Microbes and Methane
by Roberto
The three greenhouse gases that contribute most to global warming are carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). There is, of course, an urgent need to reduce the emissions of all. However, two facts point to methane emission reduction as the most impactful in the near term. First, its half-life in the atmosphere (7−12 years) is much shorter than that of CO2, which can persist for hundreds of years. Second, because of its inherent physical-chemical properties, methane's global warming potential per unit mass is 80 times greater than that of CO2. Because microbes are involved in methane production (methanogens) and consumption (methanotrophs), microbiology will undoubtedly play a huge role in methane emission mitigation. I say, we need to know as much as possible about microbes and methane.
Fig. 1. The global methane budget for year 2017 based on top-down methods for natural sources and sinks (green), anthropogenic sources (orange), and mixed natural and anthropogenic sources (hatched orange-green for 'biomass and biofuel burning'). Source. Frontispiece: from the cover of AAM report. Source
If you're looking for a primer on microbes and methane (as was I, recently) I direct you to a timely report from an American Academy of Microbiology (AAM) colloquium on the subject. It's excellent reading as it contains a treasure trove of information along with an impressive list of references, for those who want to take a deeper dive into the subject. What are the main sources of methane emissions? Large amounts of methane are released from the fossil fuel industry and sadly, they mostly come from "super-emitter events," the result of equipment failures. But in contrast to CO2 emissions, which come overwhelmingly from burning fossil fuels, agriculture and waste are the major sources of atmospheric methane. The AAM report focuses on four methane sources where the authors saw the greatest potential for mitigation in the short term: enteric fermentation in ruminants, animal wastes, rice paddies, and landfills. For each of these, the report outlines what is known about the microbes and microbial activities and which knowledge gaps need to be addressed. These are followed by descriptions of possible mitigation strategies. It is encouraging to know that, even with our still incomplete knowledge of the microbial activities involved, experts foresee ways in which microbes could be used to reduce methane emissions reasonably quickly. For any microbiologist wishing to embark in climate change research that might make a difference in the short term, this report may be more than just informative. It might lead to major changes in their research. I see plenty of opportunities in this arena.
Fig.2. Conceptual model of electrogenic sulfur oxidation in aquatic sediments by cable bacteria. Source
Here's one example of where fundamental microbiology has led to a possible methane-reducing approach in rice cultivation. Rice is not only a very water-intensive crop; growing it also releases a lot of methane. This is because the water that normally covers the planting areas in traditional rice paddies prevents oxygen from getting into the soil, rendering it anoxic. Consequently, methanogenic archaea use the products of organic matter decomposition – mainly in the form of acetate and hydrogen – to make copious amounts of methane that then seeps into the atmosphere. These methanogens do very well in the anoxic subsoil where they are the most efficient users of acetate and hydrogen. There are plenty of possible competitors present in those soils, but they do not have the substrate they need for energy generation. Sulfate reducers are one class of such competitors. Therefore, the addition of sulfate to rice paddies indeed allows the growth of sulfate reducers. As they easily outcompete methanogens, methane production is greatly decreased. The problem is that added sulfate does not last long as it is reduced to sulfide. Is there a way to cycle sulfide back to sulfate in the anoxic soil? Yes, there is. A recent paper shows that the simple addition of some very special bacteria can lead to over 90% reduction in methane emissions from rice cultivation. Who are these bacteria? The cable bacteria, described in a 2013 STC post. These Gram-negative bacteria grow as very long filaments, in the scale of several centimeters. Individual cells are still only a few microns each and bounded by their inner membrane and cell wall. But their outer membrane is continuous along the filament. These bacterial filaments can transfer electrons over centimeter distances, from sulfide oxidation at one end to oxygen reduction at the other end (Fig. 2.). In this manner cable bacteria couple the production of sulfate in the anoxic soil with oxygen respiration in the oxic region. This is but one example of the many ways in which knowledge of microbiology might be used in the future to reduce methane emissions that result from intensive agriculture.
What do the authors of this report think are the mitigation strategies that might have the most impact in the near future? In each of the areas they cover, this is what they recommend:
Enteric Fermentation in Ruminants. Enteric fermentation accounts for a quarter of anthropogenic CH4 emissions. Greater knowledge of the relationships among microbial species in the rumen microbiome will be necessary to advancing methanogen inhibitors, adjusting ruminant feedstocks, and developing vaccines against rumen methanogens.
Animal Wastes. Over 10% of agricultural CH4 emissions comes from animal wastes and manure management. A better understanding of the manure and soil microbiome from field experiments and modeling studies will be imperative for optimizing microbial communities to reduce CH4 emissions.
Rice Production. As one of the top global food staples, holistic research on the soil microbiome in relationship with the rice plant will be key to implementing the application of microbial inoculants (such as cable bacteria), managing alternate wetting and drying strategies, and co-culturing of rice and aquatic animals and alternative substrates to outcompete methanogenesis in rice paddies.
Landfills. Landfills are the third-largest source of human-related CH4 emissions in the U.S. Expanded characterization of landfill microbiome community structure and function, especially with regard to plants in phytocovers, will be important when optimizing landfill covers that effectively lower CH4 emissions. Additionally, microbial conversion of landfill gas into valuable products will create financial incentives needed to increase research and development on microbial solutions to address CH4.
We face extreme challenges when it comes to greenhouse gas emissions. But challenges always bring up opportunities. One thing is clear from this list of recommendations, there is no lack of opportunity for innovative microbiologists to contribute to reducing methane emissions!
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