Rooting for Sustainability: Development and Characterization of Microbial Consortia for Regenerative Agriculture

Abstract

The continued reliance on synthetic fertilizers and chemical pesticides in United States agriculture has raised significant concerns regarding long-term soil health, environmental sustainability, and ecosystem function. While plant growth-promoting rhizobacteria (PGPR) have demonstrated potential as biological alternatives, their widespread adoption remains limited due to inconsistent field performance, an overreliance on early-stage in vitro screening, and a lack of integrated research pipelines that advance candidate strains through field validation. These limitations are particularly evident in underrepresented systems such as peanut and turfgrass, where region-specific evaluations are scarce. Therefore, this research was designed to address these gaps by implementing a structured, efficiency-driven framework to advance PGPR from initial characterization through greenhouse and multi-year field evaluation within a single research system. Chapter II developed and applied a “biocontrol-by-design” pipeline to identify and formulate PGPR strains for suppression of Rhizoctonia solani in peanut production systems. A total of 110 strains from the DH collection were characterized for mechanisms of biocontrol, followed by greenhouse and field validation. This process resulted in the development of a single-strain treatment (Bacillus velezensis DH57) and two consortia (KSPC1 and KSPC2). Under greenhouse conditions, these treatments restored plant growth to levels comparable to azoxystrobin. During field evaluations, treatment significantly affected stand establishment at 14 (p < 0.0001), 21 (p = 0.0005), and 28 days after planting (p = 0.0151), with PGPR treatments consistently maintaining performance comparable to the fungicide standard. These results demonstrate that PGPR can provide reliable early-season disease suppression and support crop establishment under production conditions. Chapter III expanded this framework to turfgrass systems, where PGPR research remains limited, by incorporating both growth promotion and biocontrol traits into strain selection and product development. From the same collection of 110 strains, a subset including DH57, DH510, DH447, DH580, and DH588 demonstrated consistent antagonism against R. solani as well as functional traits associated with growth promotion, including nitrogenase activity. These results supported the development of a single-strain treatment (DH57) and two consortia (KSTC1 and KSTC2). In multi-season field trials, PGPR treatments significantly improved plant growth, quality, and disease suppression relative to inoculated controls (p ≤ 0.0027), while maintaining responses statistically comparable to fungicide and full-rate fertility programs (p > 0.05). Notably, PGPR treatments applied in combination with reduced nitrogen inputs sustained plant performance equivalent to conventional fertility programs, indicating improved nutrient use efficiency and supporting their integration into reduced-input management systems. Chapter IV focused on refining in vitro screening approaches to improve efficiency and reproducibility in PGPR characterization. Significant variation was observed among strains for nitrogen fixation and siderophore production (p < 0.0001), with several isolates expressing multiple functional traits associated with plant growth promotion. However, inconsistencies in phosphorus solubilization assays and variability across methodologies highlighted limitations of traditional screening approaches. These findings emphasize the need for improved, standardized methods, including microplate and liquid-based assays, to enhance sensitivity and scalability for large strain collections. Collectively, these studies demonstrate that PGPR can be systematically advanced from initial characterization to field validation within a single, integrated research pipeline, resulting in the identification of strains capable of providing plant growth promotion and disease suppression comparable to conventional management programs. More importantly, this work establishes a practical framework that prioritizes efficient screening and rapid progression to field evaluation, where environmental variability ultimately determines product performance. By shifting the focus of PGPR research from extensive in vitro characterization to field-driven validation, this approach addresses a critical barrier to the development of reliable biological products. These findings support the integration of PGPR into production systems as components of sustainable management strategies, particularly in environments where reducing chemical inputs is necessary to maintain long-term soil health and agricultural productivity.