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Regulations in British Columbia Limit Biosecurity and Waste Management Options For Poultry Producers

We encourage our local and provincial governments to consider their regulations to allow enhanced biosecurity and sustainable waste management options for the poultry industry.  The poultry industry indicates that enhanced biosecurity for poultry manure management includes:

“All manure handling must be documented. While the minimum standard is documentation of its removal, onfarm composting prior to any removal would be an enhancement. Composting must be implemented according to local environmental standards. In any case, raw manure should not be spread on fields.” (BC Poultry Association Biosecurity Committee 2006)

The poultry layer industry in British Columbia is thriving and growing. In 2012, egg sales generated $ 113 million for the egg producers, which was an increase of almost 25% during the last five years (BC Ministry of Agriculture 2012). This industry generated approximately $ 617 million in economic output, 2100 jobs and $ 25 million in taxes (Price Waterhouse Coopers 2009). Much of this production is in Abbotsford, and much of the production occurs on small properties that are not able to utilize the manure produced by the birds. None of the feed is grown on the farms. The BC Ministry of Agriculture reported production of 69 million dozen eggs in 2012 (BC Ministry of Agriculture 2012), and 65 million dozen eggs from 2.6 million birds (BC Ministry of Agriculture 2013). This translates to 36.9 million dozen eggs from 1.475 million birds (Census of Agriculture 2011) for the poultry layer industry in Abbotsford.

Given that feed input is 1.88 kg per dozen eggs (BC Ministry of Agriculture 1997), and that all the feed for poultry is imported into Abbotsford, there is an import of 69,000 tonnes of feed. With an N output as manure of 2.3 g per bird per day and a N content of 5.84%, (BC Ministry of Agriculture 1997), poultry layers in Abbotsford excrete 1238 tonnes of N in 42,406 tonnes of manure, assuming an average moisture content of 50%. Where can all this manure go?

As we consider sustainable waste management strategies for agricultural waste, and consider the biosecurity concerns for the poultry industry, we need to consider how to allow this important industry to flourish. There are currently five options for managing poultry manure in British Columbia:

  1. exporting the manure to local dairy farms – will become limited with promotion of nutrient management plans and the concern regarding animal health effects of excess potassium
  2. exporting the manure to farms in the interior – not as practical for layer manure with high moisture content and we must consider the export of potentially pathogenic and antibiotic resistant bacteria.
  3. exporting the manure for use in mushroom compost production – this is an excellent solution for poultry broiler manure, but poultry layer manure is not currently used for mushroom production
  4. composting and exporting the manure into the US – there are no legally zoned properties that have developed and adopted biosecurity measures to reduce risk of exporting diseases.
  5. composting the manure to meet Good Agricultural Practice Guidelines for use on fruit and vegetable farms in BC or elsewhere
  6. Organic fertilizer production – may involve composting
  7. Other manure processing technologies – Timmenga & Associates (2003) identified several other potential promising manure processing technologies, but as yet, none of them has come to be.

Composting the manure to allow safe and sustainable export of poultry manure meets the enhanced biosecurity protocols for the poultry industry as well as enhancing the protection of our environment and public health.

The City of Abbotsford zoning bylaw, the provincial Agricultural Waste Control Regulation and the ALC Regulations may be restricting the poultry industry’s ability to meet their enhanced biosecurity goals.

On-farm composting of poultry layer manure may require a non-farm use exclusion from the Agricultural Land Commission because the import of wood waste as a bulking agent for composting is currently not an allowed use. The addition of wood waste or other high C/N ratio materials may reduce ammonia loss during composting. This is also important in the Lower Fraser Valley because of the concerns of the high ammonia emissions from agriculture and the impact on air quality. Under the current Agricultural Waste Control Regulation (Province of British Columbia 1992), import of wood waste for composting is not an allowed use:

“20 Wood waste may only be used for (a) plant mulch, soil conditioner, ground cover, on-farm access ways, livestock bedding and areas where livestock, poultry or farmed game are confined or exercised, (b) berms for cranberry production, or (c) fuel for wood fired boilers.”

The BC Ministry of Agriculture (2014) confirmed that importing wood waste for use as a bulking agent for composting manure may require a non-farm use exclusion:

“Woodwaste is the only non agricultural waste that can be co-composted with agricultural waste and the resulting compost may be used on the farm or be sold off the farm. However, the wood waste must have been previously used on the farm for one of the allowed uses described in the Code of Agricultural Practice for Waste Management….Composting operations which fall outside the definition of composting in the Code of Agricultural Practice for Waste Management may require approval from the Agricultural Land Commission. In addition, local or regional government bylaws may require permits or applications for a composting operation to be constructed or operated on a farm. ”

The City of Abbotsford zoning bylaw states that: “The area used for processing of livestock wastes into garden compost shall not exceed 465 m2 per farm operation.”  This suggests that many poultry producers would have to request a variance to the existing Abbotsford zoning bylaw.  In addition, because the import of woodwaste to blend with the poultry litter is considered a non-farm use, the City of Abbotsford’s Consolidated Soil Removal and Deposit Bylaw 1228-2003 also applies.

In conclusion, we encourage our local and provincial government to adapt current regulations and bylaws to allow our poultry industry to flourish by meeting enhanced biosecurity measures for poultry manure management, strategies that will also have a positive benefit for environmental and human health.

BC Ministry of Agriculture. 1997. Minimizing Pollution from Poultry Manure: 1. Nitrogen. Poultry Factsheet.

BC Ministry of Agriculture. 2014. Farm Practices – Composting. Strengthening Farming – Right to Farm. Order No. 870.218-29.

BC Ministry of Agriculture. 2012. British Columbia Agri-Food Industry – Year in Review.

BC Ministry of Agriculture. 2013. Website:

BC Poultry Association Biosecurity Committee. 2006. BC Poultry Biosecurity Reference Guide.

Price Waterhouse Coopers. 2009. BC Dairy, Egg and Poultry Industries: Socio-economic impact of British Columbia’s dairy, chicken, turkey, hatching egg and table egg industries.

Province of British Columbia. 1992. Agricultural Waste Control Regulation. Includes Code of Agricultural Practice for Waste Management. B.C. Reg. 131/92.

Timmenga & Associates. (2003). Evaluation of Options for Fraser Valley Poultry Manure Utilization. Prepared for the Sustainable Poultry Farming Group.

Reducing Greenhouse Gases from Agriculture in Abbotsford

With the climate change conference in Paris this week, our country, our province and our city will be thinking about opportunities to reduce greenhouse gas emissions. We and our children will be looking for ways to feel good about making a difference and positively affect climate change.

Our community of Abbotsford is termed the City in the Country because much of our City includes agricultural land, and agriculture is important to our economy. How does our agriculture impact climate change, and is there anything we can do?

We need to keep our head in the sand, We need to pay attention to our microbes, particularly our soil microbes, because they are the ones producing the greenhouse gases. We need to understand the science in its proper context so that we can make good decisions that will mitigate climate change.

In agriculture, nitrous oxide, or laughing gas, is the greenhouse gas of greatest importance, both because of how much is produced, and because there is more that we can do to reduce it. It is produced during at least two processes where the forms of nitrogen are changed by soil microbes.

Nitrous oxide emissions to the atmosphere increased dramatically since nitrogen fertilizer was invented. In fact, 60% of the world’s nitrous oxide emission now comes from agriculture,  When we add more nitrogen to our soil than is required by the plants, we can expect more nitrous oxide emission. This is even more true when we apply manure because we are adding carbon with the nitrogen, which also changes the soil atmosphere for the microbes.  As the nitrogen surplus increases, the nitrous oxide increases all the more. We learned this 20 years ago.

Research in Europe shows that nitrous oxide emission from agriculture can be reduced by 30 to 75%, simply by balancing the nitrogen we apply to our soil with the nitrogen taken up by the plant.

In Abbotsford, of the calculated greenhouse gases coming from agriculture, two thirds of it is nitrous oxide and one third is methane.  Most of the nitrous oxide comes directly from soil after we apply manure or fertilizer, and some of it is produced indirectly from ammonia emissions from animal barns and manure storages. We learned this 20 years ago.

Nutrient management planning to optimize the nitrogen in manure and fertilizer for our crops is the simplest way to impact climate change.  This has other benefits as well, including reduced potential for air and groundwater pollution.

Another way to positively impact climate change is to balance the nitrogen that we feed to our animals with the nitrogen that they need. This reduces ammonia emission, as well as nitrous oxide emission when the manure is applied to the soil. We learned this 20 years ago as well.

You may ask, what about anaerobic digestion that captures all the methane? That is an interesting question, and guess what? We learned about that 20 years ago as well! Methane from manure storage makes up 16% of the methane produced from agriculture, and less than 5% of the greenhouse gas emission. Anaerobic digestion doesn’t reduce this emission because of leakages, and the need to import other wastes for digestion.  Germany, in spite of its thousands of anaerobic digesters, learned this several years ago.

If we want to make a positive difference for climate change,  we need to keep our head in the sand, and learn the science in its proper context.

In a circular bioeconomy, we need to recycle our nitrogen in more efficient ways to make a difference with climate change. What better time to start than now? What better place to start than right here in our own community.  Lets join together to make a positive difference for our world.

Recycling Biosolids into Agriculture – Acting Locally, Responding Globally

“Using a precautionary approach, recycling biosolids for agricultural use is an important strategy for soil health and community sustainability”.  I will unfold what this means practically in our communities. I will address the excellent questions regarding trace elements sometimes also called heavy metals, microbes, and emerging substances of concern.

“Acting Locally, Responding Globally” is a byline that states the obvious, all of us are doing this every day.  As a scientist who has worked with soil and waste for almost 30 years, I participate with others around the globe to consider how we can live more sustainability on this planet.

We need to manage our leftover food in a way that is safe for ourselves and our communities.  We in the nations who are more privileged than most in the world have the opportunity to develop, and to model sustainable management for the rest of the world. And as persons who have a shared responsibility on this planet, it is our obligation. We need to act locally, and respond globally.

A sustainable community is all about protecting and enhancing our soils. Historically, we recycled our organic matter, because we understood that it was important to return the nutrients and organic matter to the land to maintain soil health and productivity.

As our society becomes increasingly urbanized, we have separated the growing of the food from returning the unused portion back to the land to benefit the soil.  With the advent of chemicals and fertilizer, we tried to live in the illusion that the soil organic matter wasn’t really that important. Today, our world is changing again, and more of us are realizing just how important our soil and our organic matter really is. This is one of the reasons why 2015 has been designated by the United Nations to be the International Year of Soils.

There is a reason that the Soil Assocation in the UK, which promotes organic agriculture, is also considering the importance of recycling biosolids into agriculture. We will explore the global reasons for this in the next few blogs. In the meantime, there is a great documentaries that help explain the recycling of biosolids.

Water Environment Assocation of Ontario:

This blog post is the introduction of a talk that I gave at a public forum organized for the Nicola Watershed Community Round Table in Merritt on January 26, 2015. The full text, along with the accompanying references, can be accessed here: Biosolids Management Jan 26 2015 talk excerpts Oct 16

Improving our agricultural waste management in British Columbia

The proposed improvements to the Agricultural Waste Control Regulation are positive, but do not reflect the current needs of our farmers, nor our public. The BC Ministry of Environment is currently reviewing and updating the Agricultural Waste Control Regulation, and invited feedback on its 2nd Policy Intentions Paper.1 This response is based primarily on areas with where most of the farm gate receipts in British Columbia are generated, and where:

“the development of certain intensive farming practices has over time created serious agricultural pollution issues that are not encountered on the same scale elsewhere in the province.” 2

Two guiding statements used in this review include:

  1. managing our environmental and public health as a prerequisite to increase our economic viability:

Increasing importance is being placed on producing local healthy food and reducing our environmental and carbon footprint, thereby promoting the economic viability of the B.C. agriculture and food sector.3

  1. our agricultural producers need to be included in shaping our regulation and industry in light of global and local environmental and health concerns and initiatives:

“in order for producers to properly fulfill their roles as stewards and managers of agricultural lands, their awareness of environmental stewardship issues needs to be increased. Producers are a vital link in the solution making progress chain and need to be informed about alternative approaches and other interests.2

Our farmers can provide solutions that are economically viable and protect environmental and human health. We have experienced this with the Avian Flu response in British Columbia, where our farmers have worked with government agencies in developing an excellent management strategy that minimizes risk for environment and public health, and meets international requirements.

Strategies and regulation for agricultural waste management must be integrated with local and global environmental and public health concerns. These include the increasing public health concerns regarding potential pathogens and antimicrobial resistance, as well as the environmental concern regarding greenhouse gas emissions.

As farming continues to intensify to meet British Columbia’s economic goals, more food is produced on a smaller land base, resulting in more agricultural waste.  The importance of sustainable management of excess agricultural waste, already identified in 19962, is now more critical because the volumes have increased, and there are additional environmental and health concerns.

The Ministry of Environment Policy Intentions paper does not deal with provincial agencies having encouraged agricultural production but have provided few options for managing excess agricultural waste. The lack of options encourages illegally zoned waste management sites which include sites on agricultural land that do not meet environmental or land use regulations. The intentions paper also does not adequately address international food safety requirements or the increasing public health concern regarding pathogens and antimicrobial resistance.

How can we invite British Columbians into a healthy dialogue for a regulatory process that benefits our farmers, our environment and our health, and allows our agricultural industry to be world leaders in modelling economic, social and environmental sustainability?

Full response to the AWMR Intentions paper is here: John Paul Response to AWCR 2nd Intentions Paper Aug 31 2015


  1. BC Ministry of the Environment. 2015. Agricultural Waste Control Regulation Review Update
  2. Management of Agricultural Wastes in the Lower Fraser Valley Program Steering Committee. 1997. Management of Agricultural Wastes in the Lower Fraser Valley. Summary Report – A Working Document. Report 9, DOE FRAP 1996-30.
  3. C. Ministry of Agriculture. 2008. The British Columbia Agriculture Plan – Growing a Healthy Future for B.C. Families.


Does Anaerobic Digestion Reduce Nitrous Oxide Emissions?

We can expect nitrous oxide emissions to significantly increase following anaerobic digestion of animal manures, unless ammonia emission is being controlled and the digested manure is applied at a rate that optimizes the nitrogen use efficiency by the crop.

Nitrous oxide is an important greenhouse gas to consider, as more than 60% of the world’s nitrous oxide emissions come from agriculture (Smith et al. 2007). In Canada, the estimate is higher at 65% (Kebreab et al. 2006). Agriculture and Agri-Food Climate Change Table (2000) identified farm nutrient management plans as a mechanism for optimizing nitrogen applications and a strategy to reduce N2O emissions. Smith et al. (2007) concluded that:

“Improving N use efficiency can reduce nitrous oxide emisions and indirectly reduce GHG emissions from N fertilizer manufacture. By reducing leaching and volatile losses, improved efficiency of N use can also reduce off-site nitrous oxide emissions.”

European modelling suggests a 40% reduction in N2O emission by implementing anaerobic digestion (Leip et al. 2010) and a Canadian literature review suggests up to 70% reduction (Vanderzwaag et al. 2011).  Given that N2O emissions are almost 3 x higher than methane emissions from manure storages on farms (Dairy Farmers of Canada 2010), and N2O emission reduction is not included in the GHG emission protocol for dairy farms in Canada (ADFI 2008), we would conclude that there is a substantial untapped GHG emission reduction potential! We need to be cautious with this modelling.

The European modelling assumes that digested manure is applied at rates that match crop uptake. There is no mandatory nutrient management planning currently required in British Columbia, and we can expect additional nitrogen to be imported to farms that are digesting manure. This is required for economic reasons.

Excess nutrients is already a concern in British Columbia, as it is in many areas in the US.  Kruger and Frear (2008) reported that co-digestion may result in significant import of nutrients, with USDA already reporting that 36% and 55% of larger US dairies already have N and P overloads on their farmland, respectively. Frear (2010) reported that 15-20% addition of food waste would increase the total amount of nitrogen on the farm by 57%, and increase ammonia by 23%.

When digested manure is utilized as a plant nutrient source, the research comparing N2O emissions from undigested manure with digested manure shows mixed results. Important factors involved in N2O emission include the following:

  1. Carbon content in the manure – increased carbon increases N2O emission. Anaerobically digested manure contains less available carbon
  2. Ammonium concentration – higher ammonium concentrations increase N2O emission rates. Anaerobically digested manures have a higher ammonium concentration than undigested manures.
  3. Manure pH – higher pH in digestates increase NH3 losss following application to soil, which decreases direct N2O emissions.

Available carbon in manure or digestate has a significant impact on N2O emission potential. Paul et al. (1993) observed increased N2O emission from manured soils when additional carbon was added. Sommer et al. (2004) developed a model describing how additional available carbon in the manure increased the oxygen demand and hence created lower oxygen concentrations, thereby increasing N2O emission. The logical conclusion was that if available carbon was removed via anaerobic digestion, N2O emission would decrease.

Ammonium concentration in the manure or digestate also has a significant impact on N2O emission potential. Heller et al. (2010) measured a significant correlation between soil NH4+ and N2O emission. Chadwick et al. (2011) observed that N2O emission rates were correlated with readily available N in manure, and not on total N. Paul et al. (1993) measured higher N2O emission rates following addition of ammonium and acetate to soil, than following addition of nitrate and acetate to soil. This suggests that N2O emission from soil is not simply due to increased anaerobic conditions in the soil.  Digested manures typically have higher ammonium concentrations than non-digested manure.

Manure pH also has a significant impact on direct N2O emission potential from soil mostly because it will affect NH3 losses following manure application. Patni and Jui (1985) observed an increase in manure pH following disappearance of volatile fatty acids in manure slurry. Paul et al. (1993) explained how the pH of manure is balanced by volatile fatty acids that lower the pH, and ammonium that increases pH. When the volatile fatty acids are utilized to produce methane during digestion, the pH of the manure naturally increases. This also increases the potential for ammonia emission following application of digestate. This has been observed in several studies. Paul et al. (1998) observed that NH3 emission rates from dairy cattle increased with increasing manure pH.

A review of research comparing N2O emission from digested or non-digested manures shows mixed results. Amon et al. (2006) measured higher NH3 emission and N2O emission was higher from the digested manure than from the undigested manure following application to soil.

Wulf et al. (2002) measured higher N2O emission on grassland from digested manure slurry than from non-digested slurry. They observed the opposite on arable land. They too, measured higher ammonium concentration and higher pH in the digested slurry. They also measured higher NH3 emission from digested manure on grassland, and suggested that indirect N2O emissions resulting from NH3 emission may be very important in estimating greenhouse gas potential.

The 20-40% potential reduction of N2O resulting from anaerobic digestion in Europe is derived primarily from the research of Petersen (1999), who measured significantly lower N2O emissions from digested slurry compared with undigested slurry. There are two notable observations in this study. The first is that the slurry application rates were based on the NH4+ content of the slurry, not on total N, or equal application rates. This meant that the application rate of undigested slurry was significantly higher than the rate of digested slurry. The second observation was that the soil NH4+ measured shortly after manure application appeared to be significantly higher with the undigested manure. This suggests that N2O emission is very much related to NH4+ in the manure and a balancing manure or digestate application based on NH4+ concentrations becomes a very important part of waste management to reduced N2O emissions.

There are three studies with swine manure that clearly demonstrate a dramatic reduction in N2O emission following anaerobic digestion. Vallejo et al. (2006) measured a 40% reduction in N2O emission from soil following digested and separated pig slurry compared with raw pig slurry. In both of these cases, the primary factor affecting N2O emission reduction is the loss of carbon and the decreased solids associated with raw manure. In a three year study, (Chantigny et al. 2007) measured 54 to 69% and 17 to 71% lower N2O emission with digested swine manure than with raw swine manure in loam soil and in sandy loam soil cropped to forage. Bertora et al. (2008) measured a 55% reduction in N2O emission following application of digested pig slurry to soil compared with raw pig slurry. They concluded that available carbon was the primary factor and NH4+ content was the secondary factor affecting N2O emissions from organic materials applied to soil.

Collins et al. (2010) reported reduced N2O emissions from soil following application of separated dairy manure digestate compared to the undigested manure. In a field study, they observed an almost 50% emission reduction in one year, but only a very small reduction in the second year. In a laboratory study measuring N2O emission during the first 48 hours, they observed higher N2O emission from the digested manure one year, and lower N2O emission the second year, compared to the undigested manure. Crolla (2011) measured significantly higher NH3 emissions from digested manure applied to soil in the spring during two consecutive years. They measured higher N2O emissions following application of digested manure in one year, and slightly lower N2O emissions compared to undigested manure in the following year. Herrmann (2012) concluded that in some cases, N2O emission was lower in soil following application of digestate compared with raw pig slurry, and in other cases, the opposite observation was made. Lemke et al. (2012) reported higher N2O emissions from undigested manure (4% of total N applied) compared with digested swine manure (1.4% of N applied) in Saskatchewan.  Joo et al. (2013) measured slightly less N2O emissions from soil following digested manure application than undigested manure application. They also reported significant CH4 and CO2 emission from the storage lagoons following anaerobic digestion, suggesting continued decomposition of carbon.

The N2O model developed described in Sommer et al. (2004) predicted that N2O emission could be reduced by more than 50% following anaerobic digestion. Using a modelling approach (CAPRI model) for all countries in the EU, Leip et al. (2010) concluded that N2O emission following field application was up to 40% lower following anaerobic digestion. The literature does not consistently support these predictions.

The potential for N2O emission reduction following anaerobic digestion exists, however, continued VFA and CH4 production in digestate fuel N2O emission during nitrification following field application. This means that we are not able to consistently assign an N2O emission reduction factor for anaerobic digestion.

The research suggests that net N2O emissions following manure or digestate application to soil is correlated with the ammonium content of the manure or digestate, and that N2O emission increases non-linearly with increased ammonium application to soil.


There is a potential to reduce nitrous oxide emissions by anaerobically digesting the manure. This potential only applies if ammonia emissions during digestate storage and following field application is minimized, and if the manure nitrogen is applied at agronomic rates.

Currently in British Columbia, because anaerobic digesters require off-farm waste to be economically viable, and there is no mandatory nutrient management planning, we can expect that anaerobic digestion of our animal manures will significantly increase nitrous oxide emissions.


Agriculture and Agri-Food Climate Change Table. 2000. Reducing Greenhouse Gas Emissions from Canadian Agriculture – Options Report. Publication # 2028E

ADFI. 2008. Greenhouse Gas Protocol for the Canadian Dairy Industry. Dairy Farm GHG Quantification Protocol (ISO 14064-2 Compatible. Atlantic Dairy and Forage Institute.

Amon, B, V. Kryvoruchko, T. Amon and S. Zechmeister-Boltenstern.  2006. Methane, nitrous oxide and ammonia emissions during storage and after application of dairy cattle slurry and influence of slurry treatment.  Agriculture, Ecosystems and Environment 112: 153-162.

Banks, C.J., S. Heaven, Y. Zhang, M. Sapp and R. Thwaites. 2013. A review of the application of the Residual Biogas Potential (RBP) test for PAS110 as used across the UK’s Anaerobic Digestion industry, and a consideration of potential alternatives. WRAP final project report, University of Southhampton.

Bertora, C., F. Alluvione, L. Zavattaro, J.W. van Groenigen, G. Velthof and C. Grignani. 2008. Pig slurry treatment modifies slurry composition, N2O and CO2 emissions after soil application. Soil Biology and Biochemistry  40: 1999-2006.

Chadwick,  D., S. Sommer, R. Thornman, D. Fangueiro, L. Cardenas, B. Amon and T. Misselbrook. 2011. Manure management: implications for greenhouse gas emissions. Animal Feed Science and Technology 166-167: 514-531.

Chantigny, M.H., D.A. Angers, P. Rochette, G. Bélanger, D. Massé and D. Côté. 2007. Gaseous Nitrogen Emissions and Forage Nitrogen Uptake on Soils Fertilized with Raw and Treated Swine Manure. Journal of Environ. Qual. 36: 1864–1872.

Collins, H.P., J.D. Streubel, C. Frear, S. Chen, D. Granatstein, C. Kruger, A.K. Alva and S.F. Fransen. 2010. Application of AD dairy manure effluents to fields and associated impacts. CSANR Research Report 2010 – 001.

Crolla, A. C. Kinsley, E. Pattey and A. Thiam. 2011. Environmental impacts from land application of digestate. Ontario Rural Wastewater Center.

Dairy Farmers of Canada. 2010. Dairy Farmers of Canada’s Sustainable Development Strategy.

Frear, C. (2010). Co-Digestion: Opportunity and Risk – A Washington State Perspective.  Fifth AgStar National Conference April 2010.

Heller, H.,  A. Bar-Tal, G. Tamir, P. Bloom, R.T. Venterea, D. Chen, Y. Zhang, C.E. Clapp and P. Fine. 2010. Effects of Manure and Cultivation on Carbon Dioxide and Nitrous Oxide Emissions from a Corn Field under Mediterranean Conditions. J. Environ. Qual. 39:437–448.

Herrmann, A. 2012. Biogas production from grassland and arable land in Schleswig-Holstein – results of the biogas expert project. Faculty of Agricultural and Nutritional Science. Christian-Albrechts-Universitait zu Kiel.

Joo, H.S., P.M. Ndegwa, J.H. Harrison, E. Whitefield, S. Fei, X. Wang, G. Neerackal, A.J. Heber and J.Q. Ni. 2013. Potential air quality impacts of anaerobic digestion of dairy manure. Waste-2-Worth Conference. Denver, Colorado, April 3, 2013.

Kebreab, E., K. Clark, C. Wagner-Riddle and J. France. 2006. Methane and nitrous oxide emissions from Canadian animal agriculture: A review. Can. J. Animal Science 86:135-158

Kruger, C. and C. Frear. 2008. VanderHaak AD: Lessons Learned. Northwest Dairy Digester Workshop. Sunnyside WA 11/18/08.

Leip, A., F. Weiss, T. Wassenaar, I. Perez, T. Fellmann, P. Loudjani, F. Tubiello, D. Grandgirard, S. Monni, and K. Biala. 2010. Evaluation of the livestock sector’s contribution to the EU greenhouse gas emissions (GGELS) –final report. European Commission, Joint Research Centre.

Lemke, R.L., S.S. Malhi, F. Selles and M. Stumborg. 2012. Relative effects of anaerobically-digested adn conventional liquid swine manure, and N fertilizer on crop yield and greenhouse gas emissions.

Patni, N.K. and P.Y. Jiu. 1985. Volatile fatty acids in stored dairy cattle slurry. Agricultural Wastes 13: 159–178.

Paul, J.W. and E.G. Beauchamp. 1989. Relationship between volatile fatty acids, total ammonia and pH in manure slurries. Biol. Wastes. 29: 313-318.

Paul, J.W., Beauchamp, E.G., Zhang, X., 1993. Nitrous and nitric-oxide emissions during nitrification and denitrification from manure-amended soil in the laboratory. Can. J. Soil Sci. 73: 539–553.

Paul J.W., Dinn N.E., Kannangara T. and Fisher L.J. 1998. Protein content in dairy cattle diets affects ammonia losses and fertiliser nitrogen value. J. Environ. Qual. 27: 528–534.

Petersen S.O., T.H. Nielsen, A. Frostegård and T. Olesen. 1996. Oxygen uptake, carbon metabolism, and denitrification associated with manure hot-spots. Soil Biol. Biochem. 28: 341-349.

Smith, P., D. Martino, Z. Cai, D. Gwary, H. Janzen, P. Kumar, B. McCarl, S. Ogle, F. O’Mara, C. Rice, B. Scholes, O. Sirotenko. 2007. Agriculture. In Climate Change 2007: Mitigation. Contribution of Working Group III to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [B. Metz, O.R. Davidson, P.R. Bosch, R. Dave, L.A. Meyer (eds)], Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA.

Sommer, S. G., Petersen, S. O., Moller, H. B., 2004. Algorithms for calculating methane and nitrous oxide emissions from manure management. Nutr. Cycl. Agroecosyst. 69: 143-154.

Vallejo, A., U.M. Skiba, L.Garcia-Torres, A. Arce, S. Lopez-Fernandez and L. Sanchez-Martin. 2006. Nitrogen oxides emission from soils bearing a potato crop as influenced by fertilization with treated pig slurries and composts. Soil Biology and Biochemistry 38: 2782–2793

Vanderzwaag, A.C., S. Jayasundara and C. Wagner-Riddle. 2011. Strategies to mitigate nitrous oxide emissions from land applied manure. Animal Feed Science and Technology 166-167: 464-479.

Wulf, S., M. Maeting and J. Clemens. 2002. Application Technique and Slurry Co-Fermentation Effects on Ammonia, Nitrous Oxide, and Methane Emissions after Spreading: II. Greenhouse Gas Emissions. J. Environ Qual: 31: 1795-1801.

Methane Emission Leakage from Co-Digestion on Dairy Farms

Anaerobic digestion of manure is an excellent process for reducing the potential pathogens and antimicrobial resistance associated with manure management. It is also an excellent process for producing methane, but science and experience suggests that anaerobic digestion will not reduce greenhouse gas emission. We can expect that methane emission will not decrease, and nitrous oxide emissions may increase unless further processing of the liquid and solid digestate occurs following digestion. This post will focus on methane emission.

Anaerobic digestion is not cost effective using a farm’s manure alone (BC Bioprducts Association 2007, Mallon and Weersink 2007, Gregersen et al. 2007, Shumway and Bischop 2008, ECOregon 2009).  Cornwall Agri-Food Council Development Team (undated) provided modelling of anaerobic digestion in one area in the UK, and determined that anaerobic digestion was not economically viable without grants, or non-manure wastes such as potatoes or other off-farm waste.

There are three implications for methane production and emission when considering input of additional off-farm waste:

  1. methane emission reduction credit for the off-farm waste
  2. increased methane production when including off-farm waste
  3. increased “leakage” (methane emission from the digestate after it comes out of the digester).

Methane emission to the atmosphere from a dairy farm importing off-farm wastes may be higher than if the farm had no anaerobic digester. If the off-farm waste has not been going to landfill and has not been producing methane in its previous management, there are no emission reduction credits available by importing the material to the farm. With the increased methane production during anaerobic digestion, additional “leakage” can be expected.

Methane Emission Credits When Co-digesting Manure with Other Solid Wastes

If the imported off-farm waste was previously disposed of at a landfill, it is possible to claim diversion credits because this waste would have emitted methane at the landfill. Washington State’s greenhouse gas emission protocol (Cook and Kruger 2008) includes two options for off-farm waste. The first is to assume that the off-farm waste has no CO2 emissions impact and therefore provides no carbon offset credit. The second is to assume that all off-farm waste was destined to go to landfill and provide the appropriate offset credit. This would have to take into consideration any methane emission reduction strategies such as landfill gas capture already in place at the landfill.

For off-farm waste in British Columbia, unless it was residential foodwaste, it is unlikely that it has been going to landfill. Most organic waste has already been diverted for animal feeding, composting, or deposits on agricultural land. BC BioProducts (2007) was not able to confirm that any of the readily available organic wastes for co-digestion were going to landfill.  Methane emission reduction credits from off-farm waste would require verification that it was being diverted from landfill.

Methane Production Increases When Including Off-farm Waste

Off-farm organic waste can dramatically increase methane production during anaerobic digestion. The figure below shows that the methane production potential of dairy cattle manure alone is relatively low compared to the potential methane production from other organic wastes.

Potential methane production from various organic wastes (from BC Bioproducts Association 2007)

Potential methane production from various organic wastes (from BC Bioproducts Association 2007)

Frear (2010) reported that adding 15-20% food processing waste to a dairy manure digester more than doubled biogas production and increased the percentage of methane in the biogas.  Ontario Ministry of Agriculture and Food (2007) reports that addition of up to 25% off-farm waste may double or triple biogas yield. Mang (2009) summarized anaerobic digestion projects in Europe and stated that increased biogas production from co-digestion with off-farm wastes may actually make some projects economically self-sustaining. (Taglia 2010) reported that adding off-farm waste could increase the biogas production five-fold. Jepsen (undated) stated that in Denmark, adding off-farm waste to manure digesters provides up to 60% of the digester’s methane production. Crolla et al. (undated) determined that biogas yields doubled when adding off-farm substrates to anaerobic digesters in Ontario.

Increased Potential for Methane Emission From the Digestate

The BC Bioproducts Association (2007) stated that: “It is important to note that up to 15% of biogas may be produced in the digestate storage. It is paramount that digestate storage be covered to limit direct emission to the atmosphere.”  The Leipzig Institute for Energy (undated) concluded that enhanced production of methane during digestate storage results from the higher amounts of biodegradable organic matter added for co-digestion with off-farm waste.

IPCC (2006) estimated that 5-15% of the potential methane production was emitted as “leakage”.  The UNFCCC CDM (2012) then further estimates ”leakage”  from the digestate after it has been removed from the digester and distinguishes between liquid and solid digestate. This ranges from 0.05 for two stage digesters, 0.10 for covered anaerobic lagoons, 0.15 for UASB type digesters, and 0.20 for conventional digesters.  The previous protocol developed by the UNFCCC CDM which was adopted by the US EPA (2011) was 10% unless local data is available to support an alternative.

Liebetrau (2011) measured “leakage” from 10 anaerobic digesters in Germany. He measured negligible CH4 leakage from the digesters themselves, 0.4 to 2.4% CH4 leakage during gas utilization, and 0.2 to 11% of the total CH4 produced during storage of the digestate. The amount of methane emitted during storage of digestate depended on whether the storage was covered or not. Lukehurst et al. (2010) showed the residual methane yield from digestate storage following varying retention times in three different types of anaerobic digesters. They also stated that “In European countries with a developed biogas sector (e.g. Germany, Denmark and Austria) there are now financial incentives to establish covered digestate stores, with the main objective of reducing emissions.” Linke et al. (2013) developed a model for estimating methane emission from digestate following anaerobic digestion and concluded that digestate storage tanks need to be covered to reduce CH4 emission and improve CH4 recovery.

In a review of GHG emissions from agriculture in Germany, Lengers (2011) concluded that “looking at the development of methane emissions resulting from manure management, agricultural soils and enteric fermentation, abatement efforts in methane emissions failed to have major impacts.”

There are two reasons why significant methane emission following the digestion process is expected when adding off-farm waste:

  1. Increased carbon, which increases the potential of methane emission because the digestion process continues after removal from an anaerobic digester,
  2. The digestate has been inoculated with methane producing bacteria

Based on the science, the EPA recommendation and the IPPC protocols, the expected methane “leakage” following anaerobic digestion is approximately 10% of the total methane production.


Importing off-farm organic waste is critical for economic viability of anaerobic digestion in British Columbia, unless it is fully supported by taxpayer money. In BC, there is negligible methane emission reduction potential associated with including off-farm wastes because most of these wastes have not been going to landfill.

Based on the leakage estimate of 10% of the methane production, and considering that methane production has doubled, it is reasonable to expect that the net methane emission to the atmosphere from implementing anaerobic digestion is higher than the baseline emissions from manure storage alone.

This suggests that implementation of anaerobic digestion for animal manure in British Columbia will not reduce greenhouse gas emissions resulting from methane.


BC Bioproducts Association. 2007. Feasibility Study – Anaerobic Digester and Gas Processing Facility in the Fraser Valley, British Columbia.

Cook, K., and C. Kruger. 2008. Recommendations for the Development of Agricultural Sector Carbon Offsets in Washington State. Agriculture Sector Carbon Market Workgroup.

Cornwall Agri-food Council Development Team. undated. Economic Modelling of Anaerobic Digestion / Biogas Installations in a Range of Rural Scenarios in Cornwall.

Crolla, A., C. Kinsley, T. Sauvez and K. Kennedy. undated. Anaerobic Digestion of Manure with Various Co-substrates. Research Note. Ontario Rural Wastewater Center, University of Guelph.

ECOregon 2009. Dairy Manure Anaerobic Digester Feasibility Study Report. Prepared for Volbeda Dairy, Oregon.

Frear, C. 2010. Co-digestion: Opportunity and Risk – A Washington State Perspective. Fifth AgStar National Conference, Green Bay, WI April 27-28, 2010.

Gregersen, K.H., H.B. Moller, S.G. Sommer, T. Birkmose and L.H. Nielsen. 2007. Promotion of biogas for electricity and heat production in EU countries. Economic and environmental benefits of biogas from centralized co-digestion. PROBIOGAS. An EIE/Altener project, co-funded by the EU Commission.

IPCC. 2006. 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Volume 4. Agriculture, Forestry and Other Land Use. Chapter 10. Emissions from Livestock and Manure Management.

Jepsen, S-E. undated. Co-digestion of animal manure and organic household waste – the Danish experience. Ministry of Environment and Energy. Danish EPA.

Lengers, B. 2011. GHG survey of German agriculture – specific view on dairy production systems. Technical paper 2011. Institute for Food and Resource Economics, University of Bonn.

Liebetrau, J. 2011. Analysis of greenhouse gas emissions from 10 biogas plants within the agricultural sector. Deutsches Biomasse Forshungs Zentrum.

Liepzig Institute for Energy. undated. GHG Mitigation by Anaerobic Digestion.


Linke, B., I. Muha, G. Wittum and V. Plogsties. 2013. Mesophilic anaerobic c0-digestion of cow manure and biogas crops in full scale German biogas plants: A model for calculating the effect of hydraulic retention time and VS crop proportion in the mixture on methane yield from digester and from digestate storage at different temperatures. Bioresource Technology 130: 689-695.

Lukehurst, C.T., P. Frost and T. Al Seadi. 2010. Utilisation of digestate from biogas plants as biofertiliser. Task 37. IEA Bioenergy.

Mallon, S., and A. Weersink. 2007. The Financial Feasibility of Anaerobic Digestion for Ontario’s Livestock Industries. University of Guelph.

Mang, H-P. 2009. Co-digestion: Some European Experiences.  German Society for Sustainable Biogas and Bioenergy Utilization (GERBIO). 2009 AgSTAR National Conference. Baltimore, USA.

Ontario Ministry of Agriculture and Food. 2007. Anaerobic Digestion Basics. Agdex Factsheet 720/400.

Shumway, C.R., and C.P. Bishop. 2008. The Economics of Anaerobic Digestion with Co-Product Marketing. Northwest Dairy Digester Workshop. November 2008.

Taglia, P. 2010. Biogas – Rethinking the Midwest’s Potential. Clean Wisconsin.

UNFCCC/CDM. 2012. United Nations Framework Convention on Climate Change/Clean Development Mechanism. Methological Tool: Project and Leakage Emissions from Anaerobic Digesters. EB 66 Report Annex 32 (


Does anaerobic digestion reduce antibiotics or antibiotic resistance in manure?

Anaerobic digestion of animal manures reduces the amount of antibiotics and antibiotic resistant organisms but does not eliminate them. Research indicates that potential pathogens in manure can be reduced by more than 99% by anaerobic digestion, but the important point to note is that the level of potential pathogens likely remains above the safe level. We need to understand the primary objective of anaerobic digestion is not to sterilize the manure:

“Digesters are designed to produce methane, not inactivate pathogens.” (Borchardt et al. 2013)

“As long as anaerobic digestion has been considered an attractive method to promote a clean fuel from renewable feed stocks, such as animal manure, to develop a well-established technology, the optimization of anaerobic digestion processes requires effective operative control and possible correlation with reduction of pathogens” (Holm-Nielsen et al. 2009)

On-Farm Digestion Dramatically Reduces Potential Pathogens in Manure

On-farm anaerobic digestion reduces potential pathogens in the manure by over 90% in most cases. Wright et al. (2001) reported that fecal coliforms in manure on a farm in upstate New York decreased from 3.8 million to 3,400 CFU/g. Fecal coliform counts in digestate from two other farm digesters had reduced to just over 10,000 CFU/g. Harrison et al. (2005) reported that potential pathogen reduction was greater than 98% following anaerobic digestion in most cases, but that anaerobic digestion of dairy manure would not remove all biosecurity hazard. In Ontario, Crolla (2010) reported 70-95% pathogen reduction during anaerobic digestion on two dairy farms. For example, E. coli counts reduced from 1-6 million to approximately 30,000 CFU/100 mL. Pandey and Soupir (2011) reported that potential pathogens during anaerobic digestion of dairy manure in Iowa were destroyed in less than 4 days at thermophilic temperatures (52.5 C), but required 40 days at 37 C, and more than 60 days at 25 C.

Crolla et al. (2011) measured E.coli and Salmonella in drainage water following application of either raw or digested dairy cattle manure. They measured a log higher bacteria count following application of raw or digested manure compared with the control (no manure), but observed no differences between manure treatments.

Antibiotic Degradation

Degradation of antibiotics are enhanced through both higher temperatures and more biological activity (Masse et al. 2014). In this review of the research, they noted that with anaerobic digestion, thermophilic digestion was more likely to degrade antibiotics faster than mesophilic digestion. They concluded that:

“Generally, antibiotics are degraded during composting > anaerobic digestion > manure storage > soil” (Masse et al. 2014).

In recent research in China, seven antibiotics as well as antibiotic resistance genes were found in the effluent of anaerobic digestion of pig manure (Zhang et al. 2015).

Antibiotic Resistance

Mesophilic anaerobic digestion of dairy cattle manure resulted in lower potential pathogens in the manure, but the antimicrobial resistance persisted during the anaerobic digestion process (Resende et al. 2014). Others have found that thermophilic anaerobic digestion has dramatically reduced antimicrobial resistant organisms (Beneragama et. al. 2011). Ihara et al. (2013) reported that mesophilic anaerobic digestion of livestock manure reduced potential pathogens and antimicrobial resistance genes but a chemical oxidation process was required to reduce it further.

German researchers have found drug resistant E. coli in digested pig manure (von Salviati et al. 2015). Schauss et. al. (2014) reported the presence of ESBL-producing E. coli in output samples of six German biogas plants. They found that the numbers were 2-4 orders of magnitudes lower following mesophilic digestion, and in the same order of magnitude following thermophilic digestion. Wolters et al. (2015) found transferable antibiotic resistance in the output of 7 mesophilic anaerobic digesters. They concluded that:

“Since all plasmids conferred multiple antibiotic resistance and harbored integrons, they might contribute to the increasing problems caused by multi-resistant pathogens in clinical settings, nowadays threatening public health”


It appears that the risk of antibiotic resistance is reduced following anaerobic digestion of animal manures, and that the consensus is the the risks are not eliminated.

“The data point out the need of discussions to better address management of biodigesters and the implementation of sanitary and microbiological safe treatments of animal manures to avoid consequences to human, animal and environmental health.” (Resende et al. 2014)


Beneragama, N., M. Yusuke, T. Yamashiro, M. Iwasaki, L.S. Adekunle and K. Umetsu. 2011. The survival of cefazolin resistant bacteria in thermophilic co-digestion of dairy manure and waste milk. Journal of Agricultural Science and Technology A 1: 1181–1186.

Borchardt, M., S. Spencer, S. Borchardt, B. Larson and A. Ozkaynak. 2013. Inactivation of dairy manure borne pathogens by anaerobic digestion and bedding recovery units.

Crolla, A. 2010. Assessment of environmental impacts from on-farm manure digesters. Presentation at IEA Bioenergy Task 37. May 27, 2010.

Crolla, A., C. Kinsley, E. Pattey and A. Thiam. 2011. Environmental Impacts from Land Application of Digestate. Research Note. Ontario Rural Wastewater Center.

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.

Holm-Nielsen, J.B., T. Al Seadi and P. Oleskowicz-Popiel. 2009. The future of anaerobic digestion and biogas utilization. Bioresource Technology 100: 5478–5484

Daniel I. Massé, D.I., N. M. Cata Saady and Y. Gilbert. 2014. Potential of Biological Processes to Eliminate Antibiotics in Livestock Manure: An Overview. Animals 2014, 4, 146-163; doi:10.3390/ani4020146

Ihara, I., M. Yoshitake, K. Toyoda, M. Iwasaki and K. Umetsu. 2013. Risk reduction of antibiotic resistant bacterial by anaerobic digestion and electrochemical oxidation for manure application. Bio-Robotics, Volume # 1 | Part# 1.

Pandey, P.K. and M.L. Soupir. 2011. Escherichia coli inactivation kinetics in anaerobic digestion of dairy manure under moderate, mesophilic and thermophilic temperatures. AMB Express Volume 1.

Resende, J.A., V.L. Silva, T.L.R de Oliveira, S. de Oliveira Fortunato, J. da Costa Carneiro, M.H. Otenio and C.G.Diniz 2014. Prevalence and persistence of potentially pathogenic and antibiotic resistant bacteria during anaerobic digestion treatment of cattle manure. Bioresource Technology 153: 284–291.

Schauss, T., S.P. Glaeser, A. Gütschow, W. Dott and P. Kämpfer. 2014. Improved Detection of Extended Spectrum
Beta-Lactamase (ESBL)-Producing Escherichia coli in Input and Output Samples of German Biogas Plants by a Selective Pre-Enrichment Procedure. PLoS ONE 10(3): e0119791. doi:10.1371/journal.pone.0119791

von Salviati, C., H. Laube, B. Guerra, U. Roesler and A. Friese. 2015. Emission of ESBL/AmpC-producing Escherichia coli from pig fattening farms to surrounding areas. Veterinary Microbiology 175: 77-84.

Wolters, B., M. Kyselková, E. Krögerrecklenfort, R. Kreuzig and K. Small. 2015. Transferable antibiotic resistance plasmids from biogas plant digestates often belong to the IncP-1ε subgroup. Frontiers in Microbiology. January 21, 2015 doi: 10.3389/fmicb.2014.00765

Wright, P.E., S.F. Inglis, S.M. Stehman and J. Bonhotal. 2001. Reduction of selected pathogens in anaerobic digestion. 5th Annual NYSERDA Innovations in Agriculture Conference 1-11.

Zhang, S., J. Gu,  C. Wang,P. Wang, S. Jiao, Z. Li He and B. Han. 2015. Characterization of Antibiotics and Antibiotic Resistance Genes on an Ecological Farm System. Hindawi Publishing Corporation Journal of Chemistry Article ID 526143.



Does composting reduce antibiotics or antibiotic resistance in animal manure?

Composting animal manure may be the best strategy to reduce antimicrobial resistance before the manure is released into the environment. There is evidence suggesting that although antibiotic resistant pathogenic organisms are rapidly killed in a composting environment, the antimicrobial resistance genes may persist for a longer period. There is also evidence that the concentrations of most antibiotic residues in manure are significantly reduced during the composting process, although the antibiotics degrade naturally in the soil or manure with time as well.

It is important to distinguish compost from rotted or stored manure. There are some jurisdictions where the term “composting” has no particular definition other than a period of decomposition. In other areas, the term “compost” is well defined to indicate a thorough decomposition process whereby all of the material has reached temperatures of > 55-60 C for a defined period of time.

Fate of Antibiotics During Composting

It appears that concentrations of many antibiotics are significantly reduced during the composting process. In a review on the fate of antibiotics in animal manure, Masse et al. (2014) concluded that composting was more effective than anaerobic digestion, and either process was more effective than application of the raw manure directly to the land.

Storteboom et al. (2007) found that intensively managed composting process slightly reduced the degradation period for three antibiotics present in horse and dairy cattle manure, including chlortetracycline, tylosin and monensin. Dolliver et al. (2008) reported that chlortetracycline concentrations were reduced by > 99%, monensin and tylosin concentrations were reduced by 54 to 76%, and sulfamethazine concentrations were not reduced after 35 days of composting. Sura et al. (2015) measured significant reduction of antibiotics in beef cattle manure during both composting and stockpiling of the manure, but noted that temperatures of the stockpiled manure also reached > 60 C.

In a study measuring antibiotics in fresh or composted manure used for vegetable production, Kang et al. (2012) concluded:

“a practical guideline for organic producers who use conventional manure for plant nutrient source will be to (1) apply composted manure rather than fresh manure, and/or (2) let the manure sit in the soil for as long as possible before planting vegetables in the spring. This extra time will help degrade antibiotics and thus lower the concentration available for plant uptake.”

Fate of Antibiotic Resistant Microbes During Composting

Most antibiotic resistant microbes that are potentially harmful to humans are destroyed by a consistent composting process, where the temperature is carefully controlled to exceed 55-60 C in all parts of the composting material.

Sharma et al (2009) measured substantial reduction of E. coli resistant to tetracycline and ampicillin during windrow composting of beef manure but observed that the resistance genes prevailed for a much longer period of time. Wang et al. (2015) reported measured a 4 to 7 log reduction in tetracycline and erythromcyin resistant bacteria during simulated composting of swine manure compared to a 1-2 log reduction during lagoon storage. Cook and Bolster (2015) observed that enterococci concentrations decreased to below detection within 21 days of composting swine slurry. Gao et al. (2015) measured significantly lower antibiotic resistant E. coli in composted manure than in raw pig manure in China.

Fate of Antibiotic Resistant Genes During Composting

Chen et al. (2010) found that composted manure contained up to seven orders of magnitude less AMR genes than manure treated by other technologies, including lagoon, aerobic treatment, and anaerobic treatments. Wang et al. (2012) reported that the six measured classes of erythromycin resistance gens and tetracycline resistance genes declined marginally during the first 17 days of composting, but dramatically afterward within 31 days of composting swine manure. In contrast, they measured no reduction in antimicrobial resistance genes during lagoon storage of manure.

Stoorteboom et al. (20o7) concluded that more than six months of composting may be required to reduce some of the AMR genes in horse and dairy manure. Keen (2009) measured rapid disappearance of potential pathogens during composting of poultry litter, but little reduction in the concentration of tetracycline resistance genes. Sharma et al (2009) measured reduction in abundance of AMR genes following windrow composting of beef manure. Marin et al. (2014) reported that E.coli was eliminated after one or two weeks of composting sheep manure, but the virulence and/or antibiotic resistance genes persisted even after 49 days of composting. Cook and Bolster (2015) measured a 36-97% reduction in bacteria with erythromycin AR genes, a 94-99% reduction in bacteria with tetracycline resistant genes, and a 53-84% reduction in bacteria with sulfonamide resistant genes following 112-142 days of composting swine manure.

In a review of manure treatment to reduce antimicrobial resistance, Wang and Yu (2012) concluded that anaerobic lagoons  were poorest at reducing risk and composting was the best treatment option.

“because animal manure is the largest reservoir of AMR, management and treatment of animal manure provide an opportunity to contain and destruct AMR arising from food animal production” (Wang and Yu 2012)


Short of reducing antibiotic use in agriculture, composting may be the best option for managing the large reservoir of antibiotic resistance contained in animal manures.  Pruden et al. (2013) recommended composting and digestion for reducing the risks associated with animal manure. Marin et al. (2014) concluded that “composting is a practical method that can effectively eliminate pathogens in manure, or at least promote a reduction in the number of pathogenic cells.” Wang et al. (2015) concluded that “composting can be an effective and practical approach to decrease dissemination of antibiotic resistance from swine farms to the environment”. Cook and Bolster (2015) concluded that; “As concerns over antibiotic resistance and pathogens increase, composting provides a valuable manure management tool for decreasing contaminants and improving the value of this material as a soil conditioner.”

We should do all that we can to reduce the risk of increased antibiotic resistance and its impact on human and environmental health. Finley et al. (2013) concluded that “reducing this risk must include improved management of waste containing antibiotic residues and antibiotic resistant organisms” 


Chen, J., F.C. Michel Jr., S. Sreevatsan, M. Morrison, and Z. Yu. 2010. Occurrence and persistence of erythromycin resistance genes (erm) and tetracycline resistance genes (tet) in waste treatment systems on swine farms. Microbial Ecology 60:479-486.

Cook, K. and C. Bolster. 2015. Composting swine slurry to reduce indicators and antibiotic resistance genes. Animal Manure Management. http://www,

Dolliver, H., S. Gupta and S. Noll. 2008. Antibiotic degradation during manure composting. J. Environmental Quality 37: 1245-1253.

Finley, R.L., P. Collignon, D.G.J. Larsson, S.A. McEwen, X.-Z. Li, W.H. Gaze, R. Reid-Smith, M. Timinouni, E. Topp and D.W. Graham. 2013. The scourge of antibiotic resistance: the important role of the environment. Clinical Infectious Diseases, 57:  704-710.

Gao, L., J. Hu, X. Zhang, L. Wei, S. Li, Z. Miao and T. Chai. 2015.  Application of swine manure on agricultural fields contributes to extended-spectrum b-lactamase-producing Escherichia coli spread in Tai’an,China. Frontiers in Microbiology April 2015 Volume 6 Article 313.

Kang, D-H., S. Gupta, C. Rosen, V. Fritz, A. Singh, Y. Chander, and H. Murray. 2012. Antibiotic Uptake by Vegetable Crops from Manure-Applied Soils. A Report Submitted to North Central Region Sustainable Agricultural Research and Extension (SARE) Program

Keen, P.L. 2009. Seasonal dynamics of tetracycline resistance genes and antibiotics in a British Columbia agricultural watershed. PhD Thesis, University of British Columbia, Resource Management and Environmental Studies.

Marin, J.M., R.P. Maluta, C.A. Borges, L.G. Beraldo, S.A. Maesta, M.V.F. Lemos, U.S. Ruiz, F.A. Ávila and E.C. Rigobelo. 2014. Fate of non O157 Shigatoxigenic Escherichia coli in ovine manure composting. Arq. Bras. Med. Vet. Zootec., 66: 1771-1778.

Masse, D.I., N.M. Cata Saady and Y. Gilbert. 2014. Potential of Biological Processes to Eliminate Antibiotics in
Livestock Manure: An Overview. Animals 2014, 4, 146-163; doi:10.3390/ani4020146.

Pruden A, D.G.J. Larsson, A. Amézquita,  P. Collignon, K.K. Brandt, D.W. Graham, J.M. Lazorchak,  S. Suzuki, P. Silley, J.R. Snape, E. Topp, T. Zhang and Y-Guan Zhu. 2013. Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment. Environmental Health Perspectives 121: 878-885

Sharma, R., F.J. Larney, J. Chen, L.J. Yanke, M. Morrison, E. Topp, T.A. McAllister, and Z. Yu. 2009. Selected antimicrobial resistance during composting of manure from cattle administered sub-therapeutic antimicrobials. J Environmental Quality, 38: 567-575.

Storteboom, H. N.,  S.C. Kim, K.C. Doesken,  K.H. Carlson J.G. Davis and A. Pruden. 2007. Response of antibiotics and resistance genes to high-intensity and low intensity manure management. J Environmental Quality 36: 1695-703.

Sura, S., T.A. McAllister, F.J. Larney, A.J. Cessna, I.D. Amarakoon, L.D. Tymensen, J. Charest, A.F. Olson, J.V. Headley, and F. Zvomuya. 2015. The Fate of Antimicrobial Residues during Composting and Stockpiling of Manure. Compost Matters. March 4-5, 2015, Red Deer, Alberta.

Wang, L., and Z. Yu. 2012. Antimicrobial resistance arising from food-animal productions and its mitigation, antibiotic resistant bacteria. – A continuous challenge in the New Millenium, Dr. Marina Pana (Ed.), ISBN 978-953-51-0472-8 InTech.

Wang, L., Y. Oda, S. Grewal, M. Morrison, F. C. Michel Jr. and Z. Wu. 2012. Persistence of resistance to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage.  Microbial Ecology 63: 32-40

Wang, L., A. Gutek, S. Grewal, F. C. Michel Jr. and Z. Wu. 2015. Changes in diversity of cultured bacteria resistant to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage.  Letters in Applied Microbiology. May 2015


How antimicrobial resistance spreads in the environment

The safest place for untreated animal manure containing antibiotics, antibiotic resistant genes, or antibiotic resistant microbes is the soil, where the large reservoir of microorganisms is best likely able to manage them. Most microbes that are potentially pathogenic to humans do not survive long in soil because they require readily available carbohydrates and proteins and cannot compete well with other soil organisms. However, there is gene transfer from antibiotic resistant organisms in manure to non-pathogenic organisms in soil, resulting in the soil also being a large reservoir of antibiotic resistant genes.

Fate of Antibiotics, Antibiotic resistant organisms, and Antimicrobial resistant genes in Soil Following Manure Application

Concentrations of antibiotics, antibiotic resistant organisms and antimicrobial resistant genes in soil following manure application tend to increase, then decrease to background levels after some time.

Marti et al. (2014) measured an increase in antibiotic resistant genes in soil following a spring application of dairy or swine manure, and found that the gene levels decreased exponentially to background levels by the fall. Munir and Xagoraraki (2011) measured elevated antibiotic resistance genes for four months following application of manure from three farms in the U.S.  Despite reports of antimicrobial resistance genes following manure application returning to background levels, Popowska et al. (2012) measured consistently higher antibiotic resistant gene levels in agricultural soils with a history of manure application. You et al. (2012) measured tetracycline resistant genes in poultry manure amended soil for up to two years after manure application. They reported that the gene levels did decrease with time, but noted that horizontal gene transfer must have occurred into the large resident soil microbial population. You and Silbergeld (2014) provided an excellent review of the impact of low doses of antimicrobials used in agriculture on the development of the pool of antimicrobial resistance genes in the soil microbial community.

Antibiotics and antimicrobial resistant genes are taken up by plants

Leftover antibiotics in manure may be taken up by plants. Kumar et al. (2005) measured antibiotic concentrations ranging from trace levels to greater than 200 ppm in manure. Dolliver et al. (2007) found that sulfamethazine was taken up by lettuce, corn and potato plants, but that the total accumulation in plants was less than 0.1% of the amount applied to soil in manure. Seo et al. (2013) measured chlortetracycline, tylosin and sulfamethazine uptake in lettuce, tomato and hairy vetch following soil application of swine manure containing antibiotics. They noted that antibiotic uptake is dependent on antibiotic type and plant type. Kang et al. (2013) observed uptake of five antibiotics (chlortetracycline, monensin, sulfamethazine, tylosin and virginiamycin) by 11 vegetable crops in two different soils that were fertilized with raw turkey or hog manure. The uptake of the antibiotics was very low and there was no significant difference in uptake from the manured soil than from the control soil (amended with inorganic fertilizer). They concluded that antibiotic uptake by vegetable crops analyzed was not a major health concern to most adults unless one is allergic to that particular pharmaceutical.

It appears that antimicrobial resistant genes can also be taken up by plants from the soil. Marti et al. (2013) evaluated antibiotic resistant bacteria on vegetables such as tomato, cucumber, pepper, carrot, radish and lettuce. They did not find a corresponding increase in antibiotic resistant bacteria on plants following manure application, but they did report finding antibiotic resistant genes in the vegetables. They concluded that ingestion of antibiotic resistant bacteria naturally found in soil is inevitable through consumption of raw vegetables and fruits.

Antibiotics, antimicrobial resistant genes and antibiotic resistant microbes travel in the air

Recent reports have indicated that antibiotics, antibiotic resistant bacteria and antimicrobial resistance genes can be airborne on particulate matter. McEachran et al. (2015) reported measurable concentrations of monensin, tylosin, tetracycline, chlortetracycline and oxytetracycline in the airborne particulate matter measured up to 200 m downwind of ten beef feedlots in Texas. They also measured increased abundances of six tetracycline resistance genes downwind of the feedlots.

Graham et al. (2009) concluded that antimicrobial resistant organisms could be spread by flies around broiler poultry operations. Laube et al. (2014)  measured antibiotic resistant (ESBL) E. coli in the manure and surrounding air from seven poultry broiler farms in Germany, and concluded that antibiotic resistant organisms are dispersed in the exhaust air of the chicken barns.

Antimicrobial resistant genes and microbes are found in water

Holvoet et al. (2013) concluded that a significant source of antimicrobial resistant E. coli on eight vegetable farms was the irrigation water, and concluded the that antimicrobial genes in the water were of animal origin.

Krapac et al. (2004) reported increased presence of tetracycline resistance genes in groundwater near and downgradient from a swine manure storage lagoon than upgradient and further away.

Garder et al. (2012) found that 70% of the enterococci in manure samples were resistant to tylosin, but the concentrations of enterococci in the tile water were very low.

Manure must be applied at a time and in a manner that reduces the risk of runoff. Joy et al. (2013) reported runoff of both antibiotics and antibiotic resistant genes from soil amended with swine manure.

Luby (2014), following application of swine manure containing 65-100% tylosin resistant Enterococci, measured significantly increased frequency of resistance genes in the tile drains under soil receiving surface applications of swine manure. She also concluded that the increase in tylosin resistant bacteria and tylosin resistance genes in soil was short term, and reduced to background frequencies after one year.

Chow et al. (2015) reported that even low concentrations of antibiotics in aquatic environments can increase antibiotic resistance of the microbes in the water. They conclude:

“Given the huge quantities of antibiotics that are entering the environment, it is likely that this antibiotic pollution is generating antibiotic resistant organisms that may be a source of newly emerging threats to human and animal life.”


When we apply untreated manure to our agricultural soil, we are spreading antimicrobial resistance genes into the soil microbial pool, where transfer from one organism to another can take place. It is very important to manage manure in a sustainable manner, avoiding overapplication, respecting buffer zones to waterways, and applying the manure when the risk of runoff and potential pollution to ground and surface water is the lowest. Manure management to reduce greenhouse gas emissions also serves to limit the spread of antimicrobial resistance into the environment.

Denmark has been one of the first countries to limit non-therapeutic use of antimicrobials already 20 years ago. They found that if antimicrobial use was limited, there was less selective pressure for resistance, with a resulting decrease in the trait over time (Levy 2014).  This means that there is potentially good news if we reduce the amount of antimicrobials used in agriculture, particularly for non-therapeutic uses. Cogliani et al. (2011) reported that animal production continues to thrive in European countries where the ban on non-therapeutic use of antimicrobials actually led to a reduction in antimicrobial use.

We also can see a lesson from agriculture in the Netherlands. When the ban on non-therapeutic use of antimicrobials was implemented in 1999, there was no monitoring plan in place (Cogliani et al. 2011). This resulted in no change in antibiotic use, as the non-therapeutic use simply became therapeutic, until the Netherlands mandated a 50% reduction in antimicrobial use a few years ago.

“We may need to focus more resources on restricting the release of active compounds into the environment; for example, from pharmaceutical production plants, from farming activities, from hospitals and from water and sewage treatment plants, so as to restrict the selection of antibiotic resistance caused by low level exposure to drugs of the global bacterial population.” (Hughes 2015)

The soil remains a large reservoir of antimicrobial resistant genes. Although most potential pathogenic bacteria do not survive long in soil, there are a number of serious human pathogens that do. In the following posts, we will explore the effects of manure treatments, and their effect on antibiotic degradation, antimicrobial resistant organisms and antibiotic resistant genes.


Chow, L., L. Waldron and M.R. Gillings. 2015. Potential impacts of aquatic pollutants: sub-clinical antibiotic concentrations induce genome changes and promote antibiotic resistance. Frontiers in Microbiology August 5, 2015 doi: 10.3389/fmicb.2015.00803.

Cogliani, C., H. Goossens and C. Greko. 2011. Restricting Antimicrobial Use in Food Animals: Lessons from Europe. Microbe 6: 274-279.

Dolliver, H., K. Kumar and S. Gupta. 2007. Sulfamethazine uptake by plants from manure amended soil. Journal of Environmental Quality 36: 1224-1230.

Garder, J.L., M.L. Soupir adn T.B. Moorman. 2012. Occurrence and movement of antibiotic resistant bacteria, in tile drained agricultural fields receiving swine manure. ASABE Annual International Meeting, Dallas, Tx.

Graham, J.P., L.B. Price, S.L. Evans, T.K. Graczyk, and E.K. Silbergeld. 2009. Antibiotic resistant enterococci and staphylococci isolated from flies collected near confined poultry feeding operations. Science of the Total Environment 407: 2701-2710.

Holvoet, K., I. Sampers, B. Callens, J. Dewulf and M. Uyttendaele. 2013. Moderate prevalence of antimicrobial resistance in Escherichia coli isolates from lettuce, irrigation water and soil. Applied and Environmental Microbiology 79: 6677-6683.

Hughes D. Selection of resistance by very low levels of antibiotics. Presented at: AAAS Annual Meeting; Feb. 12-16, 2015; San Jose, California. Sourced at

Joy, S.R., S.L. Bartelt-Hunt, D.D. Snow, J.E. Gilley, B.L. Woodbury, D.B. Parker, D.B. Marx and X Li. 2013. Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure. Environmental Science and Technology 47: 12081-12088.

Kang, D.H., S. Gupta, C. Rosen, V Fritz, A. Singh, Y. Chander, H. Murray and C. Rohwer. 2013. Antibiotic uptake by vegetable crops from manure-applied soils. Journal of Agriculture and Food Chemistry 61: 9992-10001.

Krapac, I.G., S. Koike, M.T. Meyer, D.D. Snow, S.F.J. Chou, R.I. Mackie, W.R. Roy and J.C. Chee-Sanford. 2004. Long term monitoring of the occurrence of antibiotics residues and antibiotic resistance genes in groundwater near swine containment facilities. in Proceedings of the 4rth International conference on pharmaceuticals and endocrine disrupting chemicals in water, Minneapolis, Minn., National Groundwater Association, October 13-15, 2004.

Kumar, K., S.C. Gupta, Y. Chander and A.K. Singh. 2005. Antibiotic use in agriculture and its impact on the terrestrial environment. Advances in Agronomy 87: 1-54.

Laube, H., A. Friese, C. von Salviati, B. Guerra and U. Rosler. 2014. Transmission of ESBL/Amp C-producing Escherichia coli from broiler chicken farms to surrounding areas. Veterinary Microbiology 172: 519-527.

Levy, S. 2014. Reduced antibiotic use in livestock: How Denmark tackled resistance. Environmental Health Perspectives Vol 122: A161-165.

Luby, E.M. 2014. Fate and transport of antibiotic resistant bacteria and resistance genes in artificially drained agricultural fields receiving swine manure application. MSc thesis. Iowa State University.

Marti, R., A. Scott, Y-C Tien, R. Murray, L. Sabourin, Y. Zhang and E. Topp. 2013. Impact of manure fertilization on the abundance of antibiotic resistant bacteria and frequency of detection of antibiotic resistance genes in soil and on vegetables at harvest. Applied and Environmental Microbiology 79: 5701-5709.

Marti, R., Y-C. Tien, R. Murray, A. Scott, L. Sabourin and E. Topp,  2014. Safely coupling livestock and crop production systems: how rapidly to antibiotic resistance genes dissipate in soil following a commercial application of swine or dairy manure? Applied and Environmental Microbiology 80: 3258-3265.

McEachran, A.D., B.R. Blackwell, J.D. Hanson, K.J. Wooten, G.D. Mayor, S.B. Cox and P.N. Smith. 2015. Antibiotics, bacteria and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter. Environmental Health Perspectives

Munir, M. and I. Xagoraraki. 2011. Levels of antibiotic resistance genes in manure, biosolids, and fertilized soil. Journal of Environmental Quality 40: 248-255.

Popowska, M., M. Rzeczycka, A. Miernik, A. Krawczyk-Balska, F. Walsh and B. Duffy. 2012. Influence of soil use on prevalence of tetracycline, streptomycin and erythromycin resistance and associated resistance genes. Antimicrob. Agents Chemother. 56: 1434-1443.

Seo., Y., B. Cho, A. Kang, B. Jeong and Y-S Jung. 2013. Antibiotic uptake by plants from soil applied with antibiotic treated manure. Korean J. Soil Sci. Fert. 43:

You, Y., M. Hilpert, and M.J. Ward. 2012. Detection of a common and persistent tet(L) – carrying plasmid in chicken-waste-impacted farm soil. Appl.Environ. Microb. 78: 3203–3213. doi:10.1128/AEM.07763-11

You, Y., and E.K. Silbergeld. 2014. Learning from agriculture: understanding low dose antimicrobials as drivers of resistome expansion. Frontiers in Microbiology Volume 5, Article 284.

Pathways of antibiotics, and antimicrobial resistance genes and organisms from manure to soil

In response to the increasing human health concerns regarding antimicrobial resistance, it is helpful to understand that there is a large reservoir of beneficial microbes in a healthy soil containing active organic matter is crucial in reducing the potential harm resulting from antimicrobial use in humans and animals.

In order to understand the risks, and the important role of the soil organic matter, we need to understand some of the important pathways of antibiotics, antibiotic resistant organisms, and antibiotic resistant genes. The graphic below provides a summary of the products excreted with manure that are important in our discussions of antimicrobial resistance. It also illustrates the importance of soil organic matter in managing antimicrobial resistance resulting from animal manure. We will work through literature research documenting each of the pathways and their significance.

Pathways of antimicrobial resistant microbes, genes, and antimicrobial residue from animal manure into the environment.

Pathways of antimicrobial resistant microbes, genes, and antimicrobial residue from animal manure into the environment.

There are three potential streams of concern related to antibiotic use in agriculture and specifically manure management.

1. animals excrete antibiotics or their metabolites that may favor selection of antibiotic resistant organisms in the soil or receiving environment.

2. manure may contain potentially pathogenic organisms that are resistant to antibiotics.

3. manure may contain antibiotic resistant genes, which may be transferred to other organisms in the receiving environment.

Manure also contains readily available carbon that stimulates microbial activity in soil. We think that this is a good thing in terms of maintaining a healthy soil, but we also need to understand the dynamics of antimicrobial resistance in the soil microbial population.

Manure may contain antibiotic residue

Livestock excrete 17-90% of antibiotics into the urine or feces, either unchanged or as an active metabolite (Masse et al. 2014). In a review, EPA (2013) reported that up to 80% of tetracyclines fed to swine and poultry was excreted in the manure. They reported that up to 67% of tylosin was excreted from animals used for food production.

Masse et al. (2014) suggested that: “most of the antibiotic residues in manure form complexes with soluble organics and remain stable during manure storage.”

Furtula et al. (2010) found that antibiotics present in poultry litter on nine commercial farms in BC reflected the antibiotics in the feed. Ratsak et al. (2013) reported measured for tetracyclines, sulfonamides and fluoroquinolones in 69 manure and digestate samples in Germany. They observed that 62% of the manure samples and 80% of the digestate samples contained antibiotics. They found that pig and poultry manure contained more antibiotics than cattle manure. Zhang et al. (2015) measured the presence of seven antibiotics in pig manure in China.

It is important to note that antibiotic residue in manure decomposes likely due to the significant microbial population in manure. Joy et al. (2014) observed that the half-lives of three antimicrobials used in hog production (bacitracin, chlorotetracycline and tylosin) ranged from 1 to 10 days. Masse et al. (2014) also included a review of the persistence and biological decomposition of antibiotics in manure and soil.

Manure may contain antibiotic resistant genes

In the Fraser Valley of British Columbia, Keen (2009) measured four tetracycline resistance genes in poultry manure during storage and following field application. The resistance genes were present even though the potentially pathogenic bacteria were no longer viable. Diarrassouba (2008) found antibiotic resistant and virulence genes in E. coli and salmonella isolated from nine commercial poultry broiler farms in BC. He et al. (2014) found resistance genes in poultry litter for chloramphenicols, sulfonamides, and tetracyclines in 11 broiler operations.

Zhang et al. (2015) found 10 antibiotic resistant genes in swine manure and concluded that chlorotetracycline demonstrated the highest ecological risk. Whichmann et al. (2014) identified 80 antibiotic resistant genes in cow manure from five different cows with or without a history of antibiotic use in the US, but found that cow manure carried a lower frequency of resistance genes than poultry litter. Brooks, et al. (2014) found antibiotic resistance to Salmonella and Campylobacter spp in the manure lagoon from all 37 swine manure farms tested in the US.

Not all of the antimicrobial resistant genes are found in potentially harmful bacteria. Nandi et al. (2004) reported that antimicrobial resistant genes were found in Gram positive bacteria that constituted > 85% of the microbes in poultry litter and concluded that the antimicrobial resistance genes appear to move relatively freely among the microbial population.

Manure may contain potentially harmful antibiotic resistant microbes

In a survey of dairy cattle manure from 23 farms, Sawant et al. (2009) found that E. coli isolates were resistant to ampicillin (48%), ceftiofur (11%), chloramphenicol (20%), florfenicol (78%), spectinomycin (18%), and tetracycline (93%). They found multidrug resistance in 40% of the E.coli from healthy lactating dairy cattle.

Poultry manure was reported to contain Salmonella, E. coli and Enteroccoccus sp. that were resistant to both oxytetracycline and tetracycline (Keen 2009). It was noted that the viability of these organisms decreased during the manure storage/composting period before field application. Diarrassouba et al. (2007) found that 70% of the E. coli isolates and 14% of Salmonella isolates in the manure from nine different broiler chicken farms in the Fraser Valley of BC were multiresistant to at least nine antibiotics.   In the same study, Diarrassouba (2008) found that all of the E. coli strains isolated on the farms were resistant to penicillin, erythromycin, tylosin, clindamycin and novobiocin, and that although tetracycline is not used as a growth promoter in Canada, 74% of the E.coli were tetracycline resistant. She also found multiresistance in some of the Salmonella isolates. She concluded that:

“antibiotic resistant Salmonella carrying virulence genes can be isolated from healthy commercial broiler chickens fecal samples and letter, suggesting the potential to contaminate the environment including crops and runoff water, if litter is applied to soil as a fertilizer”

Gao et al. (2015) concluded that antibiotic resistant (extended spectrum beta-lactamase, or ESBL) E. coli contained in swine manure was the likely contributor to antibiotic resistant gene spread in the soil.  Laube et al. (2014)  measured antibiotic resistant (ESBL) E. coli in the manure and surrounding air from seven poultry broiler farms in Germany. Hartmann et al. (2012) reported ESBL producing E. coli in cattle feces during a survey of 182 farms in Burgundy, France.

Antimicrobial Genes are Everywhere 

An important fact to note is that antimicrobial genes are everywhere in nature and have been for much longer than the commercial development of antibiotics (Davies and Davies 2010). Davies and Davies (2010) also speculated whether some of these antimicrobial resistant genes have other important functions that we may not yet be aware of. Clemente et al. (2015) found antibiotic resistance genes in an isolated South American tribe with no known contact for more than 11,000 years.

Knapp et al. (2009) measured antibiotic resistant genes in soil samples that had been archived since 1940 from several experimental sites in the Netherlands. They found that the concentration of antibiotic resistant genes increased in all 18 genes studied, and that some antibiotic resistant gene concentrations increased 15 fold since 1940, likely due to increased commercial antibiotic use.

Popowska et al (2012) observed significant amounts of antimicrobial resistant genes in forest soil, compost, garden soil and farm soil. They observed that agricultural soils had a more diverse population of bacteria containing resistance genes. The composted and forest soils had lower levels of antibiotic resistance, and a lower presence of antibiotic resistant genes.

Keen (2009) measured tetracycline resistant genes in a forest soil that had not been fertilized with manure, as well as in the water from a mountain stream in the Lower Fraser Valley in British Columbia.

Manure application may stimulate growth of antibiotic resistant organisms in soil.

Udikovic-Kolic et al. (2014) found more B-lactam antibiotic resistant bacteria in soil (7.4%) than in manure (0.67%) from cows that had not been fed antibiotics. They observed higher populations of cephalothin-resistant bacteria in soil following manure application for the duration of the 94 day study. Marti et al. (2014) measured increased frequencies of antimicrobial resistance genes in soil following application of swine or dairy manure. Animal manure contains significant concentrations of readily available carbon which increases the microbial biomass population in soil (Paul and Beauchamp 1996), which are then likely to increase the number of antibiotic resistant genes in the soil.


Animal manure and how we manage it has an important impact on human health risk associated with antimicrobial resistance. You and Silbergeld (2014) summarized the concerns as follows:

“This waste contains complex constituents that are challenging to treat, including AMR determinants and low-dose antimicrobials. Unconfined storage or land deposition of a large volume of animal waste causes its wide contact with the environment and drives the expansion of the environmental resistome through mobilome facilitated horizontal genet transfer. The expanded environmental resistome, which encompasses both natural constituents and anthropogenic inputs, can persist under multiple stressors from agriculture and may re-enter humans, thus posing a public health risk to humans”.

When we add manure to our soil, our soil acts both as a reservoir for antimicrobial resistance as well as a purifier that destroys antimicrobial resistance organisms, and genes. We will explore the microbes and the soil further.


Brooks, J.P. A. Adeli, and M.R. McLaughlin. 2014. Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems. Water Research 57: 96-103.

Clemente, J.C., E.C. Pehrsson, M.J. Blaser, K. Sandhu, Z. Gao, B.Wang, M. Magris, G. Hidalgo, M. Contreras, O. Noya Alarcon, O. Lander, J. McDonald, M. Cox, J. Walter, P.L. Oh, J.F. Ruiz, S. Rodriguez, N. Shen, S.J. Song, J. Metcalf, R. Knight, G. Dantas and M.G. Dominguez-Bello. 2015. The microbiome of uncontacted Amerindians. Science Advances 2015;1:e1500183.

Davies, J. and D. Davies. 2010. Origins and evolution of antibiotic resistance. Microbiology and Molecular Biology Reviews 74: 417-433.

Diarrassouba. 2008. Impact of antimicrobial growth promoters used in broiler chicken production on the emergence of antibiotic resistance in commensal E. coli and Salmonella. MSc. thesis. University of British Columbia.

Diarrassouba, F. M.S. Diarra, S.J. Bach, P.J. Pritchard, E. Topp and B.J. Skura. 2007. Antibiotic resistance and virulence genes in commensal Escherichia coli and salmonella isolates from commercial broiler chicken farms. Journal of Food Protection 70: 1316-1327.

EPA 2013. Literature Review of Contaminants in Livestock and Poultry Manure and Implications for Water Quality. Office of Water (4304T) EPA 820-R-13-002 July 2013

Furtula, V., E.G. Farrell, F. Diarrassouba, H. Rempel, J. Pritchard and M.S. Diarra. 2010. Veterinary pharmaceuticals and antibiotic resistance of Escherichia coli isolates in poultry litter from commercial farms and controlled feeding trials. Poultry Science 89: 180-188.

Gao, L, J. Hu., X. Zhang, L. Wei, S. Li, Z. Miao, and T. Chai. 2015. Application of swine manure on agricultural fields contributes to extended spectrum B-lactamase-producing Esherichia coli spread in Tai’an, China. Frontiers in Microbiology. April 2015, Volume 6, Article 313.

Hartmann, A., A. Locatelli, L. Amoureux, G. Depret, C. Jolivet and E. Gueneau. 2012. Occurrence of CTX-M producing Escherichia coli in soils, cattle, and farm environment in France (Burgundy region). Frontiers in Microbiology Volume 3 Article 83.  doi: 10.3389/fmicb.2012.00083

He, L-Y., Y-S. Liu, H-C Su, J-L. Zhao, S-S Liu, J. Chen, W-R Liu and G-G Ying. 2014. Dissemination of antibiotic resistance genes in representative broiler feedlots environments: Identification of indicator ARGs and correlations with environmental variables. Environmental Science and Technology 48: 13120-13129

Joy, S.R., X. Li, D.D. Snow, J.E. Gilley, B. Woodbury, and S.L. Bartelt-Hunt. 2014. Fate of antimicrobials and antimicrobial resistance genes in simulated swine manure storage. Science of the Total Environment 481: 69-74.

Keen, P.L. 2009. Seasonal Dynamics of Tetracycline Resistant Genes and Antibiotics in a British Columbia Agricultural Watershed. PhD Thesis, University of British Columbia.

Knapp, C.W., J. Dolfing, P.A.I. Ehlert and D.W. Graham. 2009. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environmental Science and Technology 44: 580-587.

Laube, H., A. Friese, C. von Salviati, B. Guerra and U. Rosler. 2014. Transmission of ESBL/Amp C-producing Escherichia coli from broiler chicken farms to surrounding areas. Veterinary Microbiology 172: 519-527.

Marti, R. Y-C Tien, R. Murray, A Scot, L. Sabourin and E. Topp. 2014. Safely coupling livestock and crop production systems: how rapidly do antibiotic resistance genes dissipate in soil following a commercial application of swine or dairy manure? Applied and Environmental Microbiology 80: 3258-3265.

Masse, D.I., N.M. Cata Saady and Y. Gilbert. 2014. Potential of biological processes to eliminate antibiotics in livestock manure: an overview. Animals 2014, 4, 146-163.

Munir, M., and I. Xagoraraki. 2011. Levels of antibiotic resistance genes in manure, biosolids and fertilized soil. Journal of Environmental Quality 40: 248-255.

Nandi, S., J.J. Maurer, C. Hofacre and A.O. Summers. 2004. Gram positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter. PNAS www.pnas.orgcgidoi10.1073pnas.0306466101

Paul, J.W. and E.G. Beauchamp. 1996. Soil microbial biomass C, N mineralization, and N uptake by corn in dairy cattle slurry- and urea-amended soils. Canadian Journal of Soil Science 76: 469-472.

Popowska, M., M. Rzeczycka, A. Miernik, A. Krawcyk-Balska, F. Walsh and B. Duffy. 2012. Influence of soil use on prevalence of tetracycline, streptomycin, and erythromycin resistance and associated resistance genes. March 2012 Vol. 56. No 3.

Ratsak, C., B. Guhl, S. Zuhlke and T. Delschen. 2013. Veterinary antibiotic residues in manure and digestates in Northrhein-Westfalia. Environmental Sciences Europe 2013, 25:7.

Udikovic-Kolic, N., F. Wichmann, N.A. Broderick and J. Handelsman. 2014. Bloom of resident antibiotic resistant bacteria in soil following manure fertilization. Proceedings of the National Academy of Sciences Vol 111. No. 42. pp 15202-15207.

Whichmann, F., N. Udikovic-Kolic, S. Andrew and J. Handelsman. 2014. Diverse antibiotic resistant genes in dairy cow manure. mBio Volume 5 Issue 2, e01017-13.

You, Y. and E.K. Silbergeld. 2014. Learning from agriculture: understanding low dose antimicrobials as drivers of resistome expansion. Frontiers in Microbiology June 2014, Volume 5, Article 284.

Zhang, S., J. Gu, C. Wang, P. Wang, A. Jiao, Z.L. He and B. Han. 2015. Characterization of antibiotics and antibiotic resistance genes on an ecological farm system. Journal of Chemistry Article ID 526143.