Impact of methanotrophs, methanogens and geochemical conditions on net methane flux to the atmosphere from Arctic soils

Lead Research Organisation: Newcastle University
Department Name: Civil Engineering and Geosciences


On a global scale, soils contain more carbon than all vegetation and atmospheric sinks combined. However, this stored carbon is not permanently retained and can be readily released back to the atmosphere by biological and non-biological mechanisms (a process known as flux). In soil systems, microbial communities are the primary recyclers of carbon, including the conversion of soil carbon to gases, such as methane (CH4). This conversion is critical because CH4 is the second most significant greenhouse gas and has been rising in the atmosphere over the past forty years. Unfortunately, rates of CH4 release from Arctic soils appear to be increasing, which is significant because Arctic processes are responsible for > 25% of atmospheric CH4. As such, an urgent need exists to understand and quantify factors and mechanisms that influence Arctic CH4 flux, which will allow us to better predict climate conditions in the future.

As background, we quantified CH4 flux at 13 differing high Arctic sites near Ny-Alesund, Svalbard in 2010 in conjunction with the measurement of 58 geochemical and biological parameters in near-surface soils (work focused on the anaerobic-aerobic interface). However, statistical analyses showed only weak correlations among key near-surface microbial groups (i.e., methane-consuming methanotrophs and methane-producing methanogens), geochemical conditions, and detected CH4 flux. In fact, data suggest that phenomena deeper in the soil profile, including deep methanogenesis and gas and carbon releases from melting permafrost, may be more critical than previously thought to net CH4 release from Arctic soils. We now hypothesize that factors such as the depth of the biologically active zone (BAZ) above the permafrost; non-biological permafrost contributions; and the proportional thickness of anaerobic vs. aerobic soil layers may dominate observed CH4 release rates. Specifically, if the BAZ is deep and the anaerobic layer thick relative to the oxic layer, CH4 production will overwhelm CH4 consumption, resulting in elevated CH4 flux to the atmosphere.

In this project, we will test this alternate hypothesis via the following activities:

1. Return to Ny-Ålesund in late summer 2012 to core into and below the BAZ at specific sites with known and contrasting CH4 fluxes. Within these cores, we will quantify absolute methanogen and methanotroph abundances versus depth at each site; determine associated geochemical conditions, CH4 and oxygen profiles, permafrost depths, and permafrost CH4 and carbon content; and measure CH4 flux to correlate soil and permafrost conditions with CH4 released to atmosphere at each site;

2. Statistically compare estimated biological vs. non-biological contributors to the CH4 balance at each site, including the influence of permafrost CH4 and carbon releases associated with melting;

3. Extend local CH4 flux estimates to landscape levels around Ny-Ålesund by measuring CH4 flux at proximal sites radiating away from cored sites to more accurately estimate the relative contributions of different types of landscapes to regional CH4 flux; and

4. Sustain a successful international collaboration with a USA researcher examining methanotroph-methanogen relationships in the Arctic to increase the capacity of current and future work.

The above activities will be fulfilled via an eight-month research plan, including 10 days based at the NERC Arctic Research Station in Ny-Ålesund. Work will be performed in the late summer, which is the period of maximum permafrost thaw, and also a time when the NERC field station tends to be underutilized. A central non-technical goal of this effort will be to gain enough data to support a larger proposal aimed at EU and other international funding agencies.

Planned Impact

This project will be of primary importance to researchers studying biogeochemical cycles and climate change. However, underlying discoveries also will be of immediate value to:

1. Environmental regulators responsible for reducing carbon footprints;

2. Industrial biotechnologists that use methane cycle organisms for bioremediation and chemical biosynthesis;

3. Biochemists and medical researchers interested in biomolecules like methanobactin; and

4. The oil industry that uses related biomarkers in environmental management and bioprospecting.

Links already exist between CIs and groups involved with all of these fields, which will be promoted via activity and interactions within this project and the development of a new webpage aimed at disseminating research on methanogen-methanotroph ecology. Specific impacts are as follows.

A top priority at Defra, the Environment Agency, and the Department of Energy and Climate Change is to develop a better understanding of how different landscapes affect greenhouse gas flux to the atmosphere (see Although Arctic landscapes superficially differ from UK landscapes, the biological drivers of methane flux are similar. Therefore, any discoveries here will directly answer landscape management questions within the UK. Fortunately, our group has two guest staff members linked with Environment Agency and Defra (Drs Sean Burke and Hugh Potter), who can provide direct links for our results to policymakers at the two agencies.

A deeper understanding of methanogen-methanotroph ecology, which will be gained here, has growing importance to industrial biotechnology and the oil industry. Many new technologies are being developed that require either methane (CH4) or carbon dioxide as the carbon source, such as protein synthesis and biofuel manufacture. As such, factors that affect community selection and function will have direct value to such technologies. Further, methanotrophs and methanogens have unique molecular and chemical signatures, which are now being used for environmental management and prospecting in the oil industry. The CIs already have close associations with companies that use microbial community engineering in product development (Archventure Corporation) and bioprospecting (Envirogene), respectively, which provide immediate opportunity for commercial translation of research results. Finally, Graham's work with methanotrophs and methanobactin (mb) continues to impact medical applications related to copper transport. As examples, mb has been used as a model compound for understanding copper homeostasis in respiratory systems; synthetic analogues have been tested for copper-chelation therapy in patients with copper toxicity or deficiency diseases; and mb has been assessed as a blocking agent for patients with Alzheimer's disease. These extensions will continue as new discoveries are made.

Although results will be reported in high-impact journals and via presentations, CIs also will target new results to the popular media and literature. The CIs all have been interviewed by local (Metro Radio - Newcastle), national (BBC4) and international media sources (NPR in the US, CBC in Canada), which recently continued on 360o, the pre-eminent science news magazine show on TV2 in Switzerland. Further, the PI's work has been included in Discover and Scientific American magazines, and a simplified version of his antibiotic resistance work is included in a new children's book on science. Given this track record, we expect high educational and public interest from this current project. Impact success will be monitored against the following milestones: (1) closer engagement with environment agencies to tailor future regulatory needs; (2) presentation of findings to regulators and educators in non-university settings, including via the new webpage; and (3) increased public engagement through popular articles and local presentations.


10 25 50
Description Results from this project include:

1. The depth of thaw in 2013 was almost 0.5 m deeper than at the same sites in 2010, which resulted in problems with our permafrost coring equipment.

2. 2010 and 2013 data were combined, which resulted in two manuscripts, which shows that both microbial abundance and diversity were controlled by P availability, which was regulated by Ca and pH conditions at each site. This work has resulted in two manuscripts.

3. Because of problems in 1 above, over forty sites were cored from eight sub-areas; early data show equivalent microbial variation within the sub-areas as across sub-areas, although evidence suggests microbial abundance is limited by available P (similar to 2010).

4. Methanotrophic culturable isolates from the cores are dominated Verrucomicrobia strains, some of which are prevously unidentified.
Exploitation Route Our sample analysis is complete. We have reported on microbial abundances and local alpha versus beta diversity.

We have subsequently used these cores to develop resistomes from the samples, which is currently being prepared as manuscript and is the template for two proposals in the AMR in the Real World call.
Sectors Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

Description We ran into logistical problems in the field on the work due to our deep-coring equipment failing in the field. Therefore, we decided to use our shallow cores (40 sites) to assess the relative abundance and diversity of antibiotic resistance genes in our remote location. This work has led to some outstanding discoveries, although the actual results have not been published and the impact has not be seen as of yet. Basically, we discovered resistant genes in the high Arctic had only previously been detected in southern locales, such as India, which implies the genes are migrating in wildlife or humans to the Arctic. We submitted a new Standard NERC proposal on this discovery and we will be publishing early work in Nature Microbiology in the Spring. This report will be translated in societal and policy issues because it shows among the first true background measures of resistance in the environment, on which many other studies and decisions will ensue.
First Year Of Impact 2016
Sector Environment,Healthcare
Impact Types Societal,Policy & public services

Title Multiplex qPCR of soil samples for antibiotic resistance genes 
Description Prior to this project, no one had used multiplex qPCR for resistance genes enumeration in highly organic Arctic soils. We developed a method for extracting the organics that normally obstruct qPCR application, which allowed us to use the method for peatland, tundra and other complex matrices. 
Type Of Material Biological samples 
Year Produced 2014 
Provided To Others? Yes  
Impact We are now actively cooperating with two groups in China with the method and will use the methods on a new Arctic project proposal, if needed. 
Title 454 Sequencing Dataset for Arctic soils 
Description We sequenced nine Arctic soils, which have been deposited in the NCBI's Sequence Read Archive (SRA) and are available under the BioProject ID PRJNA308796. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact None yet. We are planning more sequencing and archiving this year. 
Description Chinese National Academy of Science - Xiamen 
Organisation Chinese Academy of Agricultural Sciences
Country China, People's Republic of 
Sector Academic/University 
PI Contribution We are working with CAS (w/ Prof Yong-Guan Zhu) on samples from this project using our extraction methods and their multiplex qPCR methods. This is an extension of on-going joint work.
Collaborator Contribution We are sharing resistome samples for comparisons between samples within this new project, our previous collabarotion on ARC AMR, and their samples from Antartica and Tibet. The goal of this additional work is to determine how background AMR gene levels compare in "remote" locations around the world.
Impact None as of yet, but are about to submit a manuscript on AMR levels in the High Arctic.
Start Year 2012
Description MERMAID EU ITN 
Organisation Danish Technological Institute
Department Department of Environmental Engineering
Country Denmark, Kingdom of 
Sector Charity/Non Profit 
PI Contribution We are joint leaders of a large EU-funded ITN consortia with DTU. The consortia includes EAWAG (Switzerland), University of Ghent, and University of Lisbon, and centres around the use of molecular biological methods for tracking pollution, including greenhouse gases, across the environment.
Collaborator Contribution Novel and new molecular methods we are now using routinely within our work at Newcastle University.
Impact This collaboration is multidisciplinary. The collaboration is on-going and, although explicit outputs are in preparation, they are not yet fulfilled.
Start Year 2014