From Below to Grow: The Power of Microbiomes

Introduction - Agriculture’s Secret Allies

Imagine an invisible world beneath your feet and within plant roots—a bustling city of microorganisms working around the clock to keep plants healthy and resilient. This microscopic community, known as the microbiome, includes a colorful mix of bacteria, fungi, archaea, viruses, and other tiny organisms that thrive in and around plants. In agriculture, these microbiomes inhabit the soil, the area immediately surrounding roots (the rhizosphere), and even plant tissues themselves, ranging from the root to the shoot surface and endosphere. It’s an invisible yet powerful world with a big impact on plant health, growth, and resilience against stress.

Think of microbiomes as a plant’s secret support team, silently providing benefits like soil fertility, nutrient cycling, and disease suppression. Today, scientists are diving deep into understanding and managing these tiny helpers, using advanced tools like e.g., metagenomics, metabolomics, and metatranscriptomics to decode their complex interactions with plants.

The Many Layers of the Microbiome: Soil, Rhizosphere, Phyllosphere, and Endosphere

Each layer in the plant’s microbiome has its specialized community, microhabitat and role:

• Soil Microbiome: The soil is the foundation, housing countless microorganisms that decompose organic matter and build soil structure, supporting plant health at the roots.
  
  
• Rhizosphere Microbiome: The rhizosphere is the narrow zone of soil that is influenced by plant roots and root exsudates, rich in nutrients and signals that foster a dynamic partnership between plants and microbes. This is where plants attract their microbial allies, exchanging resources in return for essential services. Not to forget, one important part of the rhizosphere is the rhizoplane, what addresses the area directly attached to the root.
  
  
• Phyllosphere Microbiome: The phyllosphere harbours the section of microbiome that colonizes the above ground plant compartments, in particular the shoot(s) and leaves. These microorganisms can be transmitted via the xylem originating from the seed (vertically from the mother plant), soil, root, or enter through the hydathodes, lenticels, and stomata. Likewise to the rhizoplane, we have to consider the phylloplane region.

• Endophytic Microbiome: The endosphere consists of microbes living within plant tissues (root: endorhizosphere; shoots: endophyllosphere), quietly enhancing the plant’s resilience to stress and boosting nutrient uptake from the inside out.
  
  

There are still many more microbial plant (micro-) habitats that we could dive in deeper. For instance, microbiomes can be associated to the the surrounding and inner of flowers (anthosphere), of fruits (carposphere), seeds (spermosphere), and stems (caulospehre). 

Plus, all these microbiomes can be dynamic, depending on e.g. biogeography, climate zones, weather events, vectors (like insects, animals), and anthropological practices (e.g. fertilization, irrigation, cropping systems) - all factors together forming the term of the holobiont. 

Beneficial microbiomes interact with plants at multiple levels, forming symbiotic relationships. These microbiomes improve soil structure, enhance nutrient uptake, and in return, plants provide them with food sources. Farmers can influence these interactions by selecting plant varieties that attract beneficial microbes, using treated seeds, or through strategic field management practices.

 

A Symbiotic Superpower

Plants and their microbiomes work together in a beautiful example of symbiosis. Plants release a blend of sugars, amino acids, and other compounds (e.g. via root exudates) to invite helpful microbes to settle in. In exchange, these microbes provide a range of services that help plants thrive:

• Nutrient Acquisition: Certain microbes, like mycorrhizal fungi, form extensions of the plant’s root system, improving the uptake of nutrients like phosphorus and water. Meanwhile, nitrogen-fixing bacteria transform atmospheric nitrogen into a form that plants can absorb.
• Stress Tolerance: Facing harsh conditions like drought or salty soil? Microbiomes can help by producing plant hormones (like auxins and gibberellins) or enhancing root growth to access deeper soil layers, providing plants with a lifeline in tough times.
• Pest and Disease Protection: Beneficial microbes fend off harmful pathogens by outcompeting them for resources and even producing antimicrobial compounds, giving plants a natural defense system.

 

How Managing Microbiomes Can Boost Agriculture

Cultivating a rich and diverse microbiome isn’t just about plant health; it’s about boosting productivity and sustainability on the farm. Here’s how managing microbiomes can impact agriculture:

• Better Soil Health: Microbiomes improve soil structure, water retention, and organic matter decomposition, creating a stable environment for plants.
• Reduced Reliance on Chemicals: With enhanced natural pest resistance and nutrient access, farmers can rely less on synthetic fertilizers and pesticides.
• Higher Crop Yield and Quality: A healthy microbiome means crops that are more resilient to environmental stresses, with improved yield and nutrient quality.

Looking Ahead Towards One Health

Microbiomes are essential partners in agriculture, influencing everything from nutrient uptake to disease resistance, including the suppression of food-borne diseases. Hence, they play a crucial role by achieving food quality, safety, and security, thus driving a healthy world: One Health. With modern technologies, like metagenomics, we now have powerful tools to understand these hidden communities, offering exciting opportunities to create sustainable, resilient farming systems.

This post marks the beginning of our journey into the world of microbiomes. As we go deeper, the articles will branch into two alternating storylines: 

Get ready to explore how these invisible allies are shaping the future of agriculture, one microbial interaction at a time!

Computomics can help you investigate the genetic potential of complex microbiomes.
Check out the Microbiome Solutions for your industry or contact us!
 

 

References

• Berg, G., Rybakova, D., Fischer, D. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020). https://doi.org/10.1186/s40168-020-00875-0 
• Singh, B.K., Yan, ZZ., Whittaker, M. et al. Soil microbiomes must be explicitly included in One Health policy. Nat Microbiol 8, 1367–1372 (2023). https://doi.org/10.1038/s41564-023-01386-y
• Berendsen, R. L., Pieterse, C. M., & Bakker, P. A. (2012). The rhizosphere microbiome and plant health. Trends in plant science, 17(8), 478-486.
• Mendes, R., Garbeva, P., & Raaijmakers, J. M. (2013). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS microbiology reviews, 37(5), 634-663.
• Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., & Dufresne, A. (2015). The importance of the microbiome of the plant holobiont. New Phytologist, 206(4), 1196-1206.
• Van Der Heijden, M. G., Bardgett, R. D., & Van Straalen, N. M. (2008). The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology letters, 11(3), 296-310
• Bashir I., War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res. 2022 Jan;254:126888. doi: 10.1016/j.micres.2021.126888.