Source: CLEMSON UNIVERSITY submitted to NRP
SYSTEMS APPROACH TO IMPART STRESS RESILIENCE: ENHANCING THE DROUGHT-RESILIENCE OF CROPS THROUGH CROSS-INOCULATION OF BENEFICIAL RHIZOBIOME AND COVER CROPPING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1028223
Grant No.
2022-67014-37053
Cumulative Award Amt.
$649,898.00
Proposal No.
2021-09928
Multistate No.
(N/A)
Project Start Date
May 1, 2022
Project End Date
Apr 30, 2026
Grant Year
2022
Program Code
[A1102]- Foundational Knowledge of Agricultural Production Systems
Recipient Organization
CLEMSON UNIVERSITY
(N/A)
CLEMSON,SC 29634
Performing Department
Plant & Environmental Sciences
Non Technical Summary
The increasing frequency and intensity of drought pose a major threat to crop production by reducing the arable land. Also, increasing pressure on agricultural lands to feed the growing population could be partly alleviated by bringing droughted marginal lands back to mainstream agriculture. The above two could materialize only if robust practices are formulated to enable crops to tolerate drought. Breeding for drought tolerance in crop plants is a viable, but time-consuming strategy. Microorganisms associated with plant roots have been shown to provide drought tolerance to native, ruderal plant species, which could be adopted in crop production. However, transferring these microbiomes from ruderal species to crops without losing the functional trait of drought tolerance is rarely achieved due to the complexity of plant-microbe interactions and the lower persistence of the introduced microorganisms under field conditions. The proposed research focuses on identifying the microbiome that imparts drought tolerance in ruderal plants and devising strategies to transfer the microbiome-mediated drought tolerance trait to crop plants. Using field sampling and greenhouse experiments, the researchers will select and characterize the highly drought-tolerant microbiome from the native grass Andropogon virginicus adapted to drought conditions. Further, the effectiveness of the microbiome to impart drought tolerance in corn will be tested using a series of greenhouse experiments. The challenge of supporting the beneficial microbiome under field conditions will be achieved by selecting ideal grass cover crop species that are functionally similar to andropogon and corn. This would be achieved by selecting cover crop biotypes with a similar root exudate profile as that of Andropogon, and hence would sustain a similar microbiome community. The selection of a functionally similar cover crop would provide an ideal environment to amplify the microbiome in the field before corn is planted. Field experiments will be conducted to evaluate the efficiency of cover crops to amplify the inoculum of the selected microbiome and further the potential of this microbiome to provide drought resilience to corn.Overall, the proposed approach will enable the selection and application of microbiome in crop production systems to enhance drought resilience in crops.
Animal Health Component
40%
Research Effort Categories
Basic
50%
Applied
40%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1020110107080%
1321510110320%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships; 132 - Weather and Climate;

Subject Of Investigation
1510 - Corn; 0110 - Soil;

Field Of Science
1103 - Other microbiology; 1070 - Ecology;
Goals / Objectives
Frequent and intense drought caused by changing climate presents a major threat to cropping systems worldwide. It is increasingly recognized that rhizosphere microbial communities (rhizobiome) that associate with plants can impart drought tolerance in ruderal species. However, the transfer of rhizobiome imparted drought resilience from the lab or greenhouse to the field settings is rarely achieved, which prevents the large-scale utilization of rhizobiome mediated drought resilience in agro-ecosystems.The overall goal of this project is to enhance the drought-resilience of crops through the cross-inoculation of drought-resistant rhizobiome from ruderal species and to build up the beneficial rhizobiome in agricultural fields through compatible cover cropping. The PIs postulate that 1) ruderal plants adapted to droughted conditions can select and sustain a unique rhizobiome that imparts drought resilience; 2) the observed drought resilience is an outcome of the composition of the overall rhizobiome (system property), rather than being driven by a single/few microbial species; 3) the beneficial rhizobiome of the ruderal species could be shared and sustained across closely related crop species under environmental stress, but not under optimal growing conditions; 4) specific cover crops that have similar composition of root exudates as that of the ruderal species can help assemble and amplify targeted beneficial rhizobiome in the field.The main objectives of the project are to:i) identify the beneficial rhizobiome that facilitates drought tolerance in ruderal plants that thrive in droughted environments,ii) test the cross-infection compatibility and effectiveness of the beneficial rhizobiome to impart drought resilience in phylogenetically related crop species, andiii) utilize cover crops to propagate and stabilize the beneficial rhizobiome under field conditions.
Project Methods
Rhizobiome of Andropogon virginicus will be collected from multiple sites across the southern US that experience a gradient of droughted conditions. Greenhouse experiments will be conducted to evaluate the effects of field-collected rhizobiome on the growth performance of A. virginicus under drought and ambient moisture conditions. Additional experiments will test if the observed drought tolerance is a system-property. Plant growth performance, physiological and morphological responses will be measured. The diversity of rhizosphere bacterial and fungal microbial communities will be assessed using Illumina MiSeq amplicon sequencing, targeting 16S rRNA and ITS2 genes. Functional analysis of the microbiome will be conducted using metatranscriptomic approaches. Further, greenhouse experiments will be conducted to evaluate the effects of selected rhizobiome on the growth performance of corn under drought conditions. Using hydroponics experiments, cover crop species that are functionally similar to Andropogon with respect to their root exudate profiles will be selected. Field experiments will be conducted to evaluate the efficiency of the above cover crops to multiply the selected rhizobiome in the field, and the efficiency of the resulting microbiome to impart drought resilience in corn.

Progress 05/01/23 to 04/30/24

Outputs
Target Audience:The target audience included graduate and undergraduate students. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Ph.D. students had the opportunity to conduct 16S rRNA sequence analysis and gain hands-on experience in microbial community profiling and analyzing soil physico-chemical properties. Undergraduate students got experiential learning opportunities in microbial and soil analysis. How have the results been disseminated to communities of interest?The results are being generated and are not yet ready for dissemination. The study results related to this project,published in the Plant Journal in the last reporting period, were incorporated into the undergraduate and graduate soil coursetaught by the PI. What do you plan to do during the next reporting period to accomplish the goals?The ITS sequencing did not yield satisfactory results this time, so the plan is to repeat the sequencing for fungal ITS genes. In the next reporting period, we will plant Andropogon in soil from selected sites and subject it to drought and ambient moisture conditions. Fromthe collected rhizosphere soil, the site that will provide the maximum resilience to drought-stressed Andropogon plants will be selected for thesubsequent maize experiment. In the maize experiment, wewill measure all morphological and physiological plant parameters, plant secondary metabolites, and the diversity and function of rhizosphere microbial communities in maize subjected to drought and ambient conditions.

Impacts
What was accomplished under these goals? Soil samples were collected from various sites across different states, such as South Carolina, Georgia, Texas, Alabama,Louisiana, Florida, and Oklahoma,where Andropogon virginicus L., commonly known as broomsedge bluestem grass, naturally grows. The growing sites were identified through the SERNEC (Southeast Regional Network of Expertise and Collections) data portal, and metadata was collected to obtain the necessary permissions. Rhizosphereand bulk soil samples were collected from all sites and classified as mesic or xeric based on soil particle proportions and water-retaining capacity. Total soil DNA was extracted using the OMEGA Soil DNA Kit (Omega Bio-tek, USA) and the Quick-DNA Fecal/Soil Kit (Zymo Research), following the manufacturers' instructions. The V3-V4 region of the 16S rRNA gene was PCR-amplified, purified, and sent for 16S rRNA gene amplicon sequencing. The 16S rRNA sequences were analyzed to determine the bacterial composition of soil samples. The relative abundance of various phyla was observed, and alpha diversity metrics such as Chao1, Fisher, Observed, and Shannon indicated significant differences between rhizosphere and bulk soil samples, though no significant differences were observed between xeric and mesic soils. Beta diversity analysis comparing Andropogon virginicus with other grasses revealed that Andropogon rhizosphere samples formed a distinct cluster separate from the other grasses. Additionally, a linkage clustering tree of Andropogon virginicus beta diversity showed that most rhizosphere samples formed a separate cluster from bulk soil samples, with a few exceptions. Taxonomic comparisons at the phylum level indicated differences in abundance, particularly with higher Bacteroidetes and lower Planctomycetes in earlier samples compared to current ones. Soil nutrient and texture analysis of samples from all sites wascompleted. The soils from all sites were processed by sieving through a 2mm sieve to prepare for growing Andropogon and subsequentlymaize in the next season.

Publications


    Progress 05/01/22 to 04/30/23

    Outputs
    Target Audience:The target audience includes the scientific community, undergraduate and graduate students, and postdoctoral fellows. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project provided training opportunities for threegraduate studentson various aspects of soil microbiology and analytical techniques, as well as several undergraduates. How have the results been disseminated to communities of interest?Study 1 was published in the Plant Journal (Zhang Z, Jatana B, Campbell B, Gill J, Suseela V, Tharayil N. 2022. Cross inoculation of rhizobiome from a congeneric ruderal plant imparts drought tolerance in maize (Zea mays) through changes in root morphology and proteome. The Plant Journal, doi:10.1111/tpj.15775.) The PI incorporated the results of Study 1 into courses taught at Clemson. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period, we will collect soil of Andropogon virginicus from different regions of the southern states of the USA and focus on exploring the microbiome composition and its potential to impart drought tolerance to maize. This will help us understand the effect of different climatic and edaphic conditions on the rhizobiome composition of ruderal plants and how it, in turn, affects the rhizobiome efficiency to impart drought tolerance in crops.

    Impacts
    What was accomplished under these goals? Study 1: To identify the rhizobiome that imparts drought tolerance to ruderal plants, we selected the ruderal plant Andropogon virginicus and collected its rhizobiome from the rhizosphere. We cross-inoculated this rhizobiome into maize and subjected the maize to drought to analyze the potential of the Andropogon rhizobiome to confer drought tolerance to maize. Study 2: To explore general patterns of plant responses to drought stress and assess the microbial diversity among different plants, we conducted a meta-analysis using data from the NCBI database derived from published articles. We compared this data with a study conducted in our lab by Zhang et al., 2022. All the published studies involved different host plants. We found that the microbiomes inhabiting crop plants and grass species are influenced more by host plants than by environmental factors like drought. As host plants release root exudates, specific microbial taxa colonize the rhizosphere and endosphere. The results further reinforce our understanding that microbial communities are actively and dynamically shaped by genetic variation in host plants.

    Publications

    • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2022 Citation: Zhang Z, Jatana B, Campbell B, Gill J!, Suseela V, Tharayil N. 2022. Cross inoculation of rhizobiome from a congeneric ruderal plant imparts drought tolerance in maize (Zea mays) through changes in root morphology and proteome. The Plant Journal, doi:10.1111/tpj.15775.