Source: UNIVERSITY OF HOUSTON SYSTEM submitted to NRP
PARTNERSHIP: ELUCIDATING BIOGEOCHEMICAL CYCLING OF SILICON TO IMPROVE PLANT BIOMASS, CLIMATE STRESS TOLERANCE AND CO2 SEQUESTRATION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
Reporting Frequency
Annual
Accession No.
1032174
Grant No.
2024-67020-42342
Cumulative Award Amt.
$885,789.00
Proposal No.
2023-10265
Multistate No.
(N/A)
Project Start Date
Jul 1, 2024
Project End Date
Jun 30, 2028
Grant Year
2024
Program Code
[A1401]- Foundational Program: Soil Health
Recipient Organization
UNIVERSITY OF HOUSTON SYSTEM
4800 CALHOUN ST STE 316
HOUSTON,TX 770042610
Performing Department
(N/A)
Non Technical Summary
Climate change has influenced global rainfall and water availability patterns, affecting soil chemistry and moisture. Increased incidences of drought and unprecedented heatwaves have significantly enhanced the evapotranspiration from the agricultural soil- creating soil salinization. Soil salinity is a significant factor in maintaining a sustainable crop production system. This has affected approximately 20% of the current arable land (one-third of food-producing). Adapting eco-friendlier approaches and understanding the dynamic natural soil and plant physiological systems can solve several agricultural productivity issues. Also, utilizing natural nutrient application and management can improve carbon capture and storage, which can be an ideal strategy to overcome the impacts of climate change. Silicon (Si) - is a quasi-essential soil element widely distributed in the earth's crust and accessible to plants as silicic acid, which can improve plant growth and development. Very little is known about how Si can influence carbon storage and capture in saline agricultural soils. This complex process has been extensively investigated in aquatic ecosystems; conversely, it is least explained in agricultural soil systems. Also, soil-based carbon-Si interactions during plant growth and its molecular physiology during salinity stress have not been well known, especially in soybean crops. Hence, through this project, we will understand how Si interacts with the carbon sequestration process in the rhizosphere during salinity and how it is translocated in the above-ground parts of soybean plants. The objectives of the project are: (i) elucidate the Si mobilization and uptake in the rhizosphere with reactive nutrients and sequestration of CO2, (ii) Investigate the effect of Si on physiological and molecular responses of soybean under salinity stress, (iii) determine the CO2 sequestration process and perform phenotyping and biomass production assessment during Si application. This project will use the greenhouse and field-level experiments on plant-Si-stress interactions to identify interactions with CO2 sequestration and nutrient cycling in the soil of soybean plants. The project activities will be performed by three minority-serving institutions, which will help to improve the knowledge, skills, and abilities of under-representative students in soil biogeochemistry, climate change, and molecular assessments for improving crop production.
Animal Health Component
50%
Research Effort Categories
Basic
40%
Applied
50%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1030110200020%
1021820102020%
2011820104020%
2031820105020%
1320110200010%
1020110200010%
Goals / Objectives
Goal:The long-term goal is to establish a climate-smart plant and soil health system by enhancing Si uptake and CO2 sequestration during soil salinity stress to crops. We hypothesize that silicic acid's ionization process can help Si assimilation in the rhizosphere, improving plant vigor, carbon capture, and salinity stress tolerance. Si amendments such as silicate rock can potentially reduce global warming by reducing CO2 emissions and increasing carbon sequestration in the soil. We will use lab, mesocosms, and field trails-based approaches to understand the interactions of Si-CO2 in soybean crops during saline conditions. Soil salinity hinders soybean production, an essential semi-silicious, bioenergy food crop, and it is produced relatively lower in Texas compared to other Midwest states.Objectives:This project focuses on the following specific objectives: Objective#1: Elucidate the Si mobilization and uptake in the rhizosphere with reactive nutrients and sequestration of CO2 in salinity.Objective#2: Investigate the effect of Si on physiological and molecular responses of soybean under salinity stressObjective#3: Determine the CO2 sequestration process and perform phenotyping and biomass production assessment during Si application.We hypothesize that Si-mediated physiological adjustment during salinity stress can protect root architecture and be essential in Si-based stress tolerance. However, the underlying molecular mechanisms that benefit crop yield and defenses have not been elucidated extensively. Furthermore, the field-level interactions of plant-soil salinity and Si have not been well known. Although the aquatic Si and CO2 feedback mechanisms are well-known, the mechanism by which Si interacts with the CO2 sequestration process in the terrestrial soil system, specifically the plant's rhizosphere, has been least known. There are significant knowledge gaps, and some of the main questions are outlined below:How do factors (pH and root exudation) influence Si's transport, cycling, and binding potential from primary minerals into H4SiO4 in agricultural soil systems?How does Si interact with reactive nutrients (Ca, Na, and Fe) to facilitate the mobilization and CO2 sequestration process in soil?What are the physiological and genomic responses of soybeans to the combined effects of Si application and salinity stress?How does root exudation (organic acids and isoflavones) influence Si uptake and mobilization?How can the Si-CO2 interactions help improve soil and microbial health and plant biomass in soils?To achieve the objectives, we will screen more than 30 soybean genotypes to assess their abilities in Si uptake and interactions with CO2 with or with salinity. The best genotype will be evaluated molecularly to identify pathways and gene networks for Si uptake. This will be followed by field-level cultivation to assess Si-CO2 and salinity interactome on soil health and plant biomass using Unmanned Aerial Vehicles (UAV) hyperspectral sensors at saline and non-saline agriculture fields.The project investigators from three minority-serving institutionswill manipulate plant-Si-stress physiology interactions through multi-omics (transcriptomics and metabolomics), geochemistry, and molecular analysis to explain the critical questions in Si-CO2 translocation to improve plant growth and soil salinity stress tolerance. We will involve undergraduate and graduate students to build their capacities in soil geochemistry and climate change plant biology. In addition, we will organize a training workshop every year for farmers on Si's role and potential benefits associated with increased biomass and GHG sequestration.
Project Methods
Objective#1: Elucidate the Si mobilization and uptake in the rhizosphere with reactive nutrients and sequestration of CO2.To achieve this objective, we will establish mesocosm experiments to evaluate the Si mobilization and uptake by the roots with or without reactive nutrients and ambient CO2 conditions. Advanced microscopy, chromatography, and spectroscopy approaches will be adopted to elucidate the ion compositions, distribution, and uptake from soil or substrate medium into the root and shoot parts. For this purpose, we will use several soybean cultivars (~30), which will be screened for Si uptake and NIP/LSi1 gene expressions. For this objective, our milestones will be Milestone 1.1: Determine Si mobilization and translocation in the plants with or without salinity, Milestone 1.2: Explain the Si uptake with or without the presence of reactive nutrients, Milestone 1.3: Elucidate Si and substrate nutrient management to influence rhizospheric and atmospheric carbon capture during salinity, Milestone 1.4: Elucidate the root exudation during the Si uptake in salinity. We will implement several sets of plant-Si-salinity and CO2 interaction experiments through integrative methods of explaining plant (morphology and anatomy), soil (inorganic chemistry and physical characteristics), and biogeochemical regulations. This will help to understand the Si mobilization, uptake, and translocation by soybeans during salinity stress conditions.Objectives # II - Investigate the effect of Si on the physiological and molecular responses of soybeans under salinity stress.To achieve this aim, we will perform molecular analyses based on greenhouse experiments to understand the Si-Salinity-Carbon capture potentials. We will study the two soybean genotype varieties (High- and Low Si accumulator) and their performance under Si and salinity stress based on agronomic and physiological parameters. We will also use advanced molecular tools such as mRNA- and miRNA-sequencing to identify genes and pathways regulated by both Si and salinity. In this objective, we planned milestone 2.1, which focuses on assessing the effects of Si on agronomic and physiological parameters under salinity stress conditions in greenhouse-grown soybean plants. Milestone 2.2 will help to evaluate the gene expression related to Si uptake and transport in Soybean cultivars, which will be followed by achieving milestone 2.3, to study the transcriptomic and miRNA changes in response to Si application and salinity stress and identify candidate genes and pathways responsive to the carbon capture process. Novel genes identified in these studies will be used to molecularly breed semi-silicious crops to improve salinity stress resilience and carbon capture.Objective#3: Determine the CO2 sequestration process and perform phenotyping and biomass production assessment during Si application.The milestones for this objective are to: Milestone 3.1: Assess the plant growth, root architecture, and biomass using UAV-based technologies at field levels; Milestone 3.2: Evaluate the field-level efficiencies of CO2 capture and storage in Si application; Milestone 3.3: Determine the soil and microbial health during exogenous Si; and Milestone 3.4: Determine the phytohormonal and root metabolite exudation impacts during Si. We will perform field-level experiments to replicate the beneficial impacts of Si and its broader potential to sequester CO2. In Milestone 3.1, we will focus on applying Si to soybean plants under field conditions with or without salinity and assess root architecture, plant biomass, and yield. We will use the agricultural land at the University of Houston Coastal Center (UHCC) and PVAMU. The soil is already partially saline (at UHCC), supporting the coastal area grassland ecosystem, and thus would be a fit for performing field trials. A split-plot block design will be used in this experiment with 30 plots (5 treatments x 3 replications x two sets - control and salinity). Each plot will be 2.0 m wide by 8.0 m long. We will implement two Si sources to be applied at the early V2-V3 stage of soybean growth. For this purpose, we will apply foliar Si androot zone wollastoniteapplication with and without a recommended dose of fertilizer (Fig. 11). We will use a UAV fitted with hyperspectral sensors to target Si, chlorophyll, and salinity. UH Department of Earth Science is equipped with several different classes of such UAVs. We will monitor plant biomass, root architecture, and yield levels at different growth stages of plant development. To achieve Milestone 3.2, we will evaluate the field-level efficiencies of CO2 sequestration and carbon capture during Si application. The CO2 sensors installed at different locations will record the canopy and rhizosphere compartments to understand the carbon dioxide capture and storage in soybean plants. For Milestone 3.3, we will determine the soil and microbial health using amplicon sequencing to determine microbial diversity and abundance across different treatments. Milestone 3.4 focuses on the phytohormonal (gibberellins, salicylic acid, and abscisic acid) contents in the root and shoot regions of the soybean plants. The phytohormones have been used to assess stress tolerance-related traits in soybean plants during salinity. Indeed, the metabolic activity of soybeans fluctuates due to physiological changes caused by growth conditions. Each sample will be analyzed five times to increase the level of confidence.

Progress 07/01/24 to 06/30/25

Outputs
Target Audience:Over the past year, the project has established a strong partnership among the three participating institutions (UH, UNGC, and PVAMU). This included monthly project progress discussions, presentations, and in-person lab visits. Besides establishing the resources (chemicals / consumables) to execute the work, we optimized, tested, and executed research experiments related to the three core objectives of the project. We assessed 15 soybean genotypes, and 10 more are currently in the greenhouse for data collection. The main focus of these experiments was to evaluate (i) silicate uptakes, (ii) plant biomass, (iii) CO2 fixing and storing in plant and soil, (iv) soil health (nutrients and microbial activities) in soybean plants exposed to saline conditions.We also established robust methods for soil analysis and testing using near-infrared spectroscopy and multispectral analysis alongside machine learning models. These methods will help us to predict and quantify soil health, specifically the silicates. During the project execution, two more spin-off research studies were identified that could provide more insight into the project plan. During year#1, the project research resulted in two research articles and one review paper in highly reputed and peer-reviewed journals. In addition, another review paper on combined abiotic stress (including salinity) is in the review process. These publications will provide strong knowledge to fellow scientists who are working on Silicon and soil health topics. The project activities are supporting the thesis research of two PhD students and one MS student who are focusing on soil biogeochemical cycling, salinity, soil health, and plant molecular physiology. The project activities also provided opportunities to 6 undergraduate students to perform capstone research. The project activities also helped to train a high school science teacher in soil health. In addition, the project activities were disseminated using social and electronic media using the University of Houston platforms. The project activities and research focus were also publicized on local TV and related electronic media, where the efforts of USDA-NIFA were acknowledged. The project has also strengthened collaboration across three institutions (UH, UNGC, and PVAMU) to jointly work on different aspects of this research. The monthly meeting of PD, Co-PDs, and related students involved has also increased the sharing of more knowledge and related expertise across the three institutions. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Graduate:The project activities are supporting the thesis research of two PhD students and one MS student. One PhD student is working on Silicate-Salinity and CO2 sequestration, whereas the other is working on understanding genetic mechanisms behind salinity tolerance and silicate localization in soybean crops. The MS student is working on screening around 50 vegetables, grasses, and commodity crops for silicate uptake, phytolith accumulation, and plant biomass production. Undergraduate:The project activities also provided opportunities for 6 undergraduate students to perform capstone research. These undergraduate students performed lab and greenhouse-based experiments to learn key skills related to research (planning, design, literature, data collection and analysis, communication, and problem-solving skills) and soil health-related topics. Also, we have incorporated one lecture session for undergraduate students on the importance of Soil Health as part of the Plant Biotechnology Course. School Teacher:The project activities also helped to train a high school science teacher in soil health. This is part of the teachHouston program. The teacher is undergoing training to understand the soil and soilless systems of plant growth and perform soil health analysis. Networking and Collaboration:This will help improve students' understanding of key concepts related to plant production. The project has also strengthened collaboration across three institutions (UH, UNGC, and PVAMU) to work jointly on different aspects of this research. The monthly meeting of PD, Co-PDs, and related students involved has also increased the sharing of more knowledge and related expertise across the three institutions. How have the results been disseminated to communities of interest?Over the reporting period (2024-2025), we were extensively involved in disseminating key information about project planning and implementation. Research related information on the Si and soil health was published in peer-reviewed journals. In addition, print, electronic, and social media platforms were used to disseminate project information. This information was shared on the University of Houston's and PD's labwebsite and social media accounts. In addition, the project information was shared with the public and farmers through ABC Houston reporting. 1. University of Houston Part of a $7.9M Effort to Promote Soil Health. https://www.morningagclips.com/university-of-houston-part-of-a-7-9m-effort-to-promote-soil-health/ 2. "University of Houston researchers earn USDA grant to help make crops more weather-resilient," ABC Houston. (October 10, 2024). https://abc13.com/post/university-houston-researchers-earn-grant-united-states-department-agriculture-make-crops-more-weather-resilient/15460304/#:~:text=HOUSTON%2C%20Texas%20(KTRK)%20%2D%2D,as%20heatwaves%2C%20floods%20and%20droughts. 3. US (TX): University of Houston part of $7.9M USDA grant https://www.hortidaily.com/article/9671652/us-tx-university-of-houston-part-of-7-9m-usda-grant/ 4. Doing the Dirty Work: UH Part of $7.9M Initiative to Promote Soil Health and Tackle Climate Change," UH Research. (September 2024). https://stories.uh.edu/091224-doing-the-dirty-work-soil/index.html In year 2, we will be preparing a webpage to disseminate more scientific information related to salinity, soil health, and silicon application. This will help to reach out to wider audiences. We will also planpresentations to localfarmers on Soil Health from Fort Bend and Harris Counties. For this purpose, we will collaborate with AgriLife Extension Services. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting cycle, we will complete objective#1 and start work on objective#2. The following are the objectives and their milestone that will be achieved. Objective#1: Elucidate the Si mobilization and uptake in the rhizosphere with reactive nutrients and sequestration of CO2. Milestone 1.1: Determine Si mobilization and translocation in the plants with or without salinity Milestone 1.2: Explain the Si uptake with or without the presence of reactive nutrients Milestone 1.3: Elucidate Si and substrate nutrient management to influence rhizospheric and atmospheric carbon capture during salinity Milestone 1.4: Elucidate the root exudation during the Si uptake in salinity Objective#2: Investigate the effect of Si on physiological and molecular responses of soybean under salinity stress Milestone 2.1:Assess the effect of Si on agronomic and physiological parameters under salinity stress conditions in greenhouse-grownsoybean plants. Milestone 2.1:Evaluate the gene expression related to Si uptake and transport in Soybean cultivars. Milestone 2.2:Study transcriptome-based changes in response to Si and salinity application to identify candidate genes and pathways

Impacts
What was accomplished under these goals? The project focuses on elucidating mechanisms related to rhizosphere biogeochemistry, Si uptake, CO2 fixation, and enhancing soybean plant biomass in a saline soil system. In this reporting period (2024-2025), we worked on objectives #1 and #3 and partially on 2. The following are the details of work performed during this reporting period: Objective 1: Elucidate the Si mobilization and uptake in the rhizosphere with reactive nutrients and sequestration of CO2 Milestone 1.1: High Throughput Screening of ~30 soybean cultivars for Si uptake? and salinity tolerance: We obtained soybean seeds from USDA-GRIN and identified the abiotic stress-tolerant (specifically salinity stress) genotypes. We have screened 15 genotypes out of 30, and our target is to screen at least 45 genotypes for salinity tolerance and Si uptake. These genotypes include salinity-sensitive and resistant varieties. We performed a high-throughput screening of soybean genotypes to screen them for Si influence on plant growth (biomass, chlorophyll, photosynthesis rate, stomatal conductance, and CO? assimilation rates) with or without saline conditions in soil. We screened more than 15 genotypes of soybean that were either salinity or abiotic stress tolerant. A randomized block design experiment was performed comprising (i) control, (ii) salinity (sodium chloride 18dS m−1), (iii) Si (5 g/kg soil magnesium silicates), and (iv) Si with salinity. A common agri-soil representative of Fort Bend and Harris Counties was used to grow plants till the vegetative stage-7 in greenhouse conditions. Results showed that silicon-treated plants under salinity exhibited significantly improved plant biomass (~24%; shoot-to-root length and dry root-shoot weight ratios) compared to non-Si salinity-treated plants, effectively restoring biomass levels in saline conditions. The root uptake of Si was non-significantly higher in non-saline soil conditions than in saline conditions, suggesting that salinity does not interfere with the Si uptake process. In genotypes, Lee, Lee-100, peaking, FT-abyara, NO-3093 green, Flyer, and Biloxi accumulated 2-fold higher Si content in rhizospheric soil in salinity compared to other genotypes. Similarly, the CO2 sequestration was recorded using photosynthetic efficiency and soil C-storage. Lee S-100, NO-3093 green, and FT-abyara showed a 1.5-fold rate increase in photosynthesis, with significantly higher soil organic carbon (~1.7-fold) in saline conditions for these genotypes. We are still in the process of analyzing the data, and our conclusion might change based on more screening in the coming reporting cycle. Thus, the project will assess a total of 45 genotypes. Milestone 1.2: Explain the Si uptake with or without the presence of reactive nutrients: We are in the process of performing a mesocosm experiment at the greenhouse level to understand the Si uptake in the presence of salinity and reactive nutrients (Ca, Mg, and Fe) to understand the Si mobilization and localization process in the rhizosphere. Milestone 1.3: Elucidate Si and substrate nutrient management to influence rhizospheric and atmospheric carbon capture during salinity. The changing environment and increasing CO2 levels have influenced rainfall patterns and soil chemistry. The short and long-term changes in soil chemistry impact carbon capture and storage (CCS) during plant growth. The photosynthetic process is key to CCS and maintaining plant biomass. We performed greenhouse and lab-based experiments to understand the effects of different Si sources (magnesium trisilicate and silicic acid) in combination with different soil types (agri-soil and sand). Magnesium trisilicate resulted in significantly higher biomass in agri-soil, suggesting a more effective role in promoting nutrient uptake and plant development compared to silicic acid. However, under nutrient-limited sand conditions, magnesium trisilicate-treated plants exhibited significantly improved health, shoot elongation, and biomass compared to controls. We used specialized CO2 sensor in rhizosphere and photosynthesis meter above ground to monitor CO2 capture in different soil and Si conditions during plant growth. We observed significantly higher photosynthesis rates and variable soil respiration patterns across Si sources and soil conditions. We are in the process of analyzing SOC and other soil health parameters (nutrient and microbial activities). This will be followed by nutrient management (fertilizer; NPK) and reactive nutrients to demonstrate the CCS potentials in the presence of Si and saline soil conditions. This will also help how Si application improves CCS and long-term soil health. Milestone 1.4: Elucidate the root exudation during the Si uptake in salinity. This will be performed in year 2. Objective#2: Investigate the effect of Si on the physiological and molecular responses of soybean under salinity stress. Objective#2 and the related milestones are planned for year 2 of the project. This will help elucidate the salinity tolerance and Si uptake molecular mechanisms in the most resilient soybean genotype. The team from UNGC will be performing this objective. In addition, we have also started identifying genes that are involved in Si uptake, specifically Nodulin 26-like Intrinsic Proteins (NIPs) in soybean. We are designing a gene-editing approach to clone NIPs in soybean plants using both knock-down and overexpression approaches to understand the potential physio-molecular mechanisms behind Si uptake in Soybean. This has been unexplored to date. The transgenic lines generated from this work will be evaluated for their physiological traits, including stress tolerance, silicon accumulation, and photosynthetic efficiency. Objective#3: Determine the CO2 sequestration process and perform phenotyping and biomass production assessment during Si application. Objective#3 and its related milestones are also in the process of execution and will be implemented on a large scale in year 3/4. To monitor Si and salinity, we are developing a new method using near-infrared spectroscopy (NIRS) and multispectral indices coupled with regression analysis. These spectral indices were selected because higher index values are typically indicative of improved above-ground vegetation health during salinity and Si treatments. We are in the process of optimizing and processing the protocol and analytical methods for 15 genotypes assessed (objective#1). This will help to establish a robust method for field-level analysis using multispectral analysis in year 3 of the project. For NIRS based approach, we have analyzed more than 300 soil samples from 15 genotypes during Si and salinity treatments to understand soil health parameters. The data is in the process of analysis using Partial Least Squares Discriminant Analysis in RStudio using the "pls" package with training and testing soil samples for health-related parameters. To get a better insight into the effects, we are adopting a neural network and a random forest-based machine learning approach to understand the data and make better decisions on each genotype. This will be another robust method developed for soil health, which will help in large-scale field-level analysis. In addition, a spin-off research work was also carried out to understand how Si application influences microbial health of rhizosphere. We performed next-generation sequencing approaches to show the microbiome diversity and function using Soybean plants (published). The diversity was insignificant in Si treatments; however, the bacterial diversity was found to be highly significant across soil, root, and leaf parts. We found Burkholderia and Bacillus as core species in Si supplementation, suggesting that these can play a key role in Si-solubilization in soil. We are developing a culture collection of Si-solubalizing microbes that could be used as microbial enrichment strategy to tackle salinity-related problems in agro-ecosystem.

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Khan AL. Silicon: A valuable soil element for improving plant growth and CO2 sequestration. Journal of Advanced Research. 2025 May 1;71:43-54.
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Ahmad, Waqar, Lauryn Coffman, Ram Ray, Selamawit Woldesenbet, Gurbir Singh, and Abdul Latif Khan. "Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere." Science of The Total Environment 982 (2025): 179554.
  • Type: Other Journal Articles Status: Submitted Year Published: 2025 Citation: Khan, A N., Owens, L., Khan, A.L., Complexity and dynamics of combined climate change episodes on plants. Plant Stress
  • Type: Other Journal Articles Status: Submitted Year Published: 2025 Citation: Ahmad, W, Ray, R., Khan, A.L.*, Rhizospheric Silicates regulate microbiome function and plant defense responses during temperature stress. Plant Cell Environment