Abrupt permafrost thaw triggers activity of copiotrophs and microbiome predators

Permafrost soils store a substantial part of the global soil carbon and nitrogen. However, global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1 m deep soil core consisting of up to 26 500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost, and found maximum RNA:DNA ratios in recently thawed permafrost indicating a high microbial activity. In thawed permafrost, potentially copiotrophic Burkholderiales and Sphingobacteriales, but also microbiome predators dominated the community. Overall, both thaw-dependent and long-term soil properties significantly correlated with changes in community composition, as did microbiome predator abundance. Bacterial predators were dominated in shallower depths by Myxococcota, while protozoa, especially Cercozoa and Ciliophora, almost tripled in relative abundance in thawed layers. Our findings highlight the ecological importance of a diverse interkingdom and active microbial community highly abundant in abruptly thawing permafrost, as well as predation as potential biological control mechanism

Geochemical, sedimentological and microbial diversity in two thermokarst lakes of far Eastern Siberia

Thermokarst lakes are important conduits for organic carbon sequestration, soil organic matter (soil-OM) decomposition and release of atmospheric greenhouse gases in the Arctic. They can be classified as either floating-ice lakes, which sustain a zone of unfrozen sediment (talik) at the lakebed year-round, or as bedfast-ice lakes, which freeze all the way to the lakebed in winter. Another key characteristic of thermokarst lakes are their eroding shorelines, depending on the surrounding landscape, they can play a major role in supplying the lakebeds with sediment and OM. These differences in winter ice regime and eroding shorelines are key factors which determine the quantity and quality of OM in thermokarst lake sediments. We used an array of physical, geochemical, and microbiological tools to identify the differences in the environmental conditions, sedimentary characteristics, carbon stocks and microbial community compositions in the sediments of a bedfast-ice and a floating-ice lake in Far East Siberia with different eroding shorelines. Our data show strong differences across most of the measured parameters between the two lakes. For example, the floating-ice lake contains considerably lower amounts of sediment organic matter and dissolved organic carbon, both of which also appear to be more degraded in comparison to the bedfast-ice lake, based on their stable carbon isotope composition (δ13C). We also document clear differences in the microbial community composition, for both archaea and bacteria. We identified the lake water depth (bedfast-ice vs. floating-ice) and shoreline erosion to be the two most likely main drivers of the sedimentary, microbial and biogeochemical diversity in thermokarst lakes. With ongoing climate warming, it is likely that an increasing number of lakes will shift from a bedfast- to a floating-ice state, and that increasing levels of shoreline erosion will supply the lakes with sediments. Yet, still little is known about the physical, biogeochemical and microbial differences in the sediments of these lake types and how different eroding shorelines impact these lake system

Temperature adaptation of soil bacterial communities across the Arctic

Microorganisms that inhabit soils across the Arctic are typically well adapted to low temperatures and are highly responsive to temperature increases. A change in temperature adaptation of microbial communities might affect how fast they will decompose soil organic matter in a warmed Arctic. Currently, the potential change in temperature adaptation of soil bacterial communities is under scientific debate, due to contrasting observations made in field and laboratory settings. Therefore, the overall aim of this thesis was to evaluate the current temperature adaption of soil bacterial communities in the Arctic and to investigate whether the temperature adaptation of arctic soil bacterial communities shifts when exposed to warmed conditions. In Chapter 2, the optimal growth temperature of bacterial communities increased when comparing samples from the colder sites to warmer sites. I observed that one of the most important factors for their temperature adaptation was the mean maximum soil temperature. I concluded from this study that increasing temperatures – especially summer temperatures – will likely alter the temperature adaptation of bacterial communities in arctic soils. To confirm this hypothesis, I conducted an incubation study with 8 soils collected from the (sub-) Arctic and exposed them to different temperatures, ranging between 0 and 30°C. When the soils were incubated, the bacterial communities altered their temperature adaptation depending on the incubation temperature. In the third chapter, I also found that the induced change in temperature adaptation of soil bacterial communities was accompanied by a change in the overall composition of the bacterial community. Therefore, I hypothesized that the individual response of bacterial species to soil warming might reflect the temperature adaptation. Thus, the abundance of particular bacterial species in a soil sample could be potentially used for estimating the temperature adaptation of soil bacterial communities. In chapter 4, I evaluated the use of bacterial species abundance as indicator of bacterial communities responding to soil warming. Along a natural warming gradient in Iceland, I show that, while there are changes in the composition of bacterial communities of grassland soil in response to soil warming, there are only very few bacterial species that respond to the warming through multiple and multiple levels of warming. Therefore, is limited use of bacterial abundance data in predicting the temperature adaptation and response to warming for soil bacterial communities. Overall, I did not observe bacterial species that are both 1. common amongst many soil types and 2. respond consistently to soil warming. In chapter 5, I used a trait-based model approach to test whether the current theoretical framework around thermal traits of soil bacterial species can explain the relationship between temperature adaptation of soil bacterial communities and the temperatures that they are exposed to. The model made relatively accurate predictions about the temperature adaptation of soil bacterial communities. Furthermore, I discuss which traits related to the thermal niche of a bacterial species are relevant for improved modelling. Finally, I conclude in Chapter 6 that bacterial communities will likely alter their temperature adaptation in response to long term exposure to warming. It will be important to further assess the influence of these changes on the functioning on soil bacterial communities in the Arctic. From this thesis the view emerges that changes in the temperature adaptation of soil bacterial communities are likely due to the changes in the ideal temperature range of individual bacterial species. Accurate predictions for the current and future temperature adaptation of soil bacterial communities will require more in-depth knowledge of the traits that bacteria possess related to temperature

Temperature-growth relationships Arctic soil bacterial communities - Cardinal points

Cardinal points of the temperature-growth relationships estimated for the soil bacterial communities of 12 arctic sampling sites.</p

cumulativeCO2.csv

Cumulative respiration in ug/g soil dry weight for soil from incubation experiment with Arctic soil

Soil Temperature Arctic Sample Sites.csv

Summary for the soil temperature data of 12 arctic sampling sites</p

Soil Characteristics

Measurements of soil characteristics for the 12 arctic sampling sites</p

Maximum summer temperatures predict the temperature adaptation of Arctic soil bacterial communities

Rapid warming of the Arctic terrestrial region has the potential to increase soil decomposition rates and form a carbon-driven feedback to future climate change. For an accurate prediction of the role of soil microbes in these processes, it will be important to understand the temperature responses of soil bacterial communities and implement them into biogeochemical models. The temperature adaptation of soil bacterial communities for a large part of the Arctic region is unknown. We evaluated the current temperature adaption of soil bacterial communities from 12 sampling sites in the sub- to High Arctic region. Temperature adaptation differed substantially between the soil bacterial communities of these sites, with estimates of optimal growth temperature (Topt) ranging between 23.4 ± 0.5 and 34.1 ± 3.7 ° C. We evaluated possible statistical models for the prediction of the temperature adaption of soil bacterial communities based on different climate indices derived from soil temperature records or on bacterial community composition data. We found that highest daily average soil temperature was the best predictor for the Topt of the soil bacterial communities, increasing by 0.63 ° C ° C-1. We found no support for the prediction of temperature adaptation by regression tree analysis based on the relative abundance data of the most common bacterial species. Increasing summer temperatures will likely increase Topt of soil bacterial communities in the Arctic. Incorporating this mechanism into soil biogeochemical models and combining it with projections of soil temperature will help to reduce uncertainty in assessments of the vulnerability of soil carbon stocks in the Arctic

Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming

Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature–growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) Arctic soils. The optimal growth temperature (Topt) of the soil bacterial communities increased 0.27 ± 0.039 (SE) and 0.07 ± 0.028°C per °C of warming over a 0–30°C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time-lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in Topt were accompanied by species-level shifts in bacterial community composition, which were mostly soil specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature-responsive bacterial amplicon sequence variants. This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in Arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of Arctic soil carbon stocks