Performing Department
AGRICULTURAL AND BIOSYSTEMS ENGINEERING - ENG
Non Technical Summary
Microbial functions in the rhizobiome can provide plant benefits, such as plant growth promotion, nutrient acquisition, and adaptation to stresses. We have curated a collection of bacterial isolates identified as critical rhizobiome members with high potential to benefit perennial grasses' growth and stress response. The isolates were identified based on their improved growth responses to host plant signals, their mutual compatibility, and their biogeographic prevalence. When assembled, this synthetic community is named SynCom13. We evaluate the hypothesis that SynCom13 members collectively promote plant growth via complementary mechanisms through three aims. This proposal characterizes SynCom13 isolates for their potential to provide plant benefits and develops straightforward tools for their throughput quantification in the plant environment. We will also studythe bacterial consortia's assembly, persistence, and metabolites during early plant development. Finally, we will determinethe climate resilience of plant benefits given SynCom inoculation under warming and the transferability of SynCom13 to other plants.
Animal Health Component
20%
Research Effort Categories
Basic
60%
Applied
20%
Developmental
20%
Goals / Objectives
We focus on understanding the assembly, interactions, and beneficial functions of core rhizobiome community members and assess how their plant-microbiome and microbe-microbe interactions change given climate change stress. We will take a systems-level approach that combines genomics, functional assays, plant-microbiome phenotyping experiments, and metabolic prediction to decipher the assembly dynamics, mechanistic relationships, and the interactions between key bacterial microbiome members and four focal crops (switchgrass, wheat, bean, and corn). We propose the following aims:Characterize plant benefits: quantify the bacterial consortia's functional attributes and molecular mechanisms that can benefit plants.Understanding ecosystem assembly: Characterize the bacterial consortia's assembly, persistence, and metabolites in the formative stages of plant development.Evaluating adaptability: Determine the climate resilience of plant benefits and transferability to other plants.
Project Methods
We hypothesize that these SynCom13 members engage together to promote plant growth via complementary mechanisms. The proposed work will provide new insights into the systems-level ecology and mechanisms of beneficial plant-microbiome engagements toward building a robust and transferrable bacterial synthetic community for crops. The proposed work will help us to understand molecular mechanisms and signal exchange of microbiome assembly and interactions in various environments through the relevant yet tractable lens of SynCom13. We will characterize the functional response of the interactions between SynCom13 and plant hosts under plant growth stages and warming climate conditions. This research will provide key insights into complex rhizobiome dynamics underlying plant responses to abiotic stresses of consequence for environmental change in both natural and agricultural ecosystems. Understanding the interactions between the rhizobiome, plant hosts, and the environment will also help us improve agricultural productivity. Aims 1 and 2 provide a foundational understanding of key rhizobiome players and how they are assembled and interact with plant hosts. Expanding upon this understanding, Aim 3 targets how this rhizobiome and its benefits might be transferred to other hosts and the impacts of environmental stress (i.e., temperature increases) on these benefits. Thus, our proposed studies of the multipartite interactions between the plant host, environment, and the rhizobiome will help inform how, where, and when to make management decisions to leverage plant-microbe benefits. In Aim 1, we will sequence, assemble, and annotate SynCom13 genomes; design probes specific to strains; and characterize teh potential for plant-beneficial functions.The purpose of Aim 2 is to expand who we know is there, what they are doing, and how they interact with each other, the plant, and the environment. We will explore this in a series of greenhouse experiments to determine assembly in the rhizosphere. In parallel to understanding the ecosystem assembly dynamics, we will also characterize the functional response of both SynCom13 taxa and their plant hosts (via biomass and metabolite analysis) during the early stages of switchgrass growth, which will provide insights into the interactions between bacteria, plant, and environment. In Aim 3, in thefirst part of this aim, we will test the supportive SynCom13 consortium for host benefits during climate stress, specifically warming. We will perform warming experiments of +1.5 and +3.0 degrees Celsius for both daytime and nighttime temperatures in environmental growth chambers, alongside an inoculation with an unwarmed/ambient condition control and a mock-inoculation treatment. Separately from but similar to Aim 1, we will determine the in vitro temperature ranges and growth outcomes for each of the SynCom13 members, noting any potential phenotypes of interest (e.g., dormant stages) for understanding their collective persistence and ecology in situ. We will also target 12 metatranscriptomes sampling to link the responsive functions of the SynCom13 and rhizobiome members to the warming condition. Thus, we will link the active transcripts to each member's genomes (sequenced and assembled in Aim 1) and compare those transcriptional activities to the unwarmed, inoculated treatment.