How Microbes Survive in Saturated Soils

In the last few weeks, some areas have received a considerable amount of rain, some would say excess rain. While all microbes live on water films in the soil, too much water changes the microbial community. Excess water also displaces oxygen in the soil which is detrimental to both certain types of microbes and also to plant health. Roots need to be able to absorb oxygen for respiration to break down the root sugars for energy. Oxygen is the fuel to making both fires burn hotter and also for plants and animals to burn oxygen and sugars to produce energy.

In flooded soils, the majority of obligate aerobic microbes die within 24-72 hours. As dissolved oxygen is depleted; biological activity drops by 50% within 48 hours. Then facultative and obligate anaerobic organisms take over. Obligate means that either oxygen is totally required (obligate aerobes) or not required (obligate anaerobe). Aerobe mean oxygen loving, anaerobe means absence of oxygen. Facultative microbes may live in either environment.

Many fungi and bacteria go into a dormant spore-like state when oxygen or a food source is low and may survive for weeks and months before returning to normal function when soils drain and oxygen returns. Unfortunately, in highly tilled soils, lacking roots; a compaction layer may form and this severely limits both water and oxygen or gas movement deeper into the soil. These soils tend to become anaerobic and stay that way for long periods of time. Pathogens like E. Coli and Salmonella, both gram negative bacteria; can persist for 2 to 4 months and even up to 400 days in low oxygen soil conditions because they are facultative bacteria.

How do aerobic and anaerobic bacteria survive in soil? Either with excess oxygen (highly aerobic conditions) or a near total lack of oxygen (highly anaerobic conditions)? The reason both types of microbes can survive in relatively close proximity to each other is because the soil is a micro-environment. Both aerobic and anaerobic conditions can be found close together.

Microaggregates are clusters of dense small soil particles (mainly clay) tightly packed together and they tend to be anaerobic (no or low oxygen conditions), so anaerobic microbes, especially bacteria, thrive in these conditions. The closer you get to the center of a microaggregate, the less oxygen exists. So anaerobic bacteria thrive here. Microaggregates set up like a brick wall, the soil is tight and compacted, and may be saturated with water; but have little to no oxygen for energy.

In Macroaggregates; glomalin (from arbuscular mycorrhizae fungi, AMF), root exudates, and mucilage form a protective film around groups of microaggregates, water, pockets of oxygen, plant debris, and decomposing roots and organic matter. This is a perfect environment for aerobic microbes (obligate bacteria) to thrive. Macroaggregates allow some microbes to survive at much lower numbers (less species, lower population density) for longer periods of time, even in soils that are flooded for several days.

Macroaggregates improve soil structure but the sugary films (glomalin, polysaccharides, root exudates, mucilage) is also food for the microbes. Macroaggregates break down into microaggregates, reform with the help of roots and microbes, and then break down again. It’s a temporary home for aerobic microbes to survive but if conditions stay wet too long, the aerobic diversity and density decline quickly. That is why live plant roots and microbes live together to improve the porosity of the soil environment for diverse and abundant microbial species to coexist together in their own micro-environment!

From this discussion, you might think that aerobic bacteria are better than anaerobic bacteria. Not True! They both have specific functions. Aerobic bacteria tend to improve soil structure. They colonize roots to improve nutrient recycling of soil organic matter to release plant nutrients. They also consume the easy to digest nutrients and their breakdown helps form humus, a stable organic matter that improves soil structure. In addition, they suppress harmful pathogens and diseases by out competing them for root space. Aerobic bacteria help improve the rooting environment for better soil drainage and aeration, both water infiltration and storage along with better gas exchange (think oxygen to the roots, and soil carbon dioxide flow up to the leaves.)

Anaerobic bacteria live in low oxygen or no soil oxygen regions. When they are in excess, they tend to cause disease and become pathogens. However, when they are kept in check by aerobic bacteria, they also make a lot of soil nutrients plant available. Most micro-nutrients need anaerobic bacteria to convert them to a plant available form. Taken together, keeping soils healthy requires diverse and abundant microbial species working together to produce healthy crops.