Manure Storage and Handling -- Anaerobic Digestion

Application: used to stabilize liquid manure, reduce odors, and potentially create methane rich biogas that can be used for heat and power


  • Can be used on highly concentrated manures.
  • Can be utilized to generate heat or electricity.


  • Anaerobic lagoons require large amounts of land and result in substantial loss of nitrogen.
  • Anaerobic digesters are expensive to install and maintain.



Anaerobic digestion is the process of breaking apart molecules without oxygen. Often times these are fermentation type reactions. On the subject of fermentation, what usually comes to mind is something like beer or wine making; in these processes, carbohydrates (sugars or starches) are broken down into simpler compounds (hopefully ethanol in the case of beer or wine making). In fermentation of manures, bigger substances (fibers, fats, proteins) are broken apart into smaller molecules. In this case we get a much wider assortment of other compounds formed, rather than just ethanol. Examples of the compounds formed during the fermentation of manures include volatile organic acids (like acetic acid or propionic acid, i.e., vinegar like substances), aldehydes (aldehydes are often used in fragrances), ketones (acetone is an example), amines (pieces of proteins), indoles (these are again often fragrances), and phenols (a carbon ring structure). These compounds are then broken down further by microbes in the manure.In the case of carbon, it will become methane and carbon dioxide, nitrogen will become ammonia, and sulfur will become hydrogen sulfide. Of these compounds, methane and carbon dioxide are odorless, but ammonia and sulfur bothare odorous. The intermediary compounds (those volatile organic acids, aldehydes, ketones, amines, indoles, and phenols) are many of the odorous compounds associated with partial decomposition of manures. As a result, facilitating more complete anaerobic digestion that promote the conversion of these intermediate compounds into methane and carbon dioxide can substantially reduce odor.

In agricultural settings there are generally two types of anaerobic treatment systems, these include anaerobic lagoons and anaerobic digesters. Anaerobic lagoons are large, open-topped or covered earthen storages designed to both facilitate stabilization by the anaerobic treatment process described previously, and provide long-term storage of the manure. When properly designed and managed, anaerobic lagoons will have low odor, but result in significant emission of both methane and ammonia. To maintain low odors in anaerobic lagoons that are not covered,the anaerobic digestion process must proceed to completion. Some odors should be expected from any anaerobic lagoon during the start-up period, and during spring and fall when thermal currents cause the lagoon to flip and bring decomposing manure to the surface. To minimize odor issues during these times,screen the lagoon for proper site selection that is mindful of predominant wind orientation.

In anaerobic digesters, the same microbial decomposition process that occurs in lagoons is utilized for manure stabilization, but there are several key differences. Anaerobic digesters are designed and managed in a way to optimize the bacterial decomposition of organic matter. To facilitate this, the conditions (temperature, retention time, pH) of the digester must be carefully controlled. Generally, anaerobic digesters are maintained at 35°C (95°F), and sized to provide a retention time of 21 to 30 days.As the anaerobic digester tank is sealed, almost no loss of nitrogen, phosphorus, sulfur, or odors occur during the digestion process. Moreover, since digestion is relatively complete by the time the manure is removed from the anaerobic digester, most of the potential odorants (volatile organic acids, aldehydes, ketones, amines, indoles, and phenols) have been consumed; however, as the digestion process converts nitrogen to ammonia, and sulfur to sulfides, losses of these gases can occur during subsequent storage of the manure.In general, scrubbing for hydrogen sulfide removal is required before the biogas can be combusted for power generation or storing.

Research has tended to suggest that the switch from anaerobic to aerobic conditions causes greater die-out of microbes present in the manure, when compared to manure that is immediately land applied (goes directly from excretion to aerobic conditions). In fresh manure there is a diverse array of microbes. During anaerobic storage of the manure, these microbial populations change as those who are less fit (not as well adapted for the anaerobic conditions) tend to be out- competed and die-off. When manure is taken out of storage and land-applied, the shift from anaerobic conditions to aerobic conditions occurs very quickly. Although many microbes can survive under both conditions, they generally do better under one condition than the other. Drastic changes from anaerobic conditions to aerobic conditions tend to put microbes that were present in the manure at a disadvantage where they are outcompeted by microbes that are better able to survive under aerobic conditions. This contributes greatly to reduced pathogen survival.

Overall, anaerobic lagoons have demonstrated some potential at reducing odors, but they result in loss of large amounts of ammonia, reducing the value of manure as a fertilizer source. Anaerobic digesters alleviate this problem of nitrogen loss, but they are expensive to implement on farm and have historically had a high rate of failure (~50%) when installed at animal production facilities.


Component Reduction Notes
NH3 -50 to 30% lagoons result in ammonia loss, Digesters have no ammonia loss but make manure susceptible to nitrogen loss during additional storage
H2S 0 to 10% not generally reported
Odor 50 to 85%  
Particulate Matter -- depends on how methane is handled, flaring can produce particulate
Volatile Organic Compounds (VOC) 60% not reported, expected similar to odor
Greenhouse Gases 70%  
Cost $$$ to $$$$  

Cost Considerations

Anaerobic digestion costs are high and instillation of a project will typically range from 0.5 to 2 million dollars. Estimated capital costs are $750 to 2000 per cow.


Beddoes, J.C., Bracmort, K.S., Burns, R.T., Lazarus, W.F. (2007). An analysis of energy production costs from anaerobic digestion systems on U.S. livestock production facilities. USDA NRCS Technical Note. No. 1.

Faulhaber, C.R., Raman, D.R., & Burns, R.T. (2012) An engineering-economic model for analyzing dairy plug-flow anaerobic digesters: cost structures and policy implications. Transactions of the ASABE 55(1): 201-209.


Daniel S. Andersen, Assistant Professor, Agricultural and Biosystems Engineering, Iowa State University, Jay D. Harmon & Steven J. Hoff, Professors, Agricultural and Biosystems Engineering, Iowa State University, and Angela Rieck-Hinz, Manager, Iowa Manure Management Action Group, Iowa State University Extension & Outreach

October 2014