Microbiome experts describe how to uncover contributions of microbial communities to climate change and ecosystem stability

The roles of complex microbial communities in soil and ocean environments is a relatively new area of inquiry, spurred on by the same advances in sequencing technology that have revealed the importance of human microbiomes in health. With emerging data, the importance of these microbial communities in regards to climate change and ecosystem stability has become more evident. In a new Viewpoints article published in Nature Reviews, several experts in the field, including Microbiome Insights Scientific Advisory Board member Janet Jansson, discuss the microbial contributions to climate change and, in turn, the effects a changing climate has on these communities.

For Jansson, the effect that climate change has on the diversity and function of microbial communities is evident in two climate-sensitive soil ecosystems: Arctic permafrost and grasslands. In the Arctic as temperatures rise and the permafrost thaws, soil microorganisms are becoming more active, beginning to decompose the organic carbon stored within the once-frozen environment and thereby releasing more greenhouse gases such as carbon dioxide and methane. In grasslands, changing climate patterns are leading to greater amounts of precipitation in the form of increased and more intense rainfall. This increased soil moisture affects the ability of soil microorganisms to interact and limits their ability to cycle carbon and other nutrients. Without this cycling function performed by microbes, the grasslands will suffer from a lack of key nutrients and plant derived compounds.

While Jansson’s work focuses on soil environments, climate induced changes to ocean temperatures and pH levels will similarly alter the microbes in the marine environment, changing their function or hampering their ability to perform their normal duties. When considering pathogenic viruses and bacteria found in either water or land environments, the effects of climate will be varied. Some species of viruses will be less able to tolerate warmer climates and so rates of disease caused by them may drop. However, certain pathogenic species of bacteria may respond to warmer temperatures by becoming more virulent. No matter the ecosystem or the role of the microbes within it, climate changes are poised to significantly alter the intricate ways in which thousands of these communities interact with each other, the environment and their hosts.

In order to mitigate some of the effects on soil microbial communities brought on by climate change Jansson believes there are several research approaches to consider. One avenue involves the possibility of exploiting the metabolic capabilities of soil microorganisms to capture carbon. Using synthetic biology tools, custom designed plant-soil-microorganism combinations might be used to increase carbon dioxide uptake and capture in ways that are resistant to decomposition. A second possibility is to use soil microbes to promote better plant growth under the stressful conditions brought about by climate change. Again, no matter the environment, research is needed to first understand the changes these communities are experiencing and how this alters their normal functions. From there, clever solutions such as inoculating degraded environments with microbiomes from healthy areas and other forms of ecosystem engineering or restoration can be more safely applied.

For any of this work to become reality, though, Jansson says the field needs to move beyond sequencing alone. Emerging technologies like proteomics, metabolomics and imaging need to be exploited in order to determine the functions of these interacting communities and how the functions are being altered by climate change. Again from her work on soil microbes, understanding how all types of microbes, from bacteria and viruses to protozoa and fungi, interact across trophic levels is a key area of inquiry—as is understanding how resilient the various soil microbes are to stress. Specifically, she would like to identify any tipping points after which these microbes can no longer perform their function(s).

According to Jansson, “currently, there is a disconnect between the fine-scale detail arising from microbiome studies and the larger ‘landscape’ scale resolution of most climate models.” Because of this, one of her priorities moving forward will be to incorporate knowledge about microbial biogeochemical pathways and interactions into predictive models of the impacts of climate change on the ecosystem functions of these communities.

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Microbiome Insights, Inc. is a global leader providing end-to-end microbiome sequencing and comprehensive bioinformatic analysis. The company is headquartered in Vancouver, Canada where samples from around the world are processed in its College of American Pathologist (CAP) accredited laboratory. Working with clients from pharma, biotech, nutrition, cosmetic and agriculture companies as well as with world leading academic and government research institutions, Microbiome Insights has supported over 772 microbiome studies from basic research to commercial R&D and clinical trials. The company's team of expert bioinformaticians and data scientists deliver industry leading insights including biomarker discovery, machine-learning based modelling and customized bioinformatics analysis.