Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001
Performing Department
Plant Pathology & Microbiology
Non Technical Summary
Plants actively interacting with a large diversity of bacteria, fungi and protozoans within and around them. In nature, these interactions are cooperative, and plants are heavily dependent on their microbial flora for their healthy lifestyle. Understanding this complex interaction is the major research focus of our lab. We use a range of molecular and microbiological tools to study diversity and stability of heathy plant associated microbiomes. We especially employ a systematics-based approach, so that we can identify individual organisms involved in these interactions, their biological functions, impacts on neighboring niches, and metabolic activity. The research has several direct biotechnological applications, and the research in our lab focuses on the following:Develop bioferlitizers/biopesticides: By disentangling the microbial functions that are essential for different growth stages of crop plants, we intend to develop "soil probiotics" to improve crop health. In order to achieve this, we study natural ecosystems and wild plants related to crops. The technology developed will be sustainable and environmentally friendly.Combat plant disease: Plant microbiome, especially the microorganisms that live within the plant tissue (endosphere), are major responders during infection. They assist the host's immune system to fight against disease. Thus, we are studying natural microbial interactions in the endosphere, and how it is altered during infections (dysbiosis). We intend to counter pathogens by interfering with the dysbiosis network.Discovery of novel therapeutics: Biological functions of antibiotics in nature are to communicate between different organisms. We now understand that bacteria use antibiotics to attract their niche partners, but use the same molecules to ensure that their partners do not overgrow and take over their space. By understanding this interaction network, we can develop novel antibiotics and anticancer drugs.We employ several techniques such as full SSU rRNA-metabarcoding, shot-gun metagenomics, and metatranscriptomics. To enable processing of large datasets and integrate multiple OMICS data together, we employ novel strategies in microbiome analyses using advanced computational tools. We are also developing methods to trace microbial dark matter using stable isotope labeling methods, which can also be used for plant metabolomics. Our current research focuses on early developmental stages of maize and cotton plants, and expanding into native American medicinal plant Echnecia. Additionally, we are also working on how plant-microbe interactions can help enhance pecan truffle production in Texas.
Animal Health Component
10%
Research Effort Categories
Basic
50%
Applied
10%
Developmental
40%
Goals / Objectives
Human civilization and expansion in agriculture are directly correlated. We have extensively converted natural ecosystems to farmlands (Meehan et al., 2011). Unfortunately, when it comes to cropping systems, the soils have rapidly lost their fertility and potential to support the crop plants (Pérez-Jaramillo et al., 2018). This has led to widespread use of chemical interventions such as fertilizers, pesticides and herbicides. Although such chemical applications have shown short term dividends, we now know that this practice is not sustainable and affects human health and causing severe effects on our entire planet (Tripp, 1996).Biological interventions such as biofertilizers and biocontrol agents using microorganisms have been suggested as an alternate to hazardous chemicals (Adesemoye and Kloepper, 2009). This is a sustainable approach because soil microbes are naturally interacting with plants. Although these approaches have shown great promise in controlled environments like in growth chambers and in greenhouse, they have limited applicability in actual agricultural lands. The major hurdle in such implementation is that in a field scenario, the newly introduced biofertilizer/biocontrol microbes are outsmarted by naturally occurring soil microbiota. Thus, it is important to understand how the natural interactions between soil microbes occur, and use this information to design better biological interventions in agriculture.My research strategy is to understand natural ecosystem processes and how that affects microbe-microbe interactions, and progress this into crop systems. After all, all crop plants have their wild type and land race that preexisted the current vigorous agricultural practice. I intend to use these models to develop bioinoculum. Thus, research goals are to study plant associated microbial diversity, function and bioactivity, and how they influence plant health and plant-soil feedback. I have listed three major aspects of my immediate research priorities.Objective 1. Rhizosphere microbial functions and plant-soil feed back using meta-OMICSObjective 2. Culturing novel prokaryotes associated with plants and fungiObjective 3. Drug discovery - using triangular interactions between plant-fungi-bacteriaReferences:Adesemoye AO, Kloepper JW. (2009). Plant-microbes interactions in enhanced fertilizer-use efficiency. Appl Microbiol Biotechnol 85: 1-12.Meehan TD, Werling BP, Landis DA, Gratton C. (2011). Agricultural landscape simplification and insecticide use in the Midwestern United States. Proc Natl Acad Sci U S A 108: 11500-5.Pérez-Jaramillo JE, Carrión VJ, de Hollander M, Raaijmakers JM. (2018). The wild side of plant microbiomes. Microbiome 6: 143.Tripp R. (1996). Biodiversity and modern crop varieties: Sharpening the debate. Agric Human Values 13: 48-63.
Project Methods
Objective 1. Rhizosphere microbial functions and plant-soil feed back using meta-OMICS Microorganisms follow a biogeographical pattern (Martiny et al., 2006) that are highly correlated with the plants that are supported in that ecosystem (Antony-Babu et al., 2008; Fierer and Lennon, 2011; Green et al., 2008). Interestingly, certain microorganisms can in-turn influence the presence and functions of other microbes in plant associated ecosystems, as shown by fungal associated bacteria that evolve with the host's seasonal development (Deveau et al., 2016b), assisting the fungi to build its fruiting body, and finally initiating destruction of fungal material (mycophagy) which results in releasing spores back to the soil (Antony?Babu et al., 2013). It has also been demonstrated genetic evidences that bacteria residing within fungal fruiting bodies could potentially produce aroma metabolites that attract animals to feed on the fungi and spread the spores. Thus, prokaryotes are integral part of plant-associated fungi's lifecycle. In specific, we will study variation in plant root exudates, and how it affects microbial recruitment that leads to positive and negative plant soil feed back.The proposed research would specifically address the following (also refer to figure 1):Effect of individual and consortia of root exudates on microbial recruitment: We will decipher taxonomic and functional diversity of microorganisms that are encouraged by exudate molecules. This will be achieved by using stable isotope probing and tracing. This includes use of enriched low abundance stable isotopes to replace the more abundance isotopes in a control growth chamber. By following the fate and incorporation of the isotopic labels, we will unravel the microbial functions associated with root exudation. Anaerobic bacterial and archaeal functions in plant associated soils: Anaerobic rhizosphere functions are understudied. Soil aggregation and biofilms are essential part of rhizosphere and have anoxic pockets that encourage anaerobic microorganisms. Additionally, water saturated soils (such as rice rhizosphere) are rich in anaerobes. Interestingly, anaerobic metabolism is important in drought conditions as well, since anaerobic pathways such as methanogenesis and methane oxidation produce water. We will specifically study anaerobic microbial functions in rhizosphere and its role in overall rhizosphere microbial interactions in water saturation and drought. Thus, the studies on anaerobic microbes would complement my research on microbial functional networks in 1a. Effects of exudate simulated microbes on plant phenotypic traits: We will manipulate soil microbial load and diversity by use of inoculums. These inoculums will be developed from repeated plant-soil feed backs, plant rotations, and intercropping. We will study the effects on above ground and below ground plant phenotypic traits (both above-ground and below-ground). Objective 2. Culturing novel prokaryotes associated with plants and fungiGetting microbes into culture is a rate limiting step towards developing inoculum for biointerventions in agriculture. There are three approaches that have shown great promise in my past research towards culturing earlier unknown microorganisms in vitro.Use of evolutionary systematics approach (Antony-Babu and Goodfellow, 2008)Use of interaction (Antony?Babu et al., 2013; Deveau et al., 2016a)Use of extreme niche properties (Antony-Babu, in press)The genetic and functional information obtained from the multi-OMICS data from the objective 1 will be used to develop enrichment methods for specific pathways. The enrichments would be sequentially selected to obtain reduced diversity or single organism. While developing novel culture methods, we will also be carrying out isolation based on traditional plate methods.Thereby, a diverse culture collection bioresource will be developed. An inventory of cultures will be produced. This would lay foundation for screening of bioprospecting properties in the cultures. We will also further my research interest in developing methods for effective dereplication of isolates, which would greatly help my proposed culture collection to be free of redundant maintenance of clonal strains (Antony-Babu et al., 2010, 2017).The novel methods developed would contribute towards designing inoculums for 1) biofertilizers, 2) disease suppression, and 3) antimicrobial natural products discovery (elaborated in the next section). The novel taxa in the culture collection will be formally described, and genomes would be reported as appropriate. We will also further microbial systematics concepts through this research using OMICS methods.Objective 3. Drug discovery - using triangular interactions between plant-fungi-bacteriaOne of the least studied aspects of plant-microbe interactions is to use the inter-kingdom interplay for discovery of novel therapeutic drugs. Some microorganisms produce biologically active metabolites that are used as drugs, especially antibiotics, anticancer, anti-inflammatories and immunoregulatories. It is now understood that these molecules help the producers to wade off competition and communicate with other "friendly" organisms. This is proven by the fact that many such compounds are produced only when two specific microorganisms are cultured together (a technique called "co-culture").We will carry out OMICS analyses (genome sequencing of biosynthetic genes, and decipher expression by transcriptomic and metabolomics) of mycorrhizal/wood-rot fungi/tree-lichens and their associated bacterial partners, especially actinobacteria. Initial studies would concentrate on actinobacteria owing to their track record in natural product discovery. Based on the outcomes, synthetic biology approach to engineer metabolic pathways would be carried out for expressing cryptic genes. This would advance our understanding of plant-microbe interactions and also contribute towards discovery of novel drugs. This research theme would continue on my research on lichen-associated bacteria where I showed that lichens are rich in actinobacteria (Parrot et al., 2015).Bioinformatics pipelines and analyses to meet my research goals: Computational analyses for OMICS data is an integral part of all the three research objectives. Pipelines for amplicon- and shotgun-metagenomic sequencing of microbial community will be developed. The diversity studies would be targeted towards specific genes that would include both taxonomic markers and important functional genes (especially those relevant to carbon, nitrogen and basic element cycling). Taxonomic identification for microbiomes will be advanced by use of full length 16S rRNA and long read sequences.A multifaceted approach will be used where to screen for pathways by PCR based amplicon sequencing, and also develop shotgun-metagenomic targeting using COSMID and FOSMID libraries. These screens would require database built using genomic and gene sequence data from publicly available databases. We will initially build databases for genes and pathways, which would act as reference for my studies. These databases would be made publicly available for downloads. The pipelines would not be restricted to screening for presence and expression of genes alone, but also to map pathways regulated by these genes.