Agronomy Talk


Published on Wednesday, June 30, 2021

Heavy or persistent rains can lead to saturated soils that can injure or kill a seed, seedling, or growing plant. Saturated soils have an impaired ability to exchange air between the atmosphere and soil. This deprives the seed or plant tissues of oxygen required for respiration.

The pore space of a well-granulated silt loam soil is comprised of approximately 40 to 50% micro and macropores. At
field capacity, approximately half of these pores will be occupied by water and half by air. In saturated soils, the pore
space is entirely filled with water. Thus, damage can occur even in situations without standing water - if pore space
remains 100% occupied by water.


Germination and Emergence

Successful germination requires three elements: 1) Moisture 2) Temperature 3) Oxygen

Oxygen is especially important once imbibition (water uptake to initiate germination) is completed due to increased respiration rates. This process is usually completed within a few hours but can take 24 to 48 hours depending on soil moisture and seed-to-soil contact. Ideally, zero rainfall is preferred within 48 hours post-planting. Inadequate soil oxygen can lead to seed rot or increased respiration stress, thus resulting in a lack of emergence, delayed emergence, or reduced early season vigor. 

Seedling Disease - Pythium

Pythium is often referred to as “post-emerge damping off” and is typically more prevalent in wetter areas/ fields. The survival of young corn seedlings depends on both a healthy kernel and mesocotyl. Damage to the mesocotyl tissue prior to the establishment of the nodal root system can result in stunted, weak, or dead seedlings. A developing corn seedling relies on the kernel endosperm for nourishment until the nodal root system has fully developed, V4 to V6. The mesocotyl serves as the “highway” to transport nutrients from the kernel and seminal roots to the seedling stalk and leaf tissues. Within soil water are fungal pathogens that can attack and compromise mesocotyl health. Fungal infection susceptibility increases the longer the seed is in the soil and experiences stress. Often, mesocotyl infection results in plant death. However, it is a race. If nodal root establishment can occur to support the young seedling prior to plant death, plants can survive. 

Ear Initiation

Limited oxygen in saturated soils reduces the rate of respiration, which depletes plant tissue of energy necessary
for physiological processes. This is especially impactful to younger plants, which have a higher respiration rate
due to rapid cell division and growth. Very early on in development (during the V5 to V6 growth stage), corn
determines the number of rows around the ear. A reduction in respiration at this critical yield determination stage
can negatively influence potential ear size.

Crown Rot and Premature Plant Death (PMD)

Crown rot infections are caused by both fusarium and Pythium species. These fungi enter the plant via the root
system during periods of prolonged saturation, predominately between the V2 to V7 growth stages. Crown rot
infections are not typical before the V2 growth stage with the utilization of a comprehensive fungicide seed
treatment. Because these fungi persist in higher moisture environments, soils with a propensity to remain wet are
more prone to infection. While these infections occur early in corn development, detection is difficult until later in
the grain fill period.

The crown area serves as the “pipeline” through which moisture and nutrients extracted by the root system are mobilized into the stalk. Despite infection, the plant continues to grow and develop due to the generation of new nodal and brace roots. Some may say the plant “outgrows” this infection. Newly developing roots continue to provide access to additional moisture and nutrients, and the plant survives, albeit with a reduced vascular system.

Despite the plant appearing to recover, the infection continues to progress. As it does, it further obstructs the “pipeline,” making it more difficult for the plant to mobilize nutrients and water from the roots to the rest of the plant. Plant stress is compounded throughout grain fill with the increased remobilization of nutrients to the grain. Ultimately, the plant succumbs to premature death – a condition known as PMD.

The impact of PMD typically results in smaller ears and lower test weight. It also can lead to stalk lodging and breakage at the soil level (crown region) or just above. 


Nitrogen loss due to saturated soils is directly proportional to the amount of nitrogen in the nitrate form. While nitrate nitrogen is the most readily available form of nitrogen to the plant, it is also the most vulnerable form of nitrogen to be lost due to excessive water.

The nitrate (NO3 -) form of nitrogen has a negative charge, so it does not bind with soil particles. Nitrogen in the ammonium (NH4 +) form is much more secure as it will “magnetize” or bind to negatively charged soil particles. Over time, ammonium nitrogen is then converted to nitrate nitrogen by soil bacteria.

In saturated soils, nitrate-nitrogen may be lost by way of denitrification or leaching. Leaching occurs more predominantly in coarse-textured soils. These soils allow nitrate-nitrogen within the water to readily move down through the soil profile. If the movement of nitrate-nitrogen occurs below the root zone, the nitrogen is no longer accessible.

Denitrification losses are more prevalent in fine-textured soils. These soils hold water tightly and restrict the downward movement of water and nitrate nitrogen. Denitrification is the process of soil bacteria converting nitrate nitrogen to nitrogen gas and thus, is lost upward into the atmosphere. In anaerobic conditions, a variety of bacteria utilize the oxygen in nitrate-nitrogen for respiration. Two to three days of continuous soil saturation are required for bacteria to begin denitrification. The duration of soil saturation and soil temperature influence nitrogen loss from denitrification. 


Germination and Emergence

Compared to corn, soybeans are thought to be more tolerant to flooding and saturated soils. However, germination and emergence still require the same three things: 1. moisture, 2. temperature, and 3. oxygen. Inadequate soil oxygen can lead to seed decay and increased stress resulting in a lack of emergence or a reduction in early season vigor. Stand reductions in soybeans are, however, typically less detrimental to yield in comparison to corn. Soybeans can better compensate for thinner stands by increasing pods per plant, seeds per pod, and seed size if given additional plant space.

Soil-Borne Diseases

Soybeans are continuously at risk to soil-borne pathogens, however with good growing conditions they often outpace disease infection and development. Cool, saturated conditions favor disease development while slowing soybean growth. If poor growing conditions persist, disease infection can overtake the plant resulting in weakened or dead plants. Persistently wet soils are particularly conducive to infection of Pythium and Phytophthora, often referred to as “water molds.”


Pythium can attack seedlings before emergence and produce post-emerge damping-off in saturated conditions. Pythiuminfected plants typically possess hypocotyl tissue that is soft and brownish-colored. Because this symptomology can appear much like that of seedling Phytophthora infection, lab examination is necessary for proper identification. 

Phytophthora Root and Stem Rot

Like Pythium, is referred to as a water mold due to the release of zoospores which move through the water to infect soybean roots.

  • Early-Season: Seedling death can occur prior to, or shortly after, emergence from this pathogen. Symptomology includes bruised and soft stems, rotten secondary roots, chlorotic and necrotic leaf tissue, wilted plants, and death.
  • Mid- to Late-Season: Plant death can occur throughout the growing season. Roots may have brown lesions on diseased plants. These roots may rot and degrade. Also visible is a discoloration of the stem that is dark chocolate-brown that begins just below the soil surface and stretches to the lower portions of the plant. Chlorotic leaves can persist, wilt, and often remain intact after the plant has died. Plant death usually appears in patches or in sections of rows. Tolerant varieties may appear stunted, but not die. 

Sudden Death Syndrome (SDS)

SDS is caused by the soil-borne fungus, Fusarium virgulifome. Root infection occurs early in the season, but symptoms of SDS usually are not observed until late July or August. Conducive conditions for disease development include cool and saturated soils, early planting, susceptible varieties, and soybean cyst nematode feeding.

Leaf symptoms typically begin as scattered yellow spots between the veins that expand to become brown lesions surrounded by chlorotic tissue. The edges of leaves may be curled. The leaves detach from the petioles as the disease progresses. The gray discoloration will develop in the outer stem of the vascular tissue of the lower stem. The pith remains white, which is a diagnostic feature that distinguishes SDS from brown stem rot. SDS also causes root rot, and roots may exhibit blue fungal growth in moist conditions.

While SDS can be more invasive when planting early into cool soils that may become saturated, the yield benefit of planting early often outweighs the risk of SDS. When planting into soils that are more prone to saturation, minimize the impact of SDS through variety selection, SCN management, and effective seed treatment options. 

Nitrogen Fixation and Nutrient Uptake

Anaerobic, saturated soils have a negative impact on symbiotic N fixation and the mycorrhizal colonization of soybean roots. These processes rely upon microorganism activity, which requires oxygen.

Soil bacteria, Bradyrhizobia japonicum, infect soybean root hairs and multiply to form nodules on roots where they convert atmospheric N (N2) into a form of N the soybean plant can readily utilize. Without oxygen, these bacteria struggle to survive, and nodule shed tends to occur within some soybean varieties.

Mycorrhizal fungi within soils provide soybean plants overall greater access to soil water and nutrients than roots alone. Mycorrhizae spores are not metabolically active and do not require oxygen until roots are present. Upon root development, these spores will grow, demanding oxygen and sugars from the plant roots in order to flourish.

Saturated soils are typically more detrimental to soybeans in the reproductive stages than the vegetative stages. This is due to the decreased growth rate and photosynthate production at a critical time of pod development and pod fill. 

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Author: Luke Schulte

Categories: Agronomy, Agronomy Talk


Luke Schulte

Luke Schulte

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