Source: UNIVERSITY OF ARIZONA submitted to NRP
MICROBIAL COMMUNITY EFFECTS ON THE JOINT PERFORMANCE OF COMPETING RANGELAND WEED AND FORAGE SPECIES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
Reporting Frequency
Annual
Accession No.
1030729
Grant No.
2023-67013-40169
Cumulative Award Amt.
$845,800.00
Proposal No.
2022-11080
Multistate No.
(N/A)
Project Start Date
Jul 1, 2023
Project End Date
Jun 30, 2026
Grant Year
2023
Program Code
[A1402]- Agricultural Microbiomes in Plant Systems and Natural Resources
Recipient Organization
UNIVERSITY OF ARIZONA
888 N EUCLID AVE
TUCSON,AZ 85719-4824
Performing Department
(N/A)
Non Technical Summary
Yellow starthistle (Centaurea solstitialis) is a major weed of western rangelands in the United States, causing severe economic and ecological harm. Efforts to control its invasions have not been successful to date, and the plant has evolved increased growth and seed production in these populations, further exacerbating the problem. We have found large differences in the microbial communities associated with this weed across its range, and evidence that the microbiome can alter weed performance. This research will explore the possibility that soil microbes from within the western United States could be used to hinder yellow starthistle invasions and simultaneously increase the success of valuable forage grasses, all while avoiding risks associated with importing biocontrol agents from other continents.Our work begins by forming collaborations with ranchers who are dealing with yellow starthistle invasions on the ground. We will work with these collaborators to identify sites in need of control and to collect seeds and microbes from these areas. These seeds and microbial collections will become part of our experiments. Our experiments will also include microbial communities that we have been selecting for their ability to reduce the growth of yellow starthistle. We will compare the effects of these different microbiomes on yellow starthistle performance, and on starthistle's competitive effects on a desirable forage grass. We will identify the microbes involved in different outcomes, and examine how the genetic makeup of the plants affect their performance in our experiments. Together, this work will advance our ultimate goal to understand whether microbes could be leveraged for control of yellow starthistle, and to lay a foundation for testing our solutions in the real world.?
Animal Health Component
0%
Research Effort Categories
Basic
100%
Applied
0%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2130799114040%
2010799108030%
2060799107010%
1020799110010%
1020799110210%
Goals / Objectives
Our ultimate goal is to understand whether microbes could be leveraged for control of the noxious weed yellow starthistle (YST). Across our aims, we will test the potential for microbial control across competitive situations, grazing conditions, and YST genotypes. To do this, we will work with rangeland management partners to establish collections of plants and microbes from rangelands with active invasions, experimentally test the effects of microbial community variation on the joint performance of yellow starthistle and a preferred rangeland forage grass, identify the taxonomic and functional composition of the microbial taxa influencing plant performance, and map the genetic basis of microbiome variation in the host genome. Further, our aims integrate to inform questions about weed evolution, specifically whether reduced defenses have given YST growth and competitive advantages, and whether increasing enemy interactions could target the source of this invader's success. This research will explore the possibility that microbial taxa from within an invaded range could be leveraged to simultaneously manage a pest species and promote valuable forage, while avoiding risks associated with the import of biocontrol agents from the native range.Goal 1: Collaborations with rangeland managers with active YST infestationsOur project will establish collaborations with rangeland managers to identify focal field sites in need of control measures, where we will collect seeds and live soil. These will provide field-relevant materials for our experiments testing microbial effects on YST and forage performance, and establish relationships for future testing of management options.Objective 1.1: Establish relationships with ranchers interested in collaborations and visit potential field sites.Objective 1.2: Identify field sites and obtain collections of seeds and soil.Objective 1.3: Present findings to collaborating ranchers.Goal 2: Microbial effects on YST competition with forageUsing our focal field collections, we will conduct greenhouse experiments to test the effects of selected microbial communities on the performance of YST and annual ryegrass under competition, and their fitness throughout their lifecycles.Objective 2.1: Experimentally test the competitive performance of YST and ryegrass under selected vs. natural microbial treatments.Objective 2.2: Experimentally test the effect of simulated grazing on microbial effects on competitive performance of YST and ryegrass.Objective 2.3: Analyze results and prepare manuscripts of findings.Goal 3: Genetic basis of plant-microbe interactionsWe will use a genome-phenome wide association study to map variation in microbial taxa (ASV) abundance to genetic variation in YST that is influencing these associations.Objective 3.1: Conduct GWAS panel experiment to grow a diverse panel of YST under alternative microbial soil treatments.Objective 3.2: Sequence ASVs of microbial communities.Objective 3.3: Analyze results and prepare a manuscript of findings.Goal 4: Genotype and microbial environment influences on plant phenotypeWe will use genome-wide association mapping to identify the genetic basis of YST growth and immune function trait variation under competition under each of our soil treatments. Once candidate regions have been identified under each microbial environment, we will test for genotype x environment effects on growth and immunity phenotypes. This analysis will quantify the separate effects of genotype and environment, and the extent to which they modify the effects of one another on YST traits.Objective 4.1: Phenotype GWAS panel.Objective 4.2: Analyze results and prepare a manuscript of findings.Goal 5: Microbial variant effects on plant phenotypeWe will test for ASVs that differ between soil lines used as inocula. quantify which microbial taxa (or correlated suites of taxa) have the largest effects on plant size, and whether these are independent of genotype (expected not to vary across genotypes in the field) or are genetically-based (may vary, but in predictable ways with genotypes).Objective 5.1: Analyze phenotype and ASV results from GWAS experiment and prepare a manuscript of findings.Goal 6: Metagenome reference panelWe will conduct metatgenomic sequencing to provide a reference set of more complete microbial genomes for functional and taxonomic identification. We will assemble metagenomes and annotate gene functions.Objective 6.1: Sequence metagenomes.Objective 6.2: Assembly and annotation.Objective 6.2: Incorporate annotations into analyses and publications above.Goal 7: Communication of findings to multiple audiencesAn important goal of our work is communicating our findings across audiences to which we can contribute increases in knowledge and changes in action surrounding opportunities for microbial management of weeds in rangelands.Objective 7.1: Present results from this project at professional conferences, USDA meetings, and University of Arizona seminars and poster sessions.Objective 7.2: Present results from this project to collaborating ranchers managing active invasions.Objective 7.3: Present results from this project at regional weed management meetings, including the California Invasive Plant Council.Objective 7.4: Science communication through social media.Goal 8: Mentorship of early career scientistsThis research project will employ a postdoctoral, graduate student, and undergraduate researchers. Our goal is to mentor trainees at all of these stages through a successful research experience and future careers in the field.Objective 8.1: Employ and mentor undergraduate and graduate student researchers in STEM from diverse backgrounds at the University of Arizona.Objective 8.2: Employ and mentor a postdoctoral scholar to achieve a successful career.
Project Methods
Scientific methods:A) Field collections in collaboration with range managers: We will work with ranchers managing active yellow starthistle (YST) invasions to identify collections sites for YST seeds and associated soils. These relationships will allow us to test for microbial community effects on the most relevant YST plant genotypes and in comparison to the most relevant soil microbial context. These relationships will also create opportunities for future testing of potential microbial management applications on site in active rangelands.B) Experimental tests of the effects of soil microbial communities on YST and ryegrass competition, and its interaction with grazing: Using the field collections described above, we will use greenhouse experiments to test for improved outcomes of competition between YST and annual ryegrass when exposed to our selected microbial communities. We will also assess whether simulated grazing activity alters these outcomes of microbial inocula on competition.C) Plant genetic basis of plant-microbe interactions: We will grow a diverse set of YST under microbial treatments with high and low effects on YST growth to map the genetic basis of these interactions. We will use a low-coverage whole genome sequencing approach to genotype plants. To quantify representation of microbial taxa in endophyte and rhizosphere samples, we will use amplicon sequencing as we have done previously, which offers the advantage of high depth sequencing of an amplicon region, and therefore maximum power to detect differences in abundance of amplicon sequences between samples. We will quantify variation in microbial ASV abundance and map it to genetic variation in YST that is influencing these associations, using a genome-phenome wide association study (GPWAS). GPWAS is a recently-developed approach to associating many traits (a 'phenome') with genome-wide variants while controlling experiment-wide error rates. We will conduct this analysis separately for the High and Low soil inoculum populations, and for the endophyte and rhizosphere samples, as different ASVs are expected to dominate these populations. For ASVs with significant plant genetic associations, we will categorize their inferred functional traits, and test whether these are significantly higher or lower in the High vs Low inocula, indicating the direction of their effects on YST traits.D) Genotype and environment influences on plant phenotype: We will use genome-wide association mapping (GWAS) to identify the genetic basis of YST growth and immune function trait variation under competition under each of our soil treatments. Once candidate regions have been identified under each microbial environment, we will test for genotype x environment effects on growth and immunity phenotypes using linear models that test for fixed effects of genotype at a locus, environment (microbial treatment), and their interaction. This analysis will quantify the separate effects of genotype and environment, and the extent to which they modify the effects of one another on YST traits.E) Creation of a reference set of more complete microbial genomes for functional and taxonomic identification of amplicons: We will conduct metagenomic sequencing of a reference set of samples, using shotgun sequencing on the Illumina NovaSeq PE platform. We will use the assembled contigs to reconstruct metagenome-assembled genomes (MAGs). We will annotate genes against several databases: KEGG, eggNOG, CAZy for carbohydrate-active enzymes, NCycDB for nitrogen cycling genes, Pfam for protein families, CARD for antibiotic resistance genes, and antiSMASH for secondary metabolite biosynthetic gene clusters. Metagenomic data will also include virus sequences, and we will take the opportunity to create a reference database for these as well. We will link viral contigs to MAGs using three methods: CRISPR region similarity, genomic content similarity, and tetranucleotide frequency patterns.Efforts:Mentoring of a postdoctoral scholar to achieve a successful career in agricultural sciences, as part of their involvement in these research activities.Mentoring of student researchers in STEM from diverse backgrounds at the University of Arizona, as part of their involvement in these research activities.Presenting results from this project to collaborating ranchers managing active invasions.Presenting results from this project at professional conferences, USDA meetings, and University of Arizona seminars and poster sessions.Presenting results from this project at regional weed management meetings, including the California Invasive Plant Council.Science communication through social media.Evaluation milestones:Obtaining focal field site collections of seed and soil in collaboration with rangeland managers.Completing experimental tests of selected microbial community effects on YST and annual ryegrass, using focal field site collections.Completing experimental tests of the effects of simulated grazing on plant-microbial interactions under competition.Completing plant phenotyping of diverse set of YST genotypes (GWAS panel) grown under alternative microbial treatments.Completing plant genotyping of the GWAS panel.Completing microbial genotyping of ASVs from the GWAS panel.Completing microbial metagenomic reference sequences.Presenting of results to scientific audiences.Publication of the experiments in peer-reviewed journals.Presenting of results to range management collaborators, and to broader weed management communities.Mentoring of undergraduate students, graduate students, and postdoctoral associates to achieve desirable careers in science.

Progress 07/01/23 to 06/30/24

Outputs
Target Audience:Our goals were to reach the following target audiences, and below each are noted our efforts during this reporting period: Ranchers managing active starthistle invasions. In October of 2023, we conducted a key sampling trip, as planned in this award. This involved working with extension personnel, in direct collaboration with ranchers, to sample their lands for both starthistle (weed) seeds and associated soils. We worked with ranchers to identify collection sites and gather information about land use. We will report back to these same collaborators about our results. The weed science and management communities. Throughout this project we will report results to the scientific and management communities. Year 1 was early for results but we did have lab members presenting at the meeting of the California Invasive Plant Council in Nov 2023 (Anthony Dant) and at conferences in the first summer of the award in 2024 (start of Year 2 - to be included on next report). Early career scientists. During the reporting period, three undergraduate researchers at the University of Arizona joined the project and received training in plant biology, microbiology, and genetics, as well as career mentoring. Graduate student Anthony Dant was mentored to submit his own USDA NIFA EWD predoctoral fellowship in Fall '23 on the landscape genomics of weed establishment, which was awarded to begin on July 1, 2024. Postdoctoral fellow Jessie Pelosi was mentored to submit his own USDA NIFA EWD postdoctoral fellowship in Fall '23 on invasive plant-biocontrol interactions, which was awarded to begin on Sept 1, 2024.? Changes/Problems:We have not encountered major problems in our approach. We did encounter the fortunate 'problem' of two postdoctoral fellows receiving fellowships, in succession, to conduct their own independent work in our lab. To make sure that we can proceed with experiments without further delay, we will have a current outstanding PhD candidate Rebecca Bland in the lab lead the next phase of work as part of her dissertation. We do anticipate requesting a single year of No Cost Extension to accommodate these changes. What opportunities for training and professional development has the project provided? The original postdoc named on this project, Dr. Mae Berlow, was mentored to submit her own NIFA EWD postdoctoral fellowship, which was awarded with a start in July 2023, a major success for Dr. Berlow. As a result, she did not lead this project, but is conducting related work in the lab group under her fellowship, in particular the development of the microbial culture collection and synthetic communities noted above. Dr. Jessie Pelosi was identified as an outstanding candidate to assume leadership of the project as a postdoc. Due to his PhD graduation date, Dr. Pelosi was able to start in June 2024 (the end of this reporting period, Y1). For this reason, experimental activities were shifted later and we anticipate requesting a No Cost Extension. Further, Dr. Pelosi was mentored to submit his own NIFA EWD postdoctoral fellowship, which was awarded with a start in Sep 2024. This fellowship will allow him to work with our lab on the genomics of interactions between an invasive fern and biocontrol, the focus of his independent research program. This is a major success for Dr. Pelosi, but necessitates another shift in staffing for our project. In light of this, the next phase of the project will be led by PhD candidate in the lab Rebecca Bland, who will focus a major component of her dissertation on this work. Notably, Dr. Pelosi contributed to two papers with our group while supported by this award, before starting his fellowship, including a publication of the starthistle reference genome (see Products). Dr. Pelosi is currently being mentored to apply for faculty jobs and is already receiving interview invitations. PhD candidate Anthony Dant presented research to the California Invasive Plant Council and was mentored to submit his own USDA NIFA EWD predoctoral fellowship in Fall '23 on the landscape genomics of weed establishment, which was awarded with a start of July 1, 2024. In addition, three undergraduates have been involved in the project in Y1, gaining training in plant biology, microbiology, and genetics. How have the results been disseminated to communities of interest?This is the first year of the project, but we have successfully established collaborations and presented work at conferences as planned (see Target Audiences). In addition, the project has supported participants to contribute to completing related work, resulting in three publications (see Products). What do you plan to do during the next reporting period to accomplish the goals?Continue the project as planned, with a particular focus on completing the Goal 2 microbially-mediated competition experiment and launching the Goal 3-6 GWAS experiment. We also hope to begin utilizing the synthetic microbial communities under development.

Impacts
What was accomplished under these goals? Goal 1: Collaborations with rangeland managers with active YST infestations We are on track to meet all objectives under this goal, having established collaborations, identified field sites, and obtained samples per our project design. We look forward to sharing results with our collaborators as our data become available. Goal 2: Microbial effects on YST competition with forage We have delayed this experiment one year due to postdoctoral staffing changes (see Training and Professional Development section below). We expect to utilize a No Cost Extension to accommodate these changes. In the meantime, we have been developing a collection of starthistle-associated bacteria and fungi in culture that will allow us the opportunity to utilize synthetic microbial associations in future experiments. This development will improve our experimental control of microbial communities, ability to isolate the effects of taxa on plant performance, and move quickly to potential applications as biocontrol. Goal 3-6 Relate to the GWAS experiment that is planned for next year. Our current activities and preparations are preparing us to conduct this experiment and its associated analyses as planned. Goal 7: Communication of findings to multiple audiences We are on track with communications as planned (please see Target Audiences section) Goal 8: Mentorship of early career scientists We are on track with our goals to train undergraduate students, graduate students, and postdoctoral scholars. Please see the next section on Training and Professional Development.

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Berlow, M., Mesa, M., Creek, M. et al. Plant G?ΓΏ?Microbial E: Plant Genotype Interaction with Soil Bacterial Community Shapes Rhizosphere Composition During Invasion. Microb Ecol 87, 113 (2024)
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Bryan Reatini, Jessie A Pelosi, F Alice Cang, Qiuyu Jiang, Michael T W McKibben, Michael S Barker, Loren H Rieseberg, Katrina M Dlugosch, Chromosome-scale Reference Genome and RAD-based Genetic Map of Yellow Starthistle (Centaurea solstitialis) Reveal Putative Structural Variation and QTL Associated With Invader Traits, Genome Biology and Evolution, Volume 16, Issue 12, December 2024, evae243
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Chromosome-scale reference genome of Pectocarya recurvata, a species with the smallest reported genome size in Boraginaceae. Poppy C. Northing, Jessie A. Pelosi, D. Lawrence Venable, Katrina M. Dlugosch. Applications in Plant Sciences, In Press.