Fostering Microbial Activity and Diversity in Agricultural Systems

This article is the third in a three-part series on fostering microbial activity and diversity through better management practices and strategies. Part 3 will discuss monitoring and quantification of microbial diversity, challenges for adopting sustainable practices, government policy, and scaling microbial diversity from smaller to larger agricultural systems. Soil microbial diversity is a black box and requires more intensive study to understand the effects of various strategies on ecosystem functions. The monitoring and assessment of soil microbial activity, abundance, and diversity will help us predict the associated soil properties and processes for assessing the soil health and impacts on crop production. Various methods are employed to monitor and quantify the soil microbial communities. Most of these methods need sophisticated tools and controlled environments, which may not be available for farmers but are definitely available at local university, government, and privately run labs. Plate and direct counts involve culturing microorganisms on media and counting them under a microscope, primarily detecting culturable microbes (Bakken, 1997). Phospholipid fatty acid analysis (PLFA) extracts and analyzes phospholipids from microbial cells, differentiating bacterial and fungal groups. Real-time polymerase chain reaction (PCR) measures DNA amplification to quantify the microbial community quantitatively but lacks qualitative insights. Gene sequencing assesses alpha and beta diversity, offering a qualitative understanding of microbial communities resulting from different management practices. Enzymatic activity assays are commonly used to understand soil microbial roles in carbon and nutrient cycles by breaking down compounds into simpler forms. Soil enzymes, mainly extracellular, play a crucial role in decomposing organic compounds with hydrolytic and oxidative enzymes involved in carbon, nitrogen, and phosphorus cycling. Another method, the BIOLOG EcoPlate, assesses community-level physiological profiling (CLPP) by providing 31 carbon substrates and measuring microbial metabolic potential through color development and optical density at 590 nm (Garland however, testing can be costly depending on the materials/technology necessary for analysis and the number of samples. Microbial inoculants for in situ enhancement of microbial populations may also be expensive depending on the acreage and the frequency of application needed for desired influence in the soil microbiome. Adopting cultural practices like conservation tillage, crop rotation, intercropping, and cover crops will build up microbial activity and diversity in the long run; however, they could pose a financial burden to the farmers in the short term. A recent study (Pathak et al., 2024) has shown that farmers are likely to discontinue cover cropping and conservation tillage when there is no government funding available, which shows that there is a need to support farmers financially to achieve the goal of a sustainable future through microbial farming. To test for microbial populations, farmers typically send soil samples to commercial or extension laboratories for analysis; however, testing can be costly depending on the materials/technology necessary for analysis and the number of samples. Photo by Peggy Greb. While organic fertilizers are a fantastic alternative to inorganic fertilizers for stimulating microbial activity in the soil microbiome, contaminants could be a concern depending on the fertilizer source. Photo by Rebecca Ryals and originally published here: agronomy.org/news/science-news/getting-solid-soil-response-biosolids-application. As discussed earlier, organic fertilizers are a fantastic alternative to inorganic fertilizers for stimulating microbial activity in the soil microbiome; however, depending on the source of the organic fertilizer (animal waste, compost, or biosolids), contaminants of concern such as heavy metals, pharmaceuticals, and hormones may be entering the soil and be available for plant uptake or may enter water resources (Goss et al., 2013; Urra et al., 2019). Not all organic fertilizers have these contaminants of concern as it entirely depends on the source and the treatment of these organic fertilizers in preparation for agricultural application; it is important to recognize the potential of introducing these contaminants of concern to our food and water resources. Finally, the last and probably most important challenge is educating agricultural managers, farmers, and home gardeners on the essentiality of a diverse and active soil microbiome in crop production. Microbes tend to have a bad reputation with the general public, mainly known to be harmful to human health and causing disease. While this is not inherently incorrect, it is still a misperception as there are a multitude of beneficial microbes that are necessary for everyday life. It is important to improve microbial literacy so that agricultural managers and home gardeners can make informed decisions for their agroecosystems (Bloom et al., 2024). In recent decades, there's been a notable surge in microbiome research, particularly in agricultural contexts aimed at bolstering crop production amidst climate change. While soil management is vital for climate-resilient agriculture, focusing on soil microbiome diversity is crucial for sustainability. Understanding these interactions is key to optimizing microbe benefits. Thus, a strong government policy is needed to effectively incorporate the policy of diversifying and harnessing the microbiome's potential. The soil microbiome has been further integrated to the One Health initiative where microbes are recognized as integral components of human animal and ecological health. This underscores the importance of soil microbiome research and development as a cornerstone of achieving One Health (Banerjee they have evolved together." —Charles Edwin Kellogg At this pivotal moment, optimism surrounds the evolving understanding of the role of microbes in agroecosystems, yet caution is warranted amidst increasingly complex global challenges. Embracing the task of scaling up microbial knowledge to a global level can lead to a more sustainable and resilient agricultural future. A thriving soil microbiome forms the bedrock of sustainable agriculture, driving ecological functions and contributing to nutrient cycling, soil structure maintenance, plant growth, and carbon capture. Nurturing microbial activity and diversity is vital for preserving soil fertility, mitigating climate change impacts, and ensuring long-term food security. While promising practices like reduced tillage and regenerative agriculture show potential, the future lies in harnessing plant–microbe partnerships and leveraging technologies like gene editing to engineer beneficial microbial strains. Robust policy support and advocacy efforts are needed for widespread adoption of ecological practices to enhance the soil microbiome. Farmers, policymakers, researchers, and the public must collaborate to develop comprehensive soil health strategies, implement evidence-based practices, and quantify the benefits of agroecological approaches. Through collective efforts and a commitment to soil stewardship, we can unlock the soil microbiome's full potential, restoring degraded soils, enhancing food security, and mitigating climate change for a sustainable future.