Microbiology for Agriculture: Hydroponics and More

In this blog, we’ll explore the foundational topics of microorganisms and the intersection between microbiology, agriculture, and hydroponics. Explore how this science works and applies to indoor agricultural systems like greenhouses, hydroponics, and vertical farms.

1. What is Microbiology, and Why Does It Matter to Agriculture and Hydroponics?

Microbiology is the branch of science that examines microorganisms, including bacteria, fungi, viruses, algae, and protozoa. These organisms are critical to the functioning of life on Earth. Their applications are vast and essential, from nitrogen fixation in soil to food fermentation to literally running many important nutrient cycles.

In agriculture, microbes perform vital functions, including:

• Nutrient cycling: Breaking down organic matter and releasing nutrients like nitrogen, phosphorus, and potassium for plants.
• Plant growth promotion: Certain bacteria and fungi enhance root growth and nutrient uptake.
• Disease suppression: Beneficial microbes can outcompete or inhibit pathogens in systems.

Quick Facts

It can be difficult to see the impact of one microbe, considering how tiny they are! A way to simplify their impact on systems is to look at them in a group or community, also known as the microbiome. A little fun fact: the microbiome actually describes the genomes of all the microorganisms in a specific environment, along with the environmental factors that affect them.

On the other hand, microbiota describes the just community of microorganisms that live in a specific environment, such as bacteria, viruses, fungi, or archaea.

Recently, they have been used interchangeably, but they are different! Imagine a large parking lot (representing the human body or a specific environment like the gut) filled with various types of vehicles (representing different microorganisms).

• The microbiota is represented by all the cars in the parking lot. It’s the actual collection of different vehicles present, including their makes, models, and quantities. This represents the population of microorganisms living in a particular environment.
• The microbiome is represented by all the cars in the parking lot PLUS their operating manuals and blueprints stored in each car’s trunk. These manuals contain detailed information about each car’s design, function, and maintenance. This represents not just the microorganisms themselves but also their collective genetic material and functions.

We explore the microbiome in this blog.

2. Microbiology Basics

Before understanding the interaction between microbiology, agriculture, and hydroponics, here is a quick rundown. Microorganisms exhibit incredible diversity and are classified into three domains based on genetic and biochemical characteristics: Bacteria, Archaea, and Eukarya.

Bacteria: These single-celled prokaryotes play diverse roles, including decomposing organic material and fixing nitrogen. They possess unique cell wall compositions and membrane structures.

Archaea: Also prokaryotic, archaea often thrive in extreme environments such as high-salinity soils, acidic waters, or high-temperature habitats. Their membrane lipids consist of branched hydrocarbon chains attached to glycerol by ether linkages, distinguishing them from bacteria.

Eukarya: This domain includes organisms with eukaryotic cells, such as fungi, algae, plants, and animals. Eukaryotic microbes like fungi and algae play significant roles in nutrient cycling and plant health.

Prokaryotes vs. Eukaryotes:

• Prokaryotes (Bacteria and Archaea): Microorganisms, including bacteria and archaea, that lack a distinct nucleus and membrane-bound organelles. Their genetic material is located in a nucleoid region within the cell.
• Eukaryotes: Organisms whose cells contain their genetic material in a nucleus and various membrane-bound organelles. This group includes fungi, algae, plants, and animals.

Key Cellular Components and Definitions

• Cell Wall: A rigid outer layer found in bacteria, fungi, algae, and plants.
• Nucleoid Region: The area within prokaryotic cells where DNA is located. It’s not enclosed by a membrane, unlike the nucleus in eukaryotes.
• Membrane: A flexible barrier surrounding the cell that controls what enters and exits. It’s made of a lipid bilayer and embedded proteins.
• Cytoplasm: The gel-like substance inside the cell where cellular processes occur. It contains water, nutrients, and molecules necessary for life.
• Organelles: Specialized compartments within eukaryotic cells, such as:
  • Nucleus: Houses the cell’s genetic material.
  • Mitochondria: Produces energy for the cell (the “powerhouse of the cell”).
  • Chloroplasts (in algae and plants): Carries out photosynthesis to provide sugars.

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3. Microbiology in Greenhouses, Hydroponics, and Vertical Farms

Understanding microbiology is essential for modern agriculture, particularly in controlled environments. Greenhouses, hydroponic farms, and vertical farms rely on microbiological principles to optimize plant health and yield while minimizing chemical inputs.

Microbial Roles in Controlled Agriculture:

1. Nutrient Cycling:
   • Beneficial bacteria like Rhizobium convert atmospheric nitrogen into forms plants can use.
2. Biocontrol Agents:
   • Fungi like Trichoderma spp. can protect plants from soil-borne pathogens such as Pythium or Fusarium.
3. Microbial Communities in Hydroponics:
   • Hydroponic systems are field with many types of microbial communities from biofilms (microbial layers stuck in surfaces) to free-floating to plant-related groups.

Digging Deeper in Microbiology and Hydroponics

Want to dive deeper in where microbes, agriculture and hydroponics intersect? Take a look at these papers!

• The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites (2022):
  • This study explored the phyllosphere (leaf surface) microbiome of tomatoes and strawberries in greenhouses. It revealed that bacterial diversity and abundance were low, with significant variability over time and space. Interestingly, bumblebees and predatory mites were identified as key sources of bacteria in these environments.
• Bacterial Community Dynamics of Tomato Hydroponic Greenhouses (2022):
  • Focused on bacterial communities in the tomato rhizosphere grown in rockwool under hydroponic conditions, this paper found Paenibacillus to be the most dominant genus. The study also highlighted differences between microbial communities in healthy versus diseased greenhouses.
• Water Microbiota in Greenhouses With Soilless Cultures of Tomato (2020):
  • This research analyzed microbial communities in water used for hydroponic tomato cultivation. It showed that microbial diversity varied based on water storage conditions. The study also demonstrated that slow filtration systems could reduce harmful pathogens without significantly altering microbial richness.
• The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised? (2023):
  • A comprehensive review of microbial communities in hydroponic rockwool systems, this paper discussed how these microbiomes could be harnessed for biocontrol and crop management. It emphasized the potential for “microbiome steering” to optimize plant health.
• Plants Dictate Root Microbial Composition in Hydroponics (2022):
  • This study investigated how plants influence their rhizosphere microbial communities in soil-less systems. It found that plants actively shape their root microbiomes even in hydroponic environments, highlighting the importance of plant-microbe interactions.
• Unveiling the Microbiome of Hydroponically Cultivated Lettuce: Impact of Pathogen Invasion (2024):
  • Examining the rhizosphere and root endosphere microbiomes of hydroponically grown lettuce, this research explored how the pathogen Phytophthora cryptogea affected microbial communities. The study identified certain bacterial genera associated with healthier plants.

Disclaimer

The information we present in this blog is based on collating published peer-reviewed scientific literature, and sources we think are reliable. This is by no means an exhaustive review of pathogens. This blog gives a small glimpse of what is known about pathogens. We encourage growers to do more research on the pathogens concerning their crops and hydroponic systems. We are not plant pathologists; thus, the information presented should not be used as professional advice to treat pathogens or operate your system.

David Santos is the CMO of Healthy Hydroponics InnoTech