Transformation and Agronomic Use of Nutrients From Digester Effluent

Table of Contents

Anaerobic Digestion Nutrient Transformations

Anaerobic digestion (AD) is the process in which organic compounds are broken down by naturally occurring bacteria, including methanogenic microorganisms under oxygen free conditions, transforming organic matter into biogas (methane (CH4), carbon dioxide (CO2), water vapor, ammonia, and hydrogen sulfide) (Dugba and Zhang, 1999; AgSTAR, 2010b). The end products of this process include biogas, a renewable energy source, and treated manure containing plant nutrients that can be used to replace agricultural fertilizers. The nitrogen, (N), phosphorus (P), and potassium (K) are not lost or reduced due to the AD process, but are transformed (see figure 1) from organic forms to inorganic forms while the carbon is converted to biogas (Table 1). As a result, the levels of ammonium N and inorganic P increase as a percent of total N and total P when compared to raw manure. The increase in ammonium content will vary due to pre-digester management of the manure. Data from Washington State University indicates that ~ 40% of the N going into the AD is NH4+-N, and 60 % of N coming out of the AD is NH4+-N (O’Rourke et al, 2009 SWCS presentation)

Figure 1. Transformation of nutrients passing though digester

Chemical Composition of Digested Effluent


Nitrogen that enters a digester from dairy manure is either in the ammonium or organic form. Much of the organic nitrogen is converted via nitrogen mineralization during the digestion process to ammonium, raising the overall level of ammonium in the effluent (Field et al., 1984). Although a small amount of ammonia gas will be lost to biogas, the total nitrogen leaving the digester is generally considered equal to that added to the digester. (Topper, 2006).

Nutrient content of the AD input will vary depending on the species of the contributing manure and if there is any addition of other organic feedstocks (co-digestion). Kirchmann and Witter (1992; Table 1) evaluated fresh and anaerobically digested manure from three different species for nutrient concentration. They conclude that anaerobic digestion of manure resulted in higher ammonium N concentrations (50-75% of total N) in the digested material. In a similar project with co-digestion of dairy manure and pre-consumer waste feedstocks, they observed an increase from 34% NH4 (% of total N) in pre-AD material to 58% NH4 (% of total N) post-AD material prior to liquid-solid separation  (7.3 NH4 and 21 total N lbs./ 1000gal before digestion; 9.1 NH4 and 15.8 total N lbs./1000 gal post digestion, Whitefield, 2009). Anaerobic digestion facilitates nitrogen mineralization, while carbon is converted to biogas.  Additionally, carbon is partially removed from the digested material,  reducing the C:N ratio (Kirchmann and Witter, 1992; Moller et al., 2008).

Table 1. Forms of nitrogen in fresh manure and anaerobic digestion effluent (Kirchmann et al., 1992; numbers in parenthesis are the percent of total N).


Nutrient speciation data collected from previous AD studies suggest that a high percentage of the P can be found in the inorganic form in the AD effluent (Wrigley et al., 1992; Bowers et al., 2007; Marti et al., 2008; Moody, 2009). Moody (2009) and colleagues demonstrated a 26% increase of inorganic P (PO43) in digested swine slurry compared to the raw swine slurry (1591 mg/L and 1256.2  of PO43– respectively). Inorganic P is comprised of soluble and insoluble orthophosphates and polyphosphates. When evaluating the nutrient transformation of five different types of ADs in New York, the percent change in orthophosphorus (OP) after digestion varied from 7-27% depending on the type of AD (Figure 2). The case study data from Cornell (Figure 2) also demonstrates the percent change of total Kjeldahl nitrogen (TKN), ammonia nitrogen (NH3-N), organic nitrogen (ON), and TP (Gooch et al, 2006). The positive percent change indicates a greater concentration of the nutrient in the post digested effluent compared to the influent vs. a negative percent change which indicates the nutrient is more concentrated  in the influent before digested compared to after digestion.  These data represents several farms with digesters, some with different digester models, and therefore variation would be expected. Bowers et al., (2007) demonstrated total phosphorus (TP) content ranging from 238 to 323 ppm, from which OP contributed 106 to 231 ppm of the TP in the post digestion effluent of a co-digestion dairy manure AD. Also one should not expect loss of N or P during digestion, and variability due to sampling and analyses could have caused some error in mass balance calculations.

Figure 2.  Nutrient Transformation (% change) of five different farms with digesters from a case study in NY state (Source:  Gooch et al, 2006) The percent changes was calculated as influent nutrient value minus effluent nutrient value; therefore even though there is a negative percent change of NH3-N and OP, there is a greater amount in the digested effluent compared to the influent.

pH and Chemical Oxygen Demand

The pH of the manure remains fairly neutral throughout digestion maintaining microbial stability within the digester (Wen, 2009). In a study by Wang and collegues (2010) anaerobic digestion reduced manures’ chemical oxygen demand and amount of total and volatile solids by 30-40%.

Organic nitrogen is mineralized to ammonium while conserving total nitrogen and phosphorus (Wang et al., 2010). The Danish Biogas Institute reports 25% more available NH4-N and higher pH in AD manures (Monnet, 2003).

Liquids-Solids Separation

Many AD systems are managed with the use of liquids-solids separation after the manure has been digested. Separating out the solids for use as a soil amendment or bedding can result in a small reduction of nutrients in the remaining fraction. Preliminary data from Washington State University suggests that 27 % of the solids, 6 % of the N, and 8 % of the P are removed in the solids from AD treated manure (screw type solids separator).

Potential for Increased Efficiencies

Although there is a growing body of research on anaerobic digestion and crop nutrient availability, this technology has not been extensively studied. Most work has been focused on short term nutrient recovery (1-3 years), and not the long term impacts (5+ years) of fertilizing with AD manures (Arthurson, 2009).

AD manure has been shown to have the same positive effects on yield and crop production when applied at equal rates of plant-available N as synthetic fertilizers or raw manures in corn and forage production systems (Morris and Lathwell, 2004; Loria et al., 2007), while soil quality and fertility indicators are improved relative to synthetic fertilizers (de Boer, 2008; Arthurson, 2009).

Since anaerobically digested dairy manure could provide more plant available nitrogen than untreated manure (Kirchmann and Witter, 1992; Michel et al., 2010), the potential exists for increasing agricultural efficiences (Morris and Lathwell, 2004; Moller and Stinner, 2010). Increased concentrations of NH4-N in AD manure would increase the potential for N loss in the field, so best management practices would be required to take advantage of the higher NH4-N content.

Application of AD dairy manure to corn has been shown to produce similar total plant N uptake and equivalent or greater yields than inorganic fertilizer.  Early growth/yield of corn was greater from application of AD dairy manure than from synthetic fertilizers on acidic soils (<7.0) but not on alkaline soils (Morris and Lathwell, 2004). The acidic soils restrict ammonia loss from ammonium-rich AD manure resulting in greater N uptake (Nelson, 1982).

Figure 3 summarizes information from 2 years of a study (Saunders, 2011) conducted to look at anaerobically digested dairy manure or undigested dairy manure. When anaerobically digested or undigested manure was applied at equal amounts of total nitrogen, equivalent amounts of dry matter yield (~ 7.5 tons) and similar amounts of nitrogen uptake (~ 475 pounds) were observed. The control did not receive any form of fertilizer or manure, and was stastically different (P<.05) from the manure treatments before and after digestion.

Figure 3. Average annual yield of dry matter and annual nitrogen uptake by grass receiving equal amounts of nitrogen from anaerobically digested dairy manure or undigested dairy manure.

Manure serves as a useful, low-cost source of nutrients for crop production (Sommerfeldt et al., 1988; Jokela, 1992; Ferguson et al., 2005; Nyiraneza and Snapp, 2007). Anaerobically digested manure provides sufficient nutrients to support biomass and crop yields equivalent to synthetic fertilizers and raw manures (Bittman et al., 1999; Loria et al., 2007). Some studies, (Rubaek, 1996; Chantigny et al., 2007; de Boer, 2008) have found increased yield and nitrogen availability with application of anaerobically digested material as compared to non-digested material, possibly due to increased nitrogen content and reduced carbon content, which can result in nitrogen mineralization by microbes. In addition, manure applications to soils have enhanced soil quality and fertility compared to soils receiving synthetic fertilizers (de Boer, 2008; Arthurson, 2009). A crop will typically recover <50% of applied fertilizer nitrogen (Stevens et al., 2005). Up to 46% of applied manure nitrogen may be left over in the soil at the end of the growing season, increasing the potential for loss, after multiple applications during a season (Munoz et al., 2003). Over-application of manure nitrogen in excess of crop uptake can result in nitrate leaching (Angle et al., 1993). Some studies have indicated that manure nitrogen poses an equal or slightly less risk to leaching than synthetic fertilizers (Jokela, 1992;Trindade et al., 2009). Others have determined manure increases nitrate leaching (Jemison and Fox, 1994). During winter months when plants are dormant, nitrate leaching can be the main source of N loss (Bakhsh et al., 2007). The shift in organic to inorganic nutrients during the AD process should be considered when developing a farm nutrient management plan.


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  •  Sandy Anderson, Washington State University

Cayuga County Manure Digester Virtual Tour

Anaerobic digestion is a manure treatment system that produces biogas. There are many benefits of digestion such as reductions in: odor, pathogens, and greenhouse gases (climate change). Producing biogas from manure yields useful by-products.  The economics of digestion are dependent on state energy policies and co-digestion of off-farm wastes to generate revenue.

Cayuga County Regional Digester (New York)

This virtual tour highlights the Cayuga County Soil & Water Conservation District regional digester. This facility receives manure from multiple dairy farms. The regional digester model allows smaller farms (not large enough to build their own digester) or large farms unwilling to take on the complex management of a digester to participate.sign

For more information: Cornell case study (technical details) | NRCS Newsletter (construction photos and funding information)

  • Type of digester: Pressure differential (hydraulic mix)
  • Facility began operation: March, 2012
  • Feedstocks: dairy manure, food wastes, brown fat

How Does This Anaerobic Digester Work?

The hydraulic mix or pressure differential digester type is common in Europe, but is unique in the United States. The video below explains how the material moves through the digester.

Step By Step Through The Facility

Even though we refer to this facility as an “anaerobic digester” there are actually many pieces required to make this system work. The digester is one part. The presentation below works through the entire facility.


The digester tank (photo above: left) has a capacity of one million gallons. It is estimated that 40-43,000 gallons will be added to the digester per day when it reaches full production capacity. The trucks carrying raw (undigested) manure from the farms enter on the right side of the building (photo above:right) and the manure is pumped into a holding tank (not visible in photo) and mixed with food waste.

To see the captions in the slideshow, select “full screen” (lower right side of the slide) and then click on show info (upper right corner). You can also visit this photo set at:

In the News

This digester has been in the news as the price of power has dropped and the financial side of the operation less viable.

  • Digester is shut down to re-evaluate business plan (Jan. 2015) More…
  • California company to take over Cayuga digester (June, 2015) More…

Recommended Reading on Anaerobic Digestion


Author: Jill Heemstra, University of Nebraska Extension
Reviewers: Thomas Bass, Montana State University, David Schmidt, University of Minnesota and Liz Whitefield, Washington State University

A big thank you goes to the Cornell University dairy manure management team for organizing the 2012 “Got Manure?” conference that included a real life tour on which we were able to obtain the media for this virtual tour.

This virtual tour was created by the LPELC Beginning Farmer team through funding from the USDA National Institute for Food and Agriculture (NIFA) Beginning Farmer and Rancher Development program under award #2009-49400-05871

Farm Energy Anaerobic Digestion and Biogas



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Table Of Contents

Anaerobic Digestion of Animal Manures: Understanding the Basic Processes

Animation showing breakdown of manure.

Organic Compounds Breaking Down into Biogas

The process of producing methane from manure is fairly straight forward – seal manure in an airtight container at a favorable temperature and it will break down into biogas: a mixture of Methane (CH4), Carbon dioxide (CO2), and trace amounts of other gases. Behind the apparent simplicity, though, lie complicated interactions involving several communities of microorganisms.

The Bioconversion Process (How Microbes Turn Organic Materials into Fuel)

Anaerobic digestion is a multi-stage process (Figure 1) involving two to four steps, depending on where you want to draw lines in the process.

  • Hydrolysis is the phase of anaerobic digestion where complex organic molecules are broken down into simpler organic molecules.
  • Acidogenisis is where simple organic molecules are converted into fatty acids.
  • Acetogenisis is where fatty acids are converted into acetate. This, along with acidogenisis, represents the transition from simple organic molecules to the methanogenic substrates as shown in the figure below.
  • Methanogenisis is where molecules that have been converted into a suitable food source (or substrate) for methanogenic microorganisms are converted into methane by those organisms.

Figure 1. Steps in anaerobic digestion

More than 100 different anaerobic microbes are known to contribute to the production of biogas. These microbes are organized into a number of interlinked communities. Communities of hydrolytic bacteria break complex organic matter down to simpler compounds. Acid-forming bacteria convert the simple compounds to volatile fatty acids – principally acetic acid (vinegar). Hydrolysis and acidogenisis are commonly lumped together and called anaerobic fermentation. Some microbiologists also distinguish between formation of mixed volatile fatty acids (acidosis) and reduction to Acetic acid (acetogenesis).

Figure 2. Major pathways of methane (CH4) formation

Methane forming Archaeans (very simple, single cell organisms similar to bacteria), called methanogens, take the end products of fermentation – volatile fatty acids, hydrogen gas (H2), CO2, and water (H2O) – and use them to form methane. Methanogens fall into two main camps depending on the pathway they use to produce methane (Figure 2). All methanogens can reduce CO2 and H2 into CH4 and H2O; those that use this pathway exclusively are called hydrotrophic methanogens. Methanogens that convert volatile fatty acids (and a number of other simple organic compounds) to CH4 and CO2 are called acetotrophic methanogens.

Limitations on Biological Processes

Anaerobic digestion is a living process, and like all biological communities, the microorganisms that carry out anaerobic fermentation and methanogensis do so under certain operating conditions.

Phases of Microbial Community Growth

Given an ample food supply, sufficient room to expand, the absence of predators or competing organisms, all communities of organisms – be they methanogens or human beings – grow in a pattern similar to the one shown in Figure 3. The Lag Time occurs as the organisms acclimate to their environment.

Figure 3. Generalized microbial growth curve
  • During the Growth Phase, food is not limiting, and population expands rapidly. Sometimes the Growth phase is called the Log Growth or Exponential Growth phase because the growth pattern follows an exponential curve. *Population growth slows down in the Decline Phase as the organisms meet the limit of their food supply.
  • During the Stationary Phase, the community has met the limits of its food supply. Bear in mind that reproduction does not necessarily stop during the decline and stationary phases, only that the death rate approaches the reproduction rate. In some cases the community becomes dormant or goes into hibernation during the Stationary phase.
  • Communities enter a Death or Endogenous Growth phase once a limited food supply is exhausted or an inhibiting element limits the further growth of organisms. During Endogenous Growth, the death rate exceeds the birth rate.

The inhibitory elements that cause endogenous growth are often the end products of a community’s metabolism.

The beauty of anaerobic digestion is that it is the work of a mixed community of organisms. The toxic end product of one community is the food supply of another. Acid forming bacteria consume the simple sugars that might inhibit hydrolytic communities. Methanogens use the acids formed in fermentation to produce CH4 and CO2. And in the end, CH4 and CO2 leave the digester as biogas.

Reproduction Time

Most anaerobic digesters are designed so that the microbial communities remain in exponential growth. An important concept to grasp is the doubling rate or reproduction time of an organism. This is the time needed for a population to double in size during exponential growth. In simple terms it is the time required for the organisms to replace themselves.

Hydraulic Retention Time

Anaerobic digestion generally takes place in a liquid, continuous flow reactor (Figure 4). If the reactor volume does not change, then flow out of the reactor equals flow into the reactor, and the average time that liquid remains in the reactor is its volume divided by the flow rate. This is called the hydraulic retention time of the reactor (HRT).

If the reactor is completely mixed, that is, the microorganisms are completely suspended in the reactor, then the time the cells remain in the reactor equals the HRT. If the HRT of a completely mixed reactor equals the reproduction time of the organisms living in the rector, a new cell is formed to replace each cell leaving the reactor, and the population within the reactor remains stable. If the HRT is shorter than the reproduction time, a new cell will not be there to replace the one leaving, and the population will decline, or “wash out.”

Figure 4. Relationships between Reactor Volume, Flow, Solids Mass, and Retention Times in a Completely Mixed Reactor.

Solids Retention Time

Reducing HRT decreases reactor size, and smaller reactors reduce costs; therefore, many digestion systems are designed so that microorganisms remain in the reactor longer than its HRT. For instance, we could put a screen on the outlet of the reactor in Figure 4 so that some of the microorganisms are trapped inside. We can calculate cell retention time by dividing the mass of microorganisms trapped in the reactor by the mass of organisms leaving the reactor. The microbial population is kept stable by setting cell retention time equal to reproduction time.

It is easier to measure the total mass of solid particles suspended in liquid rather than the mass of viable cells; therefore, cell retention time is approximated by Solids Retention Time (SRT), or the mass of solids in the reactor divided by the mass of solids leaving.

Steady Food Supply

Microorganisms need food to reproduce and grow. Methanogens have the uncanny ability to go dormant during periods of food shortage. This is good because you can easily restart an anaerobic digester after long periods of inactivity. On the other hand, sudden increases in feeding can cause bursts of gas production, which lead to foaming and scum formation in the digester.


Methanogens thrive in two temperature ranges. Thermophyllic (heat loving) methanogens are fast growing (reproduction time 10 to 15 days), but they operate in a fairly narrow band of temperature centered on 55 degrees C. Mesophyllic methanogens are slower growing (reproduction time up to 30 days), but they tolerate a wider range of temperatures. 35 degrees C. is optimal for mesophyllic methanogens, but they can tolerate much lower temperatures. Provided they have sufficiently long SRT, digesters operated at 20 degrees C. do not show substantial loses in gas production when compared to those operated at 35 degrees C.


Methanogens are strict anaerobes, meaning the least amount of oxygen is poison to them. Acid forming bacteria are more tolerant of oxygen. So, if oxygen gets into an anaerobic digester, methane concentration will drop and carbon dioxide concentration will increase in the biogas.


pH is an major indicator of reactor health. A complex set of naturally occurring buffers control pH within an anaerobic digester, with organic acid-ammonia and carbonate-bicarbonate being the most important buffers. The optimum pH range for anaerobic digestion is neutral to slightly basic (pH 6.6 to 7.6).

Digester Start-up

To ensure that there is a living population of methane producing microbes in a digester, materials that contain methanogens are commonly added. When these materials come from an outside source, such as sludge from an active manure treatment lagoon or biosolids from a sewage treatment plant, it is called a “hot start.” Sometimes, digesters are brought on line with a “cold start,” meaning manure is slowly added to a liquid filled digester until gas begins to form. Hot starts are generally quicker than cold starts. Depending on digester type, a hot start can take between one and six months to bring a digester on line. It may take six months to a year for a digester to reach steady-state under a cold start.

Inhibitory Substances Commonly Found in Manure

Inhibiting elements are often called toxic, but toxicity is a misnomer. Low doses of most inhibitory agents actually stimulate biological activity. The following sets of chemicals are the major inhibitory agents found in animal manures.


Antibiotics given therapeutically or fed sub-therapeutically to animals have the potential to alter the communities of microorganisms digesting manure from treated animals. The inhibitory effect of antibiotics on gas production has been shown to be minimal if high SRT is maintained and the microorganisms are given time to acclimate.


Disinfectants and cleaning agents can also cause digester imbalance, although reports of upsets have not been reported in the literature. Dilution of cleaning water or bypassing the digester after cleaning is the safest tactic for handling disinfectants. Some doses may prove to have minimal effect on performance if high SRT is maintained.


Ammonium ion (NH4+) and its gaseous relative, Ammonia (NH3), are byproducts of protein digestion and reduction of urea. Concentrations at which Ammonical Nitrogen (NH4+NH3-N) is beneficial, inhibitory, or toxic to anaerobic digestion are given in Table 1. The toxicity of ammonia is highly dependent on pH. NH3, which is the predominant form at higher pH, is more toxic than NH4+. Usually, ammonia is not a problem in manure digesters, except for reactors treating highly nitrogenous materials such as poultry manure; and some poultry manure digesters have been able to tolerate levels as high as 6,000 mg/l if the microorganisms are given time to acclimate.

Table 1. Effect of Ammonia and Sulfide Concentrations on Anaerobic Treatment
Effect on Anaerobic Treatment NH4+NH3-N mg/l S mg/l
Beneficial 50-200 <50
No Adverse Effect 200-1000 50-100
Inhibitory at higher pH values 1500-3000 100-200
Toxic >3000 >200

Sulfate and Sulfide

Sulfate (SO4) is not an inhibitory substance, per se. Its presence can reduce CH4 production because a group of bacteria called sulfate reducers can out-compete hydrotrophic methanogens for available H2. Competition with sulfate reducers does not usually reduce production from manure digesters since there is plenty of acetic acid around for acetotrophic methanogens to produce gas. The end product of sulfate reduction, Sulfide (S), can be quite toxic to anaerobic digestion. Like ammonia, the toxicity of S is dependent on digester pH. Stimulatory and inhibitory concentrations of sulfide are given in Table 1. Also, like ammonia, S- exists in a gaseous form, Hydrogen sulfide (H2S), so its control is a balance between source reduction, gas production, and pH.


The higher the soluble salt content in a digester, the harder microorganisms have to work in order to transport water in and out of their cells. Research has shown that it is mainly the cations (positive ions in solution) that inhibit microbial activity. Stimulatory and inhibitory concentrations of base cations are given in Table 2.

Table 2. Stimulatory and Inhibitory Concentrations of Base Cations
Cation Stimulatory (mg/l) Moderately Inhibitory (mg/l) Strongly Inhibitory (mg/l)
Sodium, Na+ 100-200 3500-5500 8000
Potassium, K+ 200-400 2500-4500 12,000
Calcium, Ca+ 100-200 2500-4500 8000
Magnesium, Mg+ 75-150 1000-1500 3000

Precipitation of Inhibitory Substances

It should be noted that most inhibitory substances must be in solution to reduce biological activity in digesters. Therefore, the inhibitory effect of S is reduced through precipitation of insoluble metal sulfides. Soluble Mg and NH3 are reduced by precipitation of Struvite (MgNH4PO4).

Upset Conditions and Their Control

Fermentative bacteria are generally more robust and faster growing than methanogens. The first indication that something is wrong with a digester occurs when the acid formers start to overpower the methane formers. This may show up as a drop in biogas production. First, however, the CO2 concentration in the biogas will increase, and the organic acid concentration of the reactor liquid increases. Both of these will cause a drop in pH. So, daily measurement of pH is a good method to monitor digester health. The relationship between fermentative and methanogenic communities can become so unbalanced, that even the acid formers can no longer tolerate the low pH conditions. At this point we say the digester is “stuck,” or it has “soured” or become “pickled.” Basic steps to follow in case of digester upset are:

  1. Reduce the feeding rate.
  2. Stabilize pH.
  3. Determine and correct the cause of the imbalance.
  4. Slowly increase feeding rate while maintaining neutral pH.


  • Cundiff, J.S., and K.R. Mankin. 2003. Dynamics of Biological Systems. St Joseph, MI: ASABE.
  • Darling, D. 2009. The Internet Encyclopedia of Science. Accessed May 16, 2009
  • Hamilton, D.W., P.R. Sharp, and R.J. Smith. 1985. The Operational characteristics of a manure digester for 60 beef cattle. pp 500-508, in Agricultural Waste Utilization and Management, the Proceedings of the 5th International Symposium on Agricultural Wastes. St Joseph MI: ASABE.
  • McCarty, M.L. 1964. Anaerobic waste treatment fundamentals. Public Works, Sept-Dec. 1964.
  • Mohr, M.A. 1983. Inhibition of methane production by ammonia nitrogen in the anaerobic digestion of poultry manure. MS Thesis. Madison, WS: University of Wisconsin.
  • Ndegwa, P.M., D.W. Hamilton, J.A. Lalman, and H.J. Cumba. 2007. Effects of cycle frequency and temperature on the performance of anaerobic sequencing batch reactors treating swine waste. Bioresource Technology. 99:1972-1980
  • Strauch, D. and K. Winterhalder. 1985. Effect of disinfectants, additives and antimicrobial drugs on anaerobic digestion. pp 516-522 in, Agricultural Waste Utilization and Management, the Proceedings of the 5th International Symposium on Agricultural Wastes. St Joseph MI: ASABE.
  • Varel, V.H. and A.G. Hashimoto. 1982. Methane production by fermentor cultures acclimated to waste from cattle fed Monenesin, Lasalocid, Salinomycin, or Avoparcin. Applied and Environmental Microbiology. 44(6):1415.


This document was adapted from Factsheet BAE-1747, Oklahoma State University, authored by

Peer Reviewers

Anaerobic Digesters and Biogas Safety

When manure is anaerobically digested, the biogas produced is primarily composed of methane and carbon dioxide, with lesser amounts of hydrogen sulfide, ammonia, and other gases. Each of these gases has safety issues. Overall, biogas risks include explosion, asphyxiation, disease, and hydrogen sulfide poisoning.

Image: US Municipal Supply Company.

Extreme caution is necessary when working with biogas. Adequate ventilation, appropriate precautions, good work practices, engineering controls, and adequate personal protective equipment will minimize the dangers associated with biogas. Wherever possible, digester-associated tasks and maintenance should be performed without anyone having to enter confined spaces, including pits. Systems should be initially designed so that confined space entry is not required to perform maintenance.

The information presented here is for reference purposes only. No liability is implied.

Biogas Hazards


Methane, approximately 60% of biogas, forms explosive mixtures in air. If biogas is diluted between 10% and 30% with air, there is an explosion hazard. In 2003, several explosions on Canadian swine farms were thought to have been caused by the methane in biogas exploding (Choinière, 2004). Hydrogen sulfide and ammonia are also potentially explosive.

Because of the explosion hazards, no open flames should ever be used near a digester. Also, equipment such as large engines and electric generators must be suitable to the environment so a spark will not ignite the gas. Explosion-proof equipment and electrical service, as well as non-sparking tools, should be used around digesters and biogas. There must be no smoking near the digester or related biogas lines and equipment.


Asphyxiation from biogas is a concern in an enclosed space where manure is stored. Osbern and Crapo (1981) report one case of three people who died from asphyxiation created by swine manure gas in an enclosed space. Even open-topped manure pits can generate methane at a sufficient rate to push out the air above the manure and render the space oxygen-deficient.

Never enter a facility where manure is stored or where there is a suspected biogas leak as natural ventilation cannot be trusted to dilute the explosion hazard sufficiently. Airing out a facility does not impart safety, as some of the gases produced are heavier than air. If a person is found unconscious in such a facility, do not enter the facility because you may be overcome as well. Contact emergency services so that firefighters wearing self-contained breathing apparatus (SCBA) can safely retrieve the victim.


Animal manure contains bacteria, viruses and, possibly, parasites. Biogas is generated by the anaerobic digestion of manure, which occurs because of the bacteria present in animal wastes, some of which can produce infection. When handling waste material, exercise appropriate precautions by using personal protective equipment to avoid contact with manure. Washing after working around the digester is recommended. It is particularly recommended to wash hands before eating and drinking and before touching the eyes or other mucous membranes.

Keeping the digester facility clean will reduce disease hazards as well as the spread of odors and fly populations in the digester facility.

Components of Biogas

Biogas consists mainly of 60% methane and 40% carbon dioxide, with low levels of hydrogen sulfide and other gases. Each of these gases can displace oxygen.


Methane is lighter than air and will collect toward the upper spaces of the building. It is explosive at 5% to 15% concentrations. While methane is not a toxic gas, it displaces air so that, in a confined space, it creates an oxygen-deficient atmosphere. This is how it kills.

Carbon Dioxide

Carbon dioxide is an odorless gas that is heavier than air. In a quiescent space, carbon dioxide can layer near the floor. Slightly elevated levels of carbon dioxide increase heart rate and respiration rate. Higher levels displace oxygen supply in the bloodstream, which can cause unconsciousness and death.

Hydrogen Sulfide

Hydrogen sulfide is a highly toxic gas that is heavier than air. At very low levels, it smells like rotten eggs and can produce eye irritation. At dangerous levels, it destroys the sense of smell and produces respiratory paralysis. Thus, at dangerous and fatal levels, where one can literally drop dead, there is no odor to warn of its presence.

The following table shows the health effects of hydrogen sulfide at different concentrations.

Parts per million (ppm) Possible health effects
0.01-0.3 Odor is detectable
1-10 Moderate to strong odor
Sleep loss
10-150 Irritation of the eyes

Irritation of the lungs

150-750 Severe health effects
Death becomes more likely
>750 Death may occur in minutes


Ammonia is a gas that is lighter than air, has a pungent odor, and can irritate the eyes and respiratory tract. Ammonia can displace oxygen in the bloodstream.


Manufacturer Warnings

Failure to heed manufacturer warnings may result in death or serious injury. Contact the manufacturer for maintenance and service requirements and availability of service.

Safety Walk-Throughs

A safety walk-through can help you determine potential hazards and preventative measures. Cornell University developed a comprehensive self-assessment guideline for farmers. It is intended to be used by farm owners and managers or farm staff who are responsible for the operations and/or maintenance of anaerobic digesters and their related processes. It provides guidance for process and job evaluation with suggestions based on typical potential hazards for farm digester systems and their associated preventative measures.

Gas Sensors

Explosion, suffocation, and poisonous gas hazards may be detected using gas sensors. These sensors include both disposable and electronic sensors. Electronic sensors need testing regularly, and these sensors may have a disposable component that needs periodic replacement. Only qualified people should use these sensors to determine if an area is safe.

Personal Protective Equipment

An area where manure is stored should never be entered without the appropriate personal protective equipment, which may include a self-contained breathing apparatus (SCBA). The use of protective equipment such as an SCBA is covered by OSHA regulations, and the operator must be certified in its use with equipment-fit testing and medical clearance.

For More Information

  • Pennsylvania State University: Biogas Safety. This site also has biogas and anaerobic digestion information and links.
  • Pennsylvania State University Manure Pit Safety. This site has educational videos that demonstrate manure storage hazards, the importance of monitoring manure gas levels before entry, and recommendations for the design and installation of ventilation of manure storages, emphasizing the importance of a positive pressure system for forcing fresh air into the storage. The site also has fact sheets that address manure storage hazards, monitoring for gases and oxygen, ventilating manure gases, and emergency rescue procedures. Information for accessing ANSI/ASABE S607, Ventilating Manure Storages to Reduce Entry Risk, and ASABE EP 470, Manure Storage Safety, are provided.
  • Respiratory Protection, Personal Protective Equipment. OSHA Regulation 1910.134 that applies to some anaerobic digester facilities; all operators should refer to these standards in an advisory capacity.


Brown, N.J. 2007. Conducting a safety walk-through on a farm: hazards of the manure handling system, anaerobic digester, and biogas handling system – a self-assessment guideline for farmers. Manure Management Program. Cornell Dept. of Biological and Environmental Engineering. Ithaca, NY.

Martin, J.H. 2008. A New Method to Evaluate Hydrogen Sulfide Removal from Biogas. M.S. Thesis. Raleigh, N.C.: North Carolina State University, Department of Biological and Agricultural Engineering.

Osbern, L.N., and R.O. Crapo. 1981. Dung lung: a report of toxic exposure to liquid manure. Ann. Intern. Med. 95(3):312-4.

Choinière, Y. 2004. Explosion of a deep pit finishing pig barn, investigation report on biogas production. In Proc. ASAE/CSAE Meeting. Ottawa, Ontario, Canada.

Wright, Peter. 2001. Overview of Anaerobic Digestion Systems for Dairy Farms. Natural Resource, Agriculture and Engineering Service:NRAES-143. Ithaca, NY.

Contributors to This Article


Peer Reviewers

Biogas Utilization and Cleanup


Biogas generated from anaerobic digestion processes is a clean and environmentally friendly renewable fuel. But it is important to clean, or upgrade, biogas before using it to increase its heating value and to make it useable in some gas appliances such as engines and boilers.

Biogas Utilization

While most large farms use their biogas for heat and power, it is worthwhile to consider all the options before deciding which path to take, including direct sale of biogas to an off-farm buyer.

Raw animal manure biogas contains 55 to 65% methane (CH4), 30 to 45% carbon dioxide (CO2), traces of hydrogen sulfide (H2S) and hydrogen (H2), and fractions of water vapor. For the anaerobic digestion of sludge or landfill processes, traces of siloxanes may also be found in biogas. These siloxanes mainly originate from silicon-containing compounds widely used in various industrial material or frequently added to consumer products such as detergents and personal care products. This article will not address the cleanup of biogas of siloxanes.

Biogas is about 20% lighter than air and has an ignition temperature in the range of 650 to 750 degrees C. (1,200-1,380 degrees F.). It is an odorless and colorless gas that burns with a clear blue flame similar to that of natural gas. However, biogas has a calorific value of 20-26 MJ/m3 (537-700 Btu/ft3) compared to commercial quality natural gas’ caloric value of 39 MJ/m3 (1,028 Btu/ft3).

Biogas can potentially be used in many types of equipment, including:

  • Internal Combustion (Piston) Engine – Electrical Power Generation, Shaft Power
  • Gas Turbine Engine (Large) – Electrical Power Generation, Shaft Power
  • Microturbine Engine (Small) – Electrical Power Generation
  • Stirling Heat Engine – Electrical Power Generation
  • Boiler (Steam) Systems
  • Hot Water Systems
  • Process Heaters (Furnaces)
  • Space or Air Heaters
  • Gas Fired Chiller – Refrigeration
  • Absorption Chiller – Refrigeration
  • Combined Heat and Power (CHP) – Large and Small Scale – Electrical Power and Heat
  • Fuel Cells – Electrical Power, Some Heat

There are a variety of end uses for biogas. Except for the simplest thermal uses such as odor flaring or some types of heating, biogas needs to be cleaned or processed prior to use. With appropriate cleaning or upgrade, biogas can be used in all applications that were developed for natural gas.

The three basic end uses for biogas are:

  • production of heat and steam
  • electricity generation
  • vehicle fuel

Production of heat or steam

The most straightforward use of biogas is for thermal (heat) energy. In areas where fuels are scarce, small biogas systems can provide the heat energy for basic cooking and water heating. Gas lighting systems can also use biogas for illumination.

Conventional gas burners are easily adjusted for biogas by simply changing the air-to-gas ratio. The demand for biogas quality in gas burners is low, only requiring a gas pressure of 8 to 25 mbar and maintaining H2S levels to below 100 ppm to achieve a dew point of 150 degrees C.

Electricity Generation or Combined Heat and Power (CHP)

Combined heat and power systems use both the power producing ability of a fuel and the inevitable waste heat. Some CHP systems produce primarily heat, and electrical power is secondary (bottoming cycle). Other CHP systems produce primarily electrical power and the waste heat is used to heat process water (topping cycle). In either case, the overall (combined) efficiency of the power and heat produced and used gives a much higher efficiency than using the fuel (biogas) to produce only power or heat.

Other than high initial investments, gas turbines (micro-turbines, 25-100 kW; large turbines, >100 kW) with comparable efficiencies to spark-ignition engines and low maintenance can be used for production of both heat and power. However, internal combustion engines are most cmmonly used in CHP applications. The use of biogas in these systems requires removal of both H2S (to below 100 ppm) and water vapor.

Fuel cells are considered the small-scale power plants of the future for production of power and heat with efficiencies exceeding 60% and low emissions. One of the largest digester/fuel cell units is located in Washington State. The fuel cell, located at the South Treatment Plant in Renton, WA, can consume about 154,000 ft3 of biogas a day to produce up to 1 megawatt (1,000,000 watts) of electricity. That’s enough to power 1,000 households, but it’s being used instead for the operation of the plant.

Vehicle fuel

Gasoline vehicles can use biogas as a fuel provided the biogas is upgraded to natural gas quality in vehicles that have been adjusted to using natural gas. Most vehicles in this category have been retro-fitted with a gas tank and a gas supply system in addition to the normal petrol fuel system. However, dedicated vehicles (using only biogas) are more efficient than these retro-fits.

Biogas Cleanup Or Upgrading

Biogas cleaning is important for two reasons: (1) to increase the heating value of biogas, and (2) to meet requirements for some gas appliances (engines, boilers, fuel cells, vehicles, etc). Desired biogas cleaning or upgrading purposes are summarized in Figure 1. “Full treatment” implies that biogas is cleaned of CO2, water vapor, and other trace gases, while “reforming” is conversion of methane to hydrogen.

Figure 1. Alternative biogas utilization and required cleanup

CO2 Removal

For many of the simpler biogas applications such as heaters or internal combustion engines or generator systems, carbon dioxide (CO2) removal from biogas is not necessary and CO2 simply passes through the burner or engine. For more demanding biogas/engine applications, such as vehicles that require higher energy density fuels, CO2 is routinely removed. Removing CO2 increases the heating value and leads to a consistent gas quality similar to the natural gas. Carbon dioxide can be removed from biogas economically through absorption or adsorption. Membrane and cryogenic separations are other possible processes.

Pressurized counter-current scrubbing of CO2 and H2S from biogas can be accomplished in water. For removal of CO2 in particular; pH, pressure, and temperatures are critical. High pressures, low temperature, and high pH increases CO2 scrubbing from biogas. Use of Ca(OH)2 solutions can completely remove both CO2 and H2S. Both CO2 and H2S are more soluble in some organic solvents such as polyethyleneglycol and alkanol amines that do not dissolve methane. These organic solvents can thus be used to scrub these gases from biogas even at low pressures. Systems using these kinds of organic solvents can remove CO2 down to 0.5% from the biogas.

However, use of organic solvents is much more expensive than water systems. Adsorption of CO2 on solids such as activated carbon or molecular sieves is possible although it requires high temperatures and pressures. These processes may not be cost-effective because of associated high temperature and pressure drops. Cryogenic separation is possible because at 1 atm, methane has a boiling point of -106oC, whereas CO2 has a boiling point of -78oC. Fractional condensation and distillation at low temperatures can thus separate pure methane in liquid form, which is convenient for transportation. Up to 97% pure methane can be obtained, but the process requires high initial and operational investments. Membrane or molecular sieves depend on the differences in permeability of individual gas components through a thin membrane. Membrane separations are quickly gaining in popularity. Other chemical conversions are technically viable, but their economics are poor for practical biogas-cleaning.

Water Vapor Removal

Straight from the digester, biogas will generally be saturated with vapor. Besides reducing the energy value of biogas, water can react with H2S to create ionic hydrogen and/or sulfuric acid, which is corrosive to metals. Refrigeration or sensible pipe-work design can condense and remove the water. The biogas is normally compressed before cooling to achieve high dew points. Alternative water vapor removal mechanisms include adsorption on: (1) silica gel and Al2O3 at low dew points, (2) glycol and hygroscopic salts at elevated temperatures, and 3) molecular sieves.

Removal of Hydrogen Sulfide

Hydrogen sulfide in biogas needs to be removed for all but the most simple burner applications. Hydrogen sulfide in combination with the water vapor in raw biogas can form sulfuric acid (H2SO4), which is very corrosive to engines and components. At concentrations above 100 parts per million by volume (ppmv), H2S is also very toxic. Activated carbon can be used to remove both H2S and CO2. Activated carbon catalytically converts H2S to elemental sulfur. Hydrogen sulfide can also be scrubbed out from biogas in either: NaOH, water, or iron salt solutions. A simple and inexpensive process is dosing a stream of biogas with O2, which oxidizes H2S to elemental sulfur. Oxygen dosing can reduce H2S to below 50ppm levels from biogas [Warning: IMPROPERLY DOSING A BIOGAS STREAM WITH O2 CAN CREATE AN EXPLOSION HAZARD]. Iron oxide also removes H2S as iron sulfide. This method can be sensitive to high water vapor content of the biogas. In addition to clean up of biogas of H2S after it has been produced, available methods of reducing H2S content from produced biogas include: co-digestions, multiphase digestion, reactor pH buffering, and removal of sulfur from feed substrates.


Biogas produced from animal waste can be a valuable energy resource. By combusting waste methane (biogas), a powerful greenhouse gas is eliminated that would otherwise be released. If used in simple burners for cooking or lighting the gas may not need to be treated prior to use. However, for uses that require the gas to be used in internal combustion engines, boilers or fuel cells, the biogas will probably need to be pretreated in order to remove corrosive or dangerous contaminants. The primary contaminant of biogas is hydrogen sulfide. This chemical will also react with water to form corrosive acids that can attack metals and plastics. Hydrogen sulfide is also toxic and sufficient quantities also present a possible health hazard if not treated.

Additional Resources

Intro | Feedstocks | Processing | Utilization


  • Appels, L., J. Baeyens, J. Degre`ve, R. Dewil. 2008. Principles and potential of the anaerobic digestion of waste-activated sludge. Progress in Energy and Combustion Science, 34:755–781.
  • Drewitz, M., P.Goodrich. 2005. Minnesota dairy runs hydrogen fuel cell on biogas.
  • EMG International, Inc. 2007. Biogas Clean-Up Technologies. Presentation to NYS ERDA Innovations in Agriculture.
  • FAO. 1997. A system approach to biogas technology,
  • Glub, J.C., L.F. Diaz. 1991. Biogas purification process. Biogas and alcohol fuels production, vol. II. The JP Press.
  • Hagen, M., E. Polman. 2001. Adding gas from biomass to the gas grid. Final report submitted to Danish Gas Agency, pp. 26-47.
  • Harasmowicz, M., P. Orluk, G. zakrzewska-Trznadel, A.G. Chemielewski. 2007. Application of polyimide membranes for biogas purification and enrichment. Journal of Hazardous Materials 144:698-702.
  • Kapdi, S.S., V.K. Vijay, S.K. Rajesh, R. Prasad. 2005. Biogas scrubbing, compression and storage: perspective and prospectus in Indian context. Renewable Energy 30:1195-1202.
  • Kayhanian, D.J. Hills. 1988. Membrane purification of anaerobic digester gas. Biological Wastes 23: 1-15.
  • Lastella, G., C. Testa, G. Cornacchia, M. Notornicola, F. Voltasio, V.K. Sharma. 2002. Anaerobic digestion of semi-solid organic waste: biogas production and its purification. Energy Convers. Manage., 43:63–75.
  • Leposky, G. 2005. Fuel Cell Uses Biogas from Sewage to Generate Electricity.
  • Li, K., W.K. Teo. 1993. Use of an internally staged permeator in the enrichment of methane from biogas. J. Membr Sci 1993;78:181–90.
  • Martin, J. H. 2008. A method to Evaluate Hydrogen Sulfide Removal from Biogas. MS Thesis: Biological and Agricultural Engineering, North Carolina State University, Raleigh, North Carolina.
  • Pandey, D.R., C. Fabian. 1989. Feasibility studies on the use of naturally accruing molecular sieves for methane enrichment from biogas. Gas Separation and Purification, 3:143-147.
  • Sarkar, S.C., A. Bose. 1997. Role of activated carbon pellets in carbon dioxide removal. Energy Conversions Management 38:S105-S110.
  • Stern, S.A., B. Krishnakumar, S.G. Charati, W.S. Amato, A.A. Friedmann, D.J. Fuess. 1998. Performance of a bench-scale membrane pilot plant for the upgrading of biogas in a wastewater treatment plant. J. Membr Sci, 151:63–74.
  • Walls, J.L., C. Ross, M.S. Smith, S.R. Harper. 1989. Utilization of biogas. Biomass 20: 277-290.
  • Wellinger, A., A. Lindberg. 2005. Biogas Upgrading and Utilization. Task 24: Energy From Biological Conversion of Organic Waste. IEA Bioenergy.
  • Wise, D.L. 1981. Analysis of systems for purification of fuel gas. Fuel gas production from biomas, vol. 2. Boca Raton, FL. The CRC Press.



Peer Reviewers

Uses of Solids and By-Products of Anaerobic Digestion

Anaerobic Digestate Pile at Scenic View Dairy in Fennville, MI

Anaerobic Digestate Pile, Scenic View Dairy, MI. Photo: M.C. Gould, MSU Extension

Anaerobic digestion generates a wide range of byproducts that farmers can use in their farming operations or sell. Beyond biogas used to generate electricity or as fuel, and liquids used for fertilizer or soil amendments, there are solid byproducts, which have a wide range of applications.

Table of Contents:

Value-added opportunities for fiber from digesters

Closeup of anaerobic digestate

Closeup of digestate. Photo: M.C. Gould, MSU Extension

Undigested biomass (referred to as digestate solids, fiber or biofiber) contained in the effluent (digestate) of anaerobic digesters provides opportunities for value-added byproducts. Organic fertilizer, livestock bedding, compost, fuel pellets, and construction material (medium density fiberboard and fiber/plastic composite materials) are a few examples of value-added byproducts that could be created from digestate solids.

Separating solids from the digestate

Solids can be extracted from the digestate using solid-liquid separation technologies such as slope screens, rotary drum thickeners and screw-press separators. Common solid-liquid equipment can produce digestate solids with a moisture content of 18 to 30%. The volume and the moisture content of the separated solids will vary depending on the technology used. Digestate solids are high in fiber, consisting mainly of fibrous undigested organic material (lignin and cellulose), microbial biomass, animal hair, and nutrients.


During the anaerobic digestion process, nutrients contained in the feedstock are mineralized. Mineralized nutrients are easily used by a crop. Digestate solids contain higher concentrations of plant-available nitrogen and phosphorus compared to as-excreted manure, according to research. The high carbon content of digestate solids adds organic matter to the soil and improves the water holding capacity of the soil. Actual nutrient content of digestate solids will vary depending on feedstocks, digester type, management, and solid-liquid separation technology. Digestate solids as a fertilizer source can be used “as separated” (wet), blended with other materials and composted or dried and pelletized.

Anaerobic Digester Fiber - Freestall Bedding

Digestate Solids used in freestall at Crave Brothers Dairy, WI Photo: M.C. Gould, MSU Extension

Livestock bedding

Bedding for livestock is another opportunity for putting digestate solids to use. Utilizing digestate solids for bedding provides a significant cost offset to dairy and livestock farms. In addition, excess solids may be sold to neighboring farms for bedding or soil amendment, creating a revenue stream and route for nutrient export. Bedding with digestate solids requires intensive management to ensure that a healthy environment, with low pathogen concentrations, is provided for the animals.

Other value added products using digestate solids

Digestate solids can also be used as substrate in compost, providing sources of carbon and nutrients. Solids can be dried and pelletized for use as fertilizer or fuel. The maximum energy content of livestock manure is 8,500 Btu per pound; however ash and moisture content reduce the energy potential. As excreted, livestock waste typically has an energy content between 1,000 and 2,000 Btu per pound.

Another developing opportunity for digestate solids is as a renewable construction material. Medium-density fiberboard and wood/plastic composite material have emerged as important engineered construction materials. These engineered materials can also be created using digestate solids without sacrificing mechanical or aesthetic properties, research indicates.

Organic potting soil made with digestate

Organic potting soil made with digestate as medium. Photo: M.C. Gould, MSU Extension

References & Additional Resources

  • Gould, M.C. and M.F. Crook. 2009. On-farm Anaerobic Digester Operator Handbook. Michigan State University. East Lansing, MI.
  • Kammel, D.W. 2004. Bedded Pack Housing for Dairy Cows. Minnesota/Wisconsin Engineering Notes.
  • Matuana, L. and M.C. Gould. 2006. Promoting the Use of Digestate from Anaerobic Digesters in Composite Materials: Final Report. Community Energy Project Grant No. PLA-06-42.
  • Zering, K. and B. Auvermann. April, 2009. Livestock and Poultry Environmental Learning Center. Value of Manure as an Energy Source.

Contributors to this Article


Peer Reviewers

  • Teodoro Espinosa-Solares

Environmental Benefits of Anaerobic Digestion

The manure handling system of any farm is made up of many different components, each with a different function and purpose. An anaerobic digester, although only one component of the system, can greatly improve the environmental performance and efficiency of the overall system. The main effect of anaerobic digestion is conversion of organic matter to biogas. This conversion has many potentially beneficial environmental and management side effects.

Odor reduction

By removing organic matter, the digester reduces the organic matter-loading and associated oxygen demand on downstream manure handling components. This may allow the downstream components to be smaller, operate more efficiently and function with less environmental impact. Anaerobic pretreatment may be a more economical method of converting an anaerobic lagoon to an aerobic lagoon, compared to mechanical aeration. Digester effluent is more stable than raw manure. It contains more stable organic material and less volatile odorants. Thus, storage and land application of digester effluent greatly reduces odor nuisance compared to raw manure.

Uses for digested solids

Manure solids are stabilized through anaerobic digestion. What was once reactive, partially digested material has been processed into stable microbial biomass and precipitated nutrients, although the majority of nutrients remain with the liquid. The potential to dry and transport digester solids is greatly improved over raw manure. The solids can be recycled and used for bedding or a soil amendment on the farm. The reduction in moisture content also increases the feasibility of selling the solids to farms that are greater distances away. In the right market conditions, composting the digested solids can result in a value-added product that can be sold to homeowners, gardeners or the landscape industry.

Plant nutrients

Plant nutrients are conserved and transformed during anaerobic digestion. Ammonium is created from manure proteins. This can be a benefit or a nuisance. If injected immediately into the soil, ammonium-rich effluent is highly available for plant growth. On the other hand, if digester effluent is stored under anaerobic conditions, ammonium will convert to ammonia gas and escape to the atmosphere. Since digesters are also a reducing environment, the potential exists for capture of ammonium and soluble phosphorus through precipitation as struvite.

Many metals are precipitated during anaerobic digestion. Sulfur is reduced to sulfide, which is generally a bad thing since it can escape as hydrogen sulfide gas. However, the digester environment can be manipulated so that sulfides are precipitated along with potentially harmful metals such as Ni and Zn.

Greenhouse gases

Anaerobic digestion results in the reduced emission of greenhouse gases. This may seem ironic, since the methane contained in the resulting biogas is a powerful greenhouse gas. An anaerobic digester is a controlled environment that captures the methane. After capture, it is either flared or used to generate electricity and/or heat.

When flared, the carbon dioxide formed in the combustion has less heat trapping potential than the original methane, and it is essentially recycled atmospheric carbon. What is released to the atmosphere through combustion of methane was once plant material formed through photosynthesis from atmospheric carbon dioxide.

When used for energy generation, the biogas replaces power that might have otherwise been created through conversion of fossil fuel. Regardless, if the biogas is flared or used for energy generation, the farmer may be eligible for carbon credit payments.

Anaerobic Digestion on Farms

With all of the potential benefits, one might wonder why relatively few farms utilize these systems. One major reason is that anaerobic digesters are expensive to install and operate. The economic benefits have, in the past, been limited to a reduction in electricity purchased by the farm, which is not enough to offset the costs of the system.

As the interest in renewable energy sources increases, farms are increasingly able to apply and receive carbon credits. Some farms also accept off-farm waste, collecting tipping fees, to co-digest with manure. In many states, more favorable net-metering laws have also made the economics more favorable. Power generated by the digester is valued at retail costs rather than wholesale costs.

The decision to install a digester is often driven by additional considerations, such as nuisance issues. A digester greatly reduces the odor potential of the manure, which also greatly reduces neighbors’ complaints and the potential for lawsuits.

At the current time, anaerobic digestion is slowly but surely increasing as a manure treatment method in the United States. Additional information is available at: Economics of Anaerobic Digesters for Processing Animal Manure.

Contributors To This Document

Author: Doug Hamilton, Oklahoma State University Waste Management Specialist

Contributors: Jill Heemstra, University of Nebraska

Reviewers: Mark Rice, North Carolina State University and Karl Vandevender, University of Arkansas

Pathogen Reduction in Anaerobic Digestion of Manure

Benefits of Anaerobic Digestion of Manure in Reducing Pathogens

Manure is a biologically active material that hosts and supports many microorganisms and thus can seldom be considered “pathogen free.” Certain manure handling techniques and methods, however, can limit the production and multiplication of such pathogens. Common sense must be used when making manure handling decisions. Pathogens are microbes such as bacteria, viruses, protozoa, and other organisms that cause disease. These pathogens persist commonly in animal manures. For more information about pathogens and zoonotic pathogens, see Pathogens and Potential Risks Related to Livestock or Poultry Manure. A list of animal related microorganisms (including some that are pathogens) are listed in Table 1.

Table 1. Animal Related Microorganisms
Fecal coliforms (an indicator bacteria, not all coliforms are pathogenic)
Salmonella spp. (pathogen)
Generic E. coli (not all E. coli are pathogens), including O157:H7 (pathogen)
Enterococci (not generally considered pathogenic)
Listeria (pathogen)
Clostridium (pathogen)
Mycobacterium paratuberculosis (MAP or Johne’s) (pathogen)
Enterovirus (pathogen)
Campylobacter (pathogen)
Cryptosporidium (C. parvum is the only one related to animal manure that is considered pathogenic)
Bovine Spongiform Encephalopathy (BSE) (The prions that cause BSE are not a true pathogen, but are considered an “infectious agent”)

Excessive or careless land application of manure and livestock facility runoff can contaminate surface water. This manure laden runoff can pose significant risk to human and animal health. Stored or fresh manure can be applied to land with minimal reduction of harmful pathogens, as some microorganisms can persist for long periods outside an animal’s body.

Treatment through anaerobic digestion can greatly reduce the number of pathogens within the manure and therefore limit the number of pathogens entering the environment. Anaerobic digestion (AD) of manure has a pathogen reducing effect with as much as 95-98% of common pathogens eliminated in mesophillic (~ 100 degrees Fahrenheit) digesters. The reduction in pathogens has the potential to be of benefit for: manure application in impaired watersheds when trying to manage certain pathogens such as Mycobacterium paratuberculosis (MAP or Johne’s) or salmonella, and when considering a community- based anaerobic digester where manure from multiple farms is combined, treated, and AD solids and AD effluent returned back to the farms.

Supporting Research-What We’ve Learned

There is a growing body of research which demonstrates the anaerobic digestion process can vastly reduce if not eliminate the concentration or presence of numerous organisms. Current research in this area is summarized below in Table 2.

Table 2. Potential for microbial (including pathogen) and infectious agent reduction by anaerobic digestion
Microbes Reduced By Anaerobic Digestion Microbes Not Reduced By Anaerobic Digestion
Salmonella Bovine Spongiform Encephalopathy (BSE) (Infectious agent–not a microbe)
Generic Escherichia coli  
Escherichia coli O157:H7  
Mycobacterium paratuberculosis (Johne’s)  
Bovine enterovirus (BEV)  
Fecal coliform  

Anaerobic digestion of manure has been shown to reduce the Johne’s-causing organism, Mycobacterium avium a subspecies of paratuberculosis. Thermophilic digesters operating at 135 degrees F. have shown complete elimination of Johne’s bacteria, while digesters operating at 99 degrees F with a 20-day retention time have demonstrated significant reduction [3]. Other potentially harmful pathogens to humans include Escherichia coli O157:H7, Salmonella, and the protozoan parasite Cryptosporidium parvum. These bacteria and protozoa have all been reduced in number of viable and infectious organisms after passing through a digester. Pathogen reduction of 95% is possible with a 20-day retention time under mesophilic conditions (95-105 degrees F.) with a digester [3].

Anaerobic digestion under mesophilic or thermophilic conditions has not been shown to reduce or eliminate Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease. Although little is known about this disease, it is accepted that the protein-infecting prions are resistant to heat. Even thermophilic conditions (135 degrees F.) are not sufficient to destroy BSE prions [3].

In a study in New York state, samples were taken from a plug-flow digester over a 14-month period and tested for fecal coliform and Mycobacterium avium paratuberculosis (MAP), or Johne’s disease. It was found (see Table 3) that anaerobic digestion has the potential to reduce the number of fecal indicator bacteria in dairy effluent, including in this study, by 100% reduction of MAP CFU/gram. The substantial reduction of pathogen concentrations led the authors to recommend anaerobic digestion of dairy manure when concentration of pathogens is a concern [4].

Table 3. Pathogen results from dairy manure treatment
  Fecal coliform CFU/Gram MAP CFU/Gram
Raw Manure 3,836,000 20,640
Digested Effluent 3,400 136
Wright et al. 2001

In a study conducted by Washington State University on two operating anaerobic digesters in Oregon (2004), pre-digested and post-digested samples were taken bi-weekly, for six sampling events. Samples were obtained from: manure prior to the AD system, and solids and liquids post-AD. The design of the two digesters was different: one was a plug-flow and the other, a continuous mix, each operating at 100 degrees F. and with expected retention times of ~ 21 days and 24 hours, respectively. Specific organisms selected for evaluation were: Salmonella, Generic E. coli (including 0157:H7), enterococci, Mycobacterium paratuberculosis (Johne’s), and enterovirus.


Figure 1. Generic E.Coli concentration in anaerobic digester samples


Figure 2. Enterococci concentration in anaerobic digester samples

The data indicated reductions in fecal indicator bacterial concentration was > 98% (generic E. coli, enterococci, and enterovirus) in most cases (see figure 1 and 2). While the detection of Mycobacterium paratuberculosis was reduced in post digested samples, greater than 50% of samples had detectable levels. The data from this study suggests that AD treatment of dairy manure does not completly remove all biosecurity hazards [2].

Additional Resources


  1. Spiehs, Mindy; Goyal, Sagar. Best Management Practices for Pathogen Control in Manure Management Systems. University of Minnesota Extension. 2007.
  2. Harrison, J.H., D. Hancock, M. Gamroth, D. Davidson, J.L. Oaks, J. Evermann, and T. Nennich. 2005. Evaluation of the pathogen reduction from plug flow and continuous feed anaerobic digesters. Symposium – State of the Science Animal Manure and Waste Management. San Antonio, TX. Jan. 5-7
  3. [3.0][3.1][3.2]Topper, Patrick; Graves, Robert; Richard, Thomas. The Fate of Nutrients and Pathogens during Anaerobic Digestion of Dairy Manure. Penn State Cooperative Extension. Agriculture and Biological Engineering. Extension Bulletin. 2006.
  4. Wright, P. E., S. F. Inglis, S. M. Stehman, and J. Bonhotal. “Reduction of selected pathogens in anaerobic digestion.” 5th Annual NYSERDA Innovations in Agriculture Conference (2001): 1-11.
  5. “Pathogen Overview.” Information Collection Rule. US Environmental Protection Agency, 10 Apr. 2009. Web. 7 Dec. 2009.

Contributors to this Article


  • Olivia Saunders, Crop and Soil Science, Washington State University
  • Joe Harrison, Professor, Nutrient Management Specialist, PAS, Washington State University

Peer Reviewers

Types of Anaerobic Digesters

Table Of Contents
Passive Systems
Low Rate Systems
High Rate Systems
Contributors To This Article

All anaerobic digesters perform the same basic function. They hold manure in the absence of oxygen and maintain the proper conditions for methane forming microorganisms to grow. There is a wide variety of anaerobic digesters, each performing this basic function in a subtly different way. Seven of the most common digesters are described in this article. Construction and material handling techniques can vary greatly within the main categories.

For clarity, we can divide digesters into three categories:

  • Passive Systems: Biogas recovery is added to an existing treatment component.
  • Low Rate Systems: Manure flowing through the digester is the main source of methane-forming microorganisms.
  • High Rate Systems: Methane-forming microorganisms are trapped in the digester to increase efficiency.

Passive Systems

Covered lagoon

Figure 1. First Covered Cell of a Lagoon Located on the Oklahoma State University Swine Research and Education Center.

Figure 2. Schematic Drawing of Covered Lagoon Digestion System.

This system takes advantage of the low maintenance requirement of a lagoon while capturing biogas under an impermeable cover (Figure 1). The first cell of a two-cell lagoon is covered, and the second cell is uncovered (Figure 2). Both cells are needed for the system to operate efficiently. A lagoon is a storage as well as a treatment system; the liquid level on the second cell must rise and fall to create storage, while the level on the first cell remains constant to promote manure breakdown.

Since they are not heated, the temperature of covered lagoons follows seasonal patterns. Methane production drops when lagoon temperatures dip below 20 degrees C. A covered lagoon located in the tropics will produce gas year-round, but gas production will drop considerably during the winter farther north. Since sludge is stored in lagoons for up to 20 years, methane-forming microorganisms also remain in the covered lagoon for up to 20 years. This means that much of the fertilizer nutrients, particularly phosphorus, also remain trapped in the covered lagoon for a long time. If lagoon effluent is recycled to remove manure from buildings, liquid retention time is generally 30 to 60 days – depending on the size and age of the lagoon.

Low Rate Systems

Complete Mix Digester

Figure 3. Complete Mix Digester Located on the Crave Brothers Farm in Waterloo Wisconsin (photo: Crave Brothers Farm/USEPA).

Figure 4. Schematic Drawing of a Complete Mix Digester

A complete mix digester (Figure 3) is basically a tank in which manure is heated and mixed with an active mass of microorganisms (Figure 4.). Incoming liquid displaces volume in the digester, and an equal amount of liquid flows out. Methane forming microorganisms flow out of the digester with the displaced liquid. Biogas production is maintained by adjusting volume so that liquids remain in the digester for 20 to 30 days. Retention times can be shorter for thermophyllic systems. The digester can be continuously or intermittently mixed. Intermittent mixing means the tank is stirred during feeding and only occasionally between feedings. Sometimes the process takes place in more than one tank. For instance, acid formers can break down manure in one tank, and then methane formers convert organic acids to biogas in a second tank. Complete mix digesters work best when manure contains 3 percent to 6 percent solids. Digester size can be an issue at lower solids concentrations. Lower solids mean greater volume, which means you need a larger digester to retain the microbes in the digester for 20 to 30 days.

Plug Flow Digester

Figure 5. Plug Flow Digester located on the Emerling Farm in Perry, NY (Photo Courtesy of Cornell University/USEPA).

Figure 6. Schematic Drawing of a Plug Flow Digester.

The idea behind a plug flow digester (Figure 5) is the same as a complete mix digester – manure flowing into the digester displaces digester volume, and an equal amount of material flows out (Figure 6). However, the contents of a plug flow digester manure are thick enough to keep particles from settling to the bottom. Very little mixing occurs, so manure moves through the digester as a plug – hence the name “plug flow.” Plug flow digesters do not require mechanical mixing. Total solids (TS) content of manure should be at least 10 or 15 percent, and some operators recommend feeding manure with solids as high as 20 percent. This means you may need to add extra material to manure to use a plug flow digester. This is not always a bad thing if you consider the added material may also be biodegradable. More degradable material means more biogas. Plug flow digesters are usually five times longer than they are wide. Recommended retention time is 15 to 20 days.

High Rate Systems

Solids Recycling

Figure 7. Schematic Drawing of Contact Stabilization Digester.

Returning some of the active organisms to the digester decreases digestion time. This is done in plug flow systems by pumping some of the effluent leaving the digester to the front of the digester. In complete mix systems, solids are settled in an external clarifier, and the microbe-rich slurry is recycled back to the digester. The systems are called contact stabilization digesters or anaerobic contact digesters (Figure 7).

Fixed Film Digester

Figure 8. Fixed Film Digester located on the University of Florida Dairy Research Farm (photo courtesy of Ann Wilkie, University of Florida) .

A fixed film digester (Figure 8) is essentially a column packed with media, such as wood chips or small plastic rings. Methane-forming microorganisms grow on the media. Manure liquids pass through the media (Figure 9). These digesters are also called attached growth digesters or anaerobic filters. The slimy growth coating the media is called a biofilm. Retention times of fixed film digesters can be less than five days, making for relatively small digesters. Usually, effluent is recycled to maintain a constant upward flow. One drawback to fixed film digesters is that manure solids can plug the media. A solid separator is needed to remove particles from the manure before feeding the digester. Efficiency of the system depends on the efficiency of the solid separator; therefore, influent manure concentration should be adjusted to maximize separator performance, usually 1 percent to 5 percent total solids). Some potential biogas is lost due to removing manure solids.

Figure 9. Schematic Drawing of a Fixed Film Digestion System.


Suspended Media Digesters

Figure 10. Schematic Drawing of an Upflow Anaerobic Sludge Blanket (UASB) Digester.

In these types of digesters, microbes are suspended in a constant upward flow of liquid. Flow is adjusted to allow smaller particles to wash out, while allowing larger ones to remain in the digester. Microorganisms form biofilms around the larger particles, and methane formers stay in the digester. Effluent is sometimes recycled to provide steady upward flow. Some designs incorporate an artificial media such as sand for microbes to form a biofilm; these are called fluidized bed digesters.

Suspended media digesters that rely on manure particles to provide attachment surfaces come in many variations. Two common types of suspended media digesters are the upflow anaerobic sludge blanket digester, or UASB digester (Figure 10), and the induced blanket reactor, or IBR digester (Figures 11 and 12). The main difference between these two systems is that UASB digesters are better suited for dilute waste streams (<3-percent total suspended solids); whereas, the IBR digester works best with highly concentrated wastes (6 percent to 12 percent TS).

Figure 11. Schematic Drawing of Induced Bed Reactor (IBR) Digester (Courtesy of Conly Hansen, Utah State University).


Figure12. Battery of Induced Bed Reactor (IBR) Digesters (photo courtesy of Conly Hansen, Utah State University).


Sequencing Batch Digester

Figure 13. Anaerobic Sequencing Batch Reactor (ASBR) Digester Located on the Oklahoma State University Swine Research and Education Center.

An anaerobic sequencing batch reactor (Figure 13), or ASBR digester, is a variation on an intermittently mixed digester. Methane forming microorganisms are kept in the digester by settling solids and decanting liquid. An ASBR operates in a cycle of four phases (Figure 14). The digester is fed during the fill stage, manure and microbes are mixed during the react phase, solids are settled during the settle stage, and effluent is drawn off during the decant stage. The cycle is repeated up to four times a day for nearly constant gas production. Liquid retention times can be as short as five days. Although ASBR digesters work well with manure in a wide range of solids concentrations, they are particularly well suited for very dilute manures (< 1 percent TS), and if filled with active microbes during start-up, can even produce biogas with completely soluble organic liquids. Sludge must be removed from the ASBR digester periodically. Concentrated nutrients are harvested during sludge removal.

Figure 14. Four phases of an ASBR Digester Cycle.


Contributors To This Article


Peer Reviewers