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Time to Scout for Rice Root Health

by Yeshi Wamishe, Extension Plant Pathologist - June 16, 2022

Often the effect of iron sulfide and hydrogen sulfide toxicity cause black coating and root rot in some soil types. The problem may start as early as a couple of weeks after a permanent flood is established. Problematic rice fields show yellowish lower leaves and slowed plant growth. Fields that receive cold water may show severe symptoms near ground-water inlets. Some soils with the problem may also show higher pH. 

The effect of black iron sulfide coating together with hydrogen sulfide toxicity encourages opportunistic fungi to invade and inhabit root crowns that ultimately obstruct water and nutrient translocation from the soil. At this late level, the problem is called autumn decline. 

Scouting tips for hydrogen sulfide toxicity at an early stage of rice crop

Where to scout

  • Scout in areas closer to well water inlets. Symptoms start near water inlets and fade further away.

How to scout

  • Pull out rice plants to examine roots from levees, bar ditches and/or paddies.
  • Wash the mud off rice roots.
  • Split tillers and further examine by cutting longitudinally through the root crown.
  • Compare rice roots from bar ditches, paddies and levees.


  • If hydrogen sulfide toxicity exists, roots from bar ditches and/or paddy would show black unlike roots from the levees (Figure 1).
  • Blackened roots when exposed to the air gradually change color to normal. 
  • In some fields, the flood water or roots may smell like rotten eggs or Sulphur.
  • As symptoms progress, lower leaves get yellowish and symptoms may be confused with sulfur or nitrogen deficiencies.
  • Due to yellowish lower leaves, affected fields may show a yellow cast. Rice in such fields gets stunt.
  • Often you may observe reduced root mass in affected plants compared to rice roots from levees (Figure1).
  • Root crown infection can occur at any developmental stage of the crop depending on the severity of the problems (Figure 1). 

Roots and root crowns from two rice plants. One sample taken from the levee (left) in contrast to the other sample taken from the paddy (right), having iron sulfide coating, hydrogen sulfide toxicity and invasion by opportunistic fungi.

Figure 1. Roots and root crowns from levee in contrast to paddy with iron sulfide coating, hydrogen sulfide toxicity and invasion by opportunistic fungi. 


Management tips for hydrogen sulfide toxicity

For rice fields with a history, a preventative approach is recommended.

  • Start scouting 2-3 weeks after flooding and follow the timely “drain and dry” strategy.
  • Be careful not to lose your preflood nitrogen. Before you drain, wait at least 3-4 weeks for the crop to utilize the preflood nitrogen. 
  • Drain symptomatic fields at straighthead drain-timing based on the DD50. 
  • After draining, monitor for new roots growth before re-flooding. 
  • NOTE:  It takes 3-5 days for new roots to start to grow. The concept behind draining and drying is to allow oxygen to enter the soil environment. 
  • Continue scouting. Draining more than once is not recommended. Keeping shallow flood depth may suffice to avoid adverse effects on crop yield. 

For late discovered hydrogen sulfide problem, a rescue approach is recommended.

  • If the problem is identified before midseason, drain and dry as described above. 
  • If rice is further in reproductive stages, drain the field only to lower flood depth but drying is not recommended; because rice at reproductive stages is too sensitive to drought.  
  • NOTE: Before you drain, consider the time it takes to re-flood based on the field size, your water resource and pump capacities. Big fields with this problem are often difficult to manage. 
  • Re-flood once new roots start to show up.

Consult with your county extension agent for symptom confirmation and to discuss a detailed management approach.