IP4: Carbon Bioavailability and Microbial Transformations

People: Hana Santruckova (PI), Jiri Barta (co-PI), Katerina Diakova, Iva Lacmanova, Saida Azimova, Petr Capec

Aims and Objectives

The overall goal of IP4 is to estimate SOM bioavailability in a wide range of pedons along bioclimate gradients to provide detailed information for the calculation of a vulnerability index of arctic SOM.
Specific objectives are:
(i) to survey bioavailability of SOM from subducted and regular horizons to decomposition in pedon profiles from tundra regions in Central and East Siberia,
(ii) to determine effect of abiotic factors on the interrelationship between structure and functioning of microbial community, and on the link between microbial functioning and SOM quality and availability,
(iii) to estimate effect of soil nutrient balance on microbial stoichiometry and, consequently, on microbial functioning and response to changing abiotic factors (Experiment E1).

The objectives of IP4 are embedded in objective 2 (…to identify the major SOC stabilization mechanisms in cryoturbated soils) and objective 3 (…to assess the vulnerability of SOC of cryoturbated soils in a future climate) of the CryoCARB JRP.

Methodologies and Experiments

SOM biodegradability

We intend to analyze up to 50 pedon profiles from the study sites in Cherskii and Taymyr that represent the different landcover types present in these tundra regions collected by IP1 within WP1. For each pedon, samples at 5 cm (top organic) to 10 cm (mineral) intervals down to 1 meter (or more, if deep cryoturbation is noticed) will be analyzed for SOM bioavailability using the respiratory response approach [1]. Briefly, soil is quickly dried in thin layer at room temperature immediately after sampling and kept until analyzing at low temperature. Before analysis, soil is moistened to optimum monture and incubated at 15°C for 10 days. Soil respiration is measured 2 days after moistening (flush of respiration) and at the end of incubation after soil respiration is equilibrated to “basal level”. The flush of respiration is related to easily available C pool, which can be rapidly released after soil disturbance. Basal respiration is characteristic for “steady state” C availability. Data on C bioavailability will be evaluated together with geochemical data carried up by IP1.

Laboratory Incubation Experiment (E1)

A laboratory decomposition experiment with four month incubation will be established in collaboration with AP3. In the experiment we will use surface and subducted horizons sampled at the Taymyr core site in bioclimate subzone E. Semi-intact monolites of the target horizons will be incubated in closed containers at different temperatures (0°C and 10°C), moisture regimes (50 and 100% water holding capacity) and oxygen availabilities (< 5% and 20%), respectively. The temperatures represent low and high range of the field temperatures, and moisture simulating optimum and maximum water content favors aerobic and anaerobic metabolism, respectively. Oxygen concentration below 5% is a threshold concentration for functioning of aerobic microorganisms. CO2 gas exchange will be measured weekly by gas chromatography during the incubation. In the treatments with temperature and moisture manipulation, containers will be always opened after gas exchange measurement to change headspace atmosphere and adjust moisture if necessary. We intend to measure biodegradability of SOM, net rates of C, N and P transformations. In addition, the samples will be used for analysis of bacterial and archaeal community (IP5), gross rates of N transformation, methane production and microbial community composition by PLFAs (IP3) and SOM quality and degradability (IP2).

– Biodegradability of SOM will be measured as heterotrophic respiration of bulk soil and individual physical fractions; the natural abundance of 13C in 13CO2 will be analysed in cooperation with IP3. In addition simple chemical fractionation will be applied to separate SOM according mobility and potential availability [2].

– Microbial C and N transformation activities: microbial biomass (N, C using CFE method [3,4]), heterotrophic respiration rate, net N mineralization [5,6] and net methane exchange (gas chromatography) ; key genes of denitrification using qPCR will be detected to get better insight into microbial N transformation [7,8].

– Microbial P transformation activity: P mineralization rate measuring microbial P [9], available P, MUF-phosphatase activity [10].


[1] Šantrůčková et al., 2005 In: Binkley D (Ed) Trees and Soil Interactions, Implications to Global Climate Change., Kluwer Acad Press, Dordrecht, 229. [2] Uhlířová et al., 2007, Soil Biol Biochem 39: 1978. [3] Vance et al., 1987, Soil Biol Biochem 19: 689. [4] Cabrera & Beare, 1993, Soil Sci Soc Am J 57: 1007. [5] Ste-Marie & Paré, 1999, Soil Biol Biochem 31: 1579. [6] Šantrůčková et al., 2009, Biol Fertil Soils: DOI 10.1007/s00374-008-0349-4. [7] López-Gutiérrez et al., 2004, J Microbiol Meth 57: 399. [8] Sharma et al., 2007, J Microbiol Meth 68: 445. [9] Brookes et al., 1982, Soil Biol Biochem 14: 319. [10] Šantrůčková et al., 2004, Soil Biol Biochem 36:1569.