Increased levels of methane, a potent greenhouse gas, are a main driver of climate change. Methane’s warming power is ~80 times stronger than carbon dioxide over a 20 year period, which makes the reduction of methane an effective way to slow greenhouse warming in the near term. As microbes are major contributors to methane levels, microbiologists can play a significant role in developing microbial innovations to combat rising methane emissions. To understand the current state of science and knowledge gaps, the American Academy of Microbiology (Academy) and the American Geophysical Union (AGU) held a colloquium on The Role of Microbes in Mediating Methane Emissions. Experts outlined a research roadmap for how to use microbes to combat increasing methane emissions and encourage research for 4 main sectors.

  1. Enteric Fermentation in Ruminants
  2. Enteric Fermentation in Ruminants

    Ruminant animals have a unique digestive system that includes a large fermentation compartment, known as the rumen, where a diverse population of microbes convert plant matter to fatty acids that provide energy for the host ruminant. Anaerobic archaea known as methanogens also consume these fatty acids to regenerate electron carriers for fermenting microbes and, in the process, produce methane. 

    More than 50% of methane emissions results from agricultural practices, such as raising livestock, with most of this methane generated by the enteric rumen microbiome. In the U.S., 25% of all anthropogenic methane comes from enteric fermentation. Since the 1890s, methane emissions from ruminants increased over 300%. Thus, effective strategies to reduce methane emissions from ruminant livestock are needed to cut global methane levels.  

    First-Order Priorities
    • Launch more academic training programs in anaerobic microbiology and physiology to increase the number of scientists skilled in isolating and characterizing methanogens.  
    • Establish rumen microbiome collection repositories to support the rumen research community. 
    • Develop genetic tools and non-model organisms to facilitate work with unique microbes found in the rumen. 
    • Design transdisciplinary research consortiums for a holistic characterization of the rumen microbiome and methanogen inhibitors.
    • Expand research about dietary additives and probiotics to reduce methane emissions, including research on directing the energy away from methanogenesis and into alternative, energetically favorable electron sinks. 
    • Invest in design of vaccines against rumen methanogens or protozoa. 

    Major Knowledge Gaps
    • Distribution of and relationship among rumen bacteria, protozoa, fungi, viruses and archaeal methanogens. 
    • How the rumen microbiome comprehensively responds to feed additives that inhibit methanogenesis. 
    • Effects of ruminant type (dairy, beef) and animal genetics on the rumen microbiome.  

    Current Technologies

  3. Enteric Fermentation in Ruminants
  4. Animal Wastes and Manure Management
  5. Animal Wastes and Manure Management

    Manure includes both dung and urine produced by livestock. Manure management refers to all activities used to handle, store and dispose of feces and urine from livestock. When manure is stored or treated in anaerobic conditions, microbes can produce methane by degrading organic matter found in manure. Manure management contributes about 10% of agricultural methane. Livestock farming is projected to increase worldwide, leading to increased amounts of animal wastes and methane emissions. Therefore, microbial innovations can be develped to mediate emissions from landfills.

    First-Order Priorities
    • Increase research on the influence of rumen fermentation management on subsequent manure land applications to optimize composting and anaerobic digestion strategies. 
    • Develop models to look at manure management practices and outcomes to optimize the approach for each area. 
    • Expand research on manure treatment, such as acidification or methanotroph inoculation, and how those treatments impact the manure microbiome with regard to methane and nitrous oxide emissions. 
    • Increase field-based studies from more diverse locations to understand the viability of sustainable practices in low-income areas and inform global climate-smart practices. This will require collaboration of scientists and local farmers. 
    • Standardize guidelines about manure production and application to foster sustainability and minimize methane and nitrous oxide emissions, such as diverting manure from anaerobic lagoons to composting sites.  

    Major Knowledge Gaps
    • Holistic life cycle perspective of methane and nitrous oxide emissions from solid waste composting and its ensuing soil application. 
    • How rumen fermentation management impacts subsequent manure methane emissions.  
    • Effect of inoculating manure storage with methanotrophs, and/or prebiotic additions to enrich for desirable methanotrophs, on reducing overall methane emissions. 

    Current Technologies
    • Composing and directing manure away from storage lagoons can reduce overall methane emissions, but infrastructure, investment and lack of research on its applicability across diverse climatic and socio-economic contexts is a major challenge. 
    • Acidification of manure can decrease emissions from slurry ponds, although it may increase emissions of nitrous oxide. 
    • Anaerobic digestion by microbes converts manure into biogases that can be used for energy, though high costs of investment pose a barrier to widespread adoption. 

  6. Animal Wastes and Manure Management
  7. Rice Farming
  8. Rice Farming

    Rice is a semi-aquatic plant that must be flooded for optimal crop production. Methanogenic archaea found in wetlands and flooded rice paddy fields produce methane by anaerobic degradation of organic matter. Rice production accounts for over 10% of global methane emissions. Rice is a staple food and critical source of calories and nutrients for more than half the world’s population. Global rice production has increased more than 300% from 1961. Rice will be an important crop to meet the nutritional needs of an expanding global population, making climate-smart and sustainable rice production practices necessary to reduce greenhouse gas emissions.

    First-Order Priorities
    • Comprehensive investigations, encompassing entire ecosystems and involving multiple kingdoms, to gain a deeper understanding of carbon cycling within rice paddies. This includes understanding the interactions between rice plants, prokaryotes and eukaryotes, such as fungi and protozoa.   
    • Research and design of alternative substrates (i.e., iron) or addition of microbial inoculants to promote the growth of microorganisms that outcompete methanogens. For example, adding filamentous cable bacteria to rice paddy fields decreased methane emissions by 93%
    • Develop user-friendly and scalable methane flux measurement equipment for continuous monitoring of intervention. The effectiveness of such strategies will require partnerships with farmers and industry.  
    • Expand rice plant breeding programs to increase availability of low-methane emitting cultivars, which will also involve cooperation of farmers and researchers. 
    • Adopt optimized water management practices, such as alternating wet-dry irrigation. 

    Major Knowledge Gaps
    • Complete relationship among rice microbial community members and nutrient cycling. This includes more research on syntrophic fermenters and their methanogenic partners, iron and sulfur reducers that compete with methanogens for acetate and H2, and microbes involved in anaerobic methane oxidization. 
    • How rice plants recruit specific microbial communities to inform rice breeds that promote methanotrophy. 
    • Effect of cultivar breeding on rice plant production and greenhouse gas emissions. 

    Current Technologies

  9. Rice Production
  10. Landfills
  11. Landfills

    Landfills are highly engineered sites to store and surround waste with impermeable liners that reduce environmental harm. Microbes naturally found in the waste and soil of landfills break down the biodegradable waste and generate high amounts of methane and carbon dioxide gases in the process. In fact, landfills are the third largest source of anthropogenic methane emissions in the U.S. People produce more trash now than ever, with global waste expected to increase with an increasing global population. Landfills, and their greenhouse gas emissions, will need to grow to meet future trash levels, making microbial solutions in landfills critical to reduce emissions.  

    First-Order Priorities
    • Increased research into microbial community composition and activity within landfills to understand and control methane production and consumption.  
    • Studies that explicitly consider microbe-microbe and plant-microbe interactions that either inhibit methanogenesis and/or enhance methanotrophy to inform mitigation strategies. 
    • More research and use of landfill covers, such as biocovers, biofilters or biowindows
    • Optimized methods for measuring landfill methane emissions, such as using satellite monitoring.  
    • Expanded installation of gas collection infrastructure in all new landfills to improve efficiency of methanotrophs. 

    Major Knowledge Gaps
    • More detailed analyses of methanotrophic, methanogenic and fermentative populations found in landfills. 
    • More accurate estimates of methane emissions from landfills and effectiveness of mitigation strategies.  
    • Soil-microclimate controls on methanotrophy in wider range and diversity of microclimates. 
    • Anaerobic methane oxidation (AOM) populations in landfills and the extent to which this process occurs in cover soils to inform approaches to exploit AOM to reduce methane fluxes. 

    Current Technologies
    • Diverting organic materials from landfills to compost is effective at limiting greenhouse gas emissions, but lack of information on composting scalability and applicability across diverse climatic and socio-economic contexts limits wider spread use.
    • Covers made of porous and organic layers to oxidize methane, known as biocovers or biofilters, can be added to landfills to reduce methane emissions, but they are costly and commercial use is limited.
    • Some methane produced in landfills can be a source of renewable energy known as biogas. However, if concentrations are too low to make it economically feasible to capture and use, the biogas is burned off. 


  12. Landfills