UNIVERSITY PARK, Pa. — Decades of research has shown promise for using microbiome science to solve several problems facing agriculture, but these findings have not yet been translated to practical recommendations for growers, according to a team of scientists in Penn State’s College of Agricultural Sciences.
The researchers authored a paper in the journal Applied and Environmental Microbiology on how scientists and growers could translate microbiome research from theory to practical applications in crop production.
In the Q&A below, a few of the authors — Carolee Bull, professor of bacterial systematics and plant pathology; Alex Vompe, postdoctoral scholar; Mozhde Hamidizade, postdoctoral scholar; and Kevin Hockett, associate professor of microbial ecology — spoke about where science stands with microbiome research in agriculture and how it could be used to benefit crop production.
Q: What is a microbiome and why do they matter in agriculture?
Bull: A microbiome is the community of microorganisms — including bacteria, archaea, viruses and microeukaryotes, including fungi — that inhabit a specific habitat, which may be a specific organism. When we’re talking about plants, we also refer to the phytobiome, which is a system that includes the interactions between the plant, the diversity of microbes that inhabit the plant and soil around the plant.
Previous research has shown promise for microbiome science to help find solutions for multiple problems facing agriculture. For example, studies have demonstrated that plant growth-promoting microorganisms can mitigate the effects of environmental stresses and plant disease on crop performance.
Food safety is also an important challenge in agricultural systems, and the use of microbes to mitigate the risk of foodborne illness shows great potential. Additionally, microbiomes could be used to reduce chemical pesticide use, which would lower the exposure of farm workers and others to chemical pesticides, minimizing potential impacts to their health. Microbial pesticides also could be employed to manage pest populations that are resistant to chemical pesticides.
Still, while microbiome manipulations and microbial inoculants present promising solutions, their practical application has so far proven challenging.
Q: How can microbiome science solve these problems?
Vompe: There are several strategies that can use microbiomes to improve agricultural outcomes. The first is adding microbial communities or substrate that promotes a beneficial microbial community to plant systems with the goal of promoting improved plant health and crop productivity, such as prebiotics and probiotics.
One example of successful probiotic use in agriculture includes applying certain bacteria to seeds to give the plants resistance against a different, pathogenic bacteria. Another is applying specific bacteria to soybeans to either partially or completely replace nitrogen fertilizers, which are linked to environmental and health issues.
In addition to providing benefits, microbiomes also may help plants by inhibiting detrimental microbes. For example, bacteriophages are important predators in agricultural systems and could be used to effectively reduce target bacterial populations.
Hockett: Microbiomes also can be shaped through selective pressure over time, in a process called “passaging.” This refers to repeatedly subjecting a microbial community to the same environment and its associated pressures, typically with the goal of enhancing a trait, such as increasing plant salt tolerance or disease suppression.
Hamidizade: Finally, seed microbiomes can act as microbial reservoirs that can impact plants for generations. They can improve germination rates, seedling health and influence important plant functional traits. They also may enhance nutrient availability and uptake while increasing tolerance to biotic and abiotic stress.
Q: What are some of the challenges putting these solutions into practice?
Hamidizade: Supplementing hosts or environments with functional microbial communities presents several challenges.
First, the host or environment may have to be re-supplemented with microbes multiple times. This is because the persistence of these microbe strains can be unpredictable in complex, real-world ecosystem. Second, existing microbiome probiotics are usually limited to bacteria, which ignores the potential benefits of organisms such as archaea, micro-eukaryotes and viruses.
Third, these introduced communities potentially can harbor genes for antibiotic resistance and other undesirable traits. Finally, standards for evaluating probiotic effectiveness, consistency and safety across conditions remain limited and need further development and validation.
Q: How do we put these solutions into practice, and what’s next for microbiome science in agriculture?
Vompe: Some of these solution approaches are more mature and broadly used, while others are more novel and face challenges to translation due to biological complexity and novelty. We believe there are a series of core objectives that must be met to most effectively apply microbiomes translationally.
First, precision agriculture should be a priority. For microbiome-informed treatments to be successful, we will need to be able to provide personalized treatments for crops, treating individual fields, parts of fields and, potentially, individual plants.
Second, microbiome products for growers must be regulated and commercialized. This process will set standards for product safety, effectiveness and reproducibility. Additionally, we must develop relationships and trust with stakeholders. Grower acceptance is a major hurdle, and extension research remains a major bridge toward grower acceptance. Participatory research, in which growers are co-designers of research, is a successful approach leading to acceptance and adoption.
Finally, the best tools at scientists’ disposal to address the above objectives are carefully designed, long-term experiments in locations with a variety of soil and climate conditions to represent the diversity of agricultural systems. By providing both time and diversity of conditions, scientists will be able to better understand the influence of microbiome interventions on crop health.