Dispersal vs. Adherence: tradeoffs in ecological drivers of colonization fitness in hydroponic systems

Controlled Environment Agriculture (CEA) is a soilless cultivation technique that promotes high yields by tightly controlling growth conditions, including nutrient availability, temperature, and light intensity. However, these systems do not typically manage the microbiome beyond scheduled or emergency sterilization routines. CEA systems acquire a microbiome in an uncontrolled manner that reflects diverse abiotic (e.g., water systems, humans) and biotic sources (e.g., plants, insects). When undesired plant or human pathogens enter the system, they spread rapidly and unchecked until they are discovered by routine monitoring. Sanitation and monitoring are necessary but do not provide the fullest set of available safeguards. This research investigates the development of ‘positive biofilms,’ a defined microbial community to colonize growth tanks, outcompete undesirable microbes, add a layer of biosafety, and build towards microbiome management in CEA systems with potential benefits to plant production.

CEA systems are dominated by biofilms that harbor diverse microbes with a distribution of traits involved in colonization and dispersal. This thesis examines dispersal-colonization trade-offs and their effect on microbial colonization success on surfaces in hydroponic systems to identify key microbial traits for developing a positive biofilm. Firstly, we develop and validate a model, a high-throughput dispersal-colonization selection system (DCSS), to test whether members of the hydroponic microbiome possess complementary or specialized traits for dispersal and surface colonization (Chapter 1). Subsequently, we sampled a commercial hydroponic farm to assess the prevalence of microbes with divergent traits in real-world conditions (Chapter 2). Finally, we conducted a meta-analysis to identify global trends in the phylogenetic background of populations with different dispersal-colonization traits in CEA systems (Chapter 3).

Our results show that the DCSS can enrich colonization-competent microbes from a microbial community. Our detailed account of the compartments in a commercial hydroponic facility revealed the predominance of biofilm-forming microbial populations, including members of Pseudomonas and Sphingobium. These taxa have been linked to plant growth-promoting benefits in conventional soil-based agriculture and are prevalent surface colonizers in water distribution systems. We confirmed that these populations were present across diverse CEA systems, illustrating their membership in the core CEA microbiome. This research highlights the potential populations and their respective traits for colonization and dispersal, aiming to develop a positive biofilm that can rapidly and repeatedly colonize CEA systems. In doing so, we seek to build the foundation for advanced microbiome-based strategies that enhance CEA safeguards against plant and human pathogens and future microbiome technologies that promote plant health and productivity.