination of genetics, biochemistry, live imaging, cell biology, and genome editing is used to uncover the roles of EVs in these interactions. This research, primarily using Arabidopsis and the fungal pathogen Botrytis cinerea as model systems, aims to reveal how EVs influence plant defense and pathogen strategies. Dr. He also extends his studies about EVs to key crops like cotton and maize, with the goal of developing innovative methods for controlling fungal diseases.

Dr. Thomas Isakeit

Topic: Extension program in agronomic and vegetable crops

Dr. Isakeit’s extension program addresses significant and current problems affecting agronomic and vegetable crops in Texas, with an emphasis on cotton, corn, sorghum, and watermelon. Students learn how to isolate and culture bacterial and fungal pathogens from different crops, and how to set up and evaluate field experiments. One student in 2017 was responsible for isolating and studying the growth of Pithomyces sp., a fungus implicated in causing a photosensitivity problem in cattle when they graze on contaminated pastures. In 2020, one student was responsible for determining the identity and survival of a Stemphylium fungal species that was causing losses from leaf spots produced on aquaponically-produced organic lettuce. The projects were tailored to the abilities of students, and these results helped Dr. Isakeit to better inform the growers and stakeholders.

Dr. Young-Ki Jo

Topic: Extension in turfgrass, rice, and pecan diseases

The Jo Lab’s extension program is directed to the discovery of best management practices for turfgrass, rice and pecan diseases and the convey of this information to agricultural industries. The attempt to develop holistic disease management strategies with a minimal risk of causing adverse environmental impact is responding to current important issues in Texas agriculture. For achieving this goal, pathogen populations have been studied for the control strategies since the populations continuously evolve to survive and adapt to a given environment condition affected by agricultural practices. The Jo lab has developed the integrated pest management (IPM) programs for economically important plant diseases based on proper diagnosis, environmentally friendly approaches, alternative agricultural methods and chemical management practices. Students will learn validation and characterization of pathogens and beneficial microbes in plant health.

Dr. Mike Kolomiets

Topic: Oxylipins in plant defense, plant growth and signaling

The Kolomiets Lab studies plant signaling, including how plants communicate within and between themselves and other plants and organisms. Plants produce oxylipin (oxidized lipids) signals for communication. Oxylipins in humans are known as eicosanoid hormones that regulate most physiological and pathological processes. It is expected that oxylipins in plants play pivotal roles in many if not all aspects of biology and serve as signals to normally grow and develop and to properly respond to biotic and abiotic stresses. The lab has created an extensive and unique library of corn mutants disrupted in the biosynthesis of volatile and non-volatile oxylipins and has been testing these mutants for any changes in (1) growth and development, (2) for their ability to communicate via volatiles with other plants, and for their response to (3) pathogens, (4) insect herbivores, (5) root colonizing symbiotic microorganisms, and (6) drought and salt stress. The students will be able to learn diverse reverse genetics, plant molecular biology, physiology and genomics tools, biological assays for testing stress resilience of corn, and analytical chemistry.

Dr. Kevin Ong

Topic: Extension in emerging diseases and plant disease diagnostics

Dr. Kevin Ong directs the Texas Plant Disease Diagnostic Lab (TPDDL-CS), a National Plant Diagnostic Network member lab. This service lab based in College Station has been providing interested undergraduate students opportunities to work, intern and gain practical experiences in a diagnostic service lab environment. His Applied Research Unit (TPDDL-ARU) help to provide development, optimization and validation of molecular diagnostic tests. The TPDDL-ARU also functions as a National Clean Plant Center for Roses, conducting virus screening to ensure the “cleanliness” of Old Garden and Heritage Rose stock materials. Current projects at the TPDDL-ARU includes development and optimization of pathogen detection in seeds, focusing on pathogen of regulatory concerns. Partnership with Texas Department of Agriculture (TDA) provides an avenue for student to gain further experience in the field with TDA inspectors. Students will have opportunities to participate in development, improvement and implementation of plant diagnostic methods.

Dr. Clint Magill

Topic: Plant host/pathogen interactions, sorghum resistance to fungal pathogens

The Magill Lab investigates the genetic mechanisms underlying host-pathogen interactions in sorghum, focusing on resistance and susceptibility to fungal diseases. By leveraging genome sequencing of both sorghum and its pathogens, the lab aims to identify key genes involved in host specificity and disease resistance. Current research includes identifying resistance genes in sorghum against anthracnose, head smut, and downy mildew, as well as uncovering the genetic basis of race specificity in the causal pathogens. This work contributes to developing disease-resistant sorghum cultivars for sustainable agriculture. Undergraduate experience will include media preparation and growth of fungal pathogens under sterile conditions, PCR verification of prospective heterokaryons or diploids, recovery of pure cultures, and similar experiments.

Dr. Won Bo Shim

Topic: Fungal plant pathogens

The Shim lab is focused on determining key genetic mechanisms associated with crop diseases caused by diverse Fusarium species and finding innovative management strategies. Key diseases we are currently addressing are Fusarium ear rot of corn and Fusarium wilt of cotton. Crop losses as well as regulatory, testing, and management costs associated with mycotoxins due to corn ear rots tops $1 billion annually in the US. The recent emergence of Fusarium wilt of Pima cotton in Texas is raising huge concern for $7 billion Texas and US cotton growers. For cotton Fusarium wilt, we are developing next-generation biocontrol tools by deciphering genetic and metabolic communication in plant rhizosphere. We have established strong collaborations with AgriLife, TEEX, and international colleagues to expand our research scope and broaden the impact of technological advancements. For instance, the Shim lab and Texas A&M Engineering collaborators are identifying plastic-degrading fungi and their associated enzymes that can degrade polyethylene and polystyrene plastics. The program is aggressively pursuing opportunities to solve global agricultural and environmental issues.

Dr. Joseph Edwards

Topic: Plant and soil microbiomes

The Edwards Lab investigates the intricate relationships between plants and their root microbiomes, focusing on beneficial, commensal, and pathogenic microorganisms that influence plant health and resilience. This research explores how host genetic factors shape microbiome assembly in bioenergy and native grasses, as well as the staple crop rice. By leveraging metagenomic sequencing, bacterial isolation and genome sequencing, GWAS and QTL mapping, and transcriptomics, we aim to uncover the genetic and molecular mechanisms governing plant-microbe interactions. Our goal is to develop microbiome-informed strategies to enhance plant immunity, improve crop productivity, and promote sustainable agriculture. Through interdisciplinary collaborations, we strive to advance fundamental knowledge and translate discoveries into innovative agricultural solutions.

Dr. Brian Shaw

Topic: Fungal growth and development

The Shaw Lab uses advanced microscopy to investigate the cellular and molecular basis for fungal growth and development. In fungi, production of hypha utilizes two cellular structures unique to fungi: a tip body called a Spitzenkorper that concentrates exocytosis to the cell apex, and a sub-apical collar enriched for endocytosis found just behind the Spitzenkorper. Students will use fusion PCR to create constructs to insert coding sequence for fluorescent proteins (GFP and mCherry) into the genomic native locus for genes of interest in the maize pathogen Colletotrichum graminicola. Students will then image transformants using a laser scanning confocal microscope to document the dynamic localization of the proteins within the growing cell to these unique fungal structures. We also have found that C. graminicola conidia produce an adhesive in only one region of the spore. Adherence at this region triggers germination. Spores that do not make contact with the substrate in this region do not attach and therefore can be dispersed further until they settle onto the surface at their adhesive region. Students will investigate the cellular basis for spore attachment and develop models for how this selectivity enhances spore dispersal in the field.

Dr. Jeanmarie Verchot

Topic: Plant virology and biotechnology

The Verchot lab has developed pipeline for screening Arabidopsis mutant lines for bZIP transcription factors that regulate virus resistance. Arabidopsis is the principal model for plant genome analysis, studying plant-virus co-evolution, and the molecular genetics of virus resistance and pathogenicity. This proposed research investigates the critical genetic responses underlying anti-viral defenses in plants.  We reported the Turnip mosaic virus (TuMV; a potyvirus) and Plantago asiatica mosaic virus (PlAMV; a potexvirus) induce the expression of three bZIP TFs (bZIP17, bZIP28, and bZIP60) in Arabidopsis.  In this research, undergraduate students will be screening a library of Arabidopsis KO mutant plants by inoculating them with GFP containing virus infectious clones, TuMV-GFP and PlAMV-GFP. They will collect digital images of GFP and between 5- and 14-day post inoculation to record changes in host susceptibility. They will learn to use IMAGE J to quantify GFP fluorescence and conduct statistical analysis of the data to identify host genes that restrict or exacerbate virus infection.