Beneath the surface: how microbes degrade stable tundra organic matter

The swampy plains of an arctic tundra exude a cold stillness in a seemingly lifeless landscape. But beneath the surface copious microorganisms exist and whether these organisms are active or dormant is typically governed by the thawed or frozen state of the soil.
Published in Microbiology
Beneath the surface: how microbes degrade stable tundra organic matter

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Many soil microorganisms feed on soil organic carbon (SOC), for which the tundra currently serves as one of the largest global banks. Under climate change, tundra experiences longer periods of thaw and the thaw depth becomes increasingly deeper. If and how the microorganisms in the tundra begin actively decomposing the SOC will have a huge impact on whether this carbon decays and is released in the form of greenhouse gasses. In the best scenario, the SOC is resistant to decomposition, and remains abundant even with warming-stimulated increases in microbial activity. In worse scenarios, the resident microbes can completely decompose the SOC.

Aiming to provide better resolution on tundra SOC vulnerability under warming, several projects have utilized the Carbon in Permafrost Experimental Heating Project (CiPEHR) site in Central Alaska. These novel studies examined relationships between soil microbial communities and SOC decomposition in thawed tundra (PNAS; NCC; SB&B). For this research, published in ISMEJ, we profiled soil microbial community functional genes and taxa and SOC decomposition parameters during one of the longest running lab incubations of tundra soils.

The tundra soil incubated in this project was collected from the CiPEHR site in Central Alaska (pictured above). Photo credit: Ted Schuur, Ph.D., Center for Ecosystem Science and Society, Northern Arizona University.

There were some obstacles to overcome. For example, there is so much carbon in these soils, that extracting DNA from them is tricky. The brownish-black color in soil DNA extracts, loathed because it is indicative of organic matter contamination, was as thick and dark as extracts taken from tar pits. But, with curated extraction methodology and multiple clean-up rounds, quality DNA was plentiful.

A general issue in assaying SOC emerges when partitioning SOC into fractions that are considered more- or less-microbially accessible. Methods often rely on mixing the soil into a slurry, then chemically evaluating the carbon. But these soil slurries disrupt the structure of the soil. So, for example, carbon in the interior of a stable aggregate may appear to be labile and available when, in reality, it was physically protected from microbial decomposition. Hence, there is a disconnect between what we see and what the microorganisms experienced.

Using a 3-year laboratory incubation, we were able to monitor respiration kinetics of tundra soils that were partitioned into chunks of relatively in-tact soil cores, sampled from three depths. This allowed us to model valuable parameters for the pool sizes and decomposition kinetics of three carbon pools (fast, slow, and passive) from each soil depth. Using metagenomic techniques we profiled microbial taxa and traits involved in carbon cycling at four time points during the incubation.

The integration of estimated SOC decomposition parameters and microbial omics data, provided unique insights into what components of the SOC microbes were accessing and which microbial taxa and traits were important when slow SOC dominated the respiration. Traveling deeper below the surface, there were more associations between slow and passive SOC parameters and microbial community characteristics, potentially indicating a community that excels in accessing stable carbon pools.

So, we understand that the barren tundra landscape is teeming with life and the tundra SOC is vulnerable to decomposition. Ideally, this will enhance our respect of this landscape, provided the positive feedback it can impose on global climate change.

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