The interaction of soil phototrophs and fungi with pH and their impact on soil CO2, CO18O and OCS exchange

Abstract

The stable oxygen isotope composition of atmospheric CO2 and the mixing ratio of carbonyl sulphide (OCS) are potential tracers of biospheric CO2 fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (α, β and γ) may have different affinities to CO2 and OCS and their expression should also vary between different microbial groups, differences in the community structure could impact the ‘community-integrated’ CA activity differently for CO2 and OCS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO2, CO18O and OCS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototrophs. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO2 sink and the CA-driven CO2-H2O isotopic exchange rates correlated with phototrophs abundance. OCS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. Our findings demonstrate that soil-atmosphere CO2, OCS and CO18O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and supports the idea that different members of the microbial community express different classes of CA, with different affinities to CO2 and OCS.

Disentangling the rates of carbonyl sulphide (COS) production and consumption and their dependency with soil properties across biomes and land use types

“…1, from measurements of the soil-to-air COS flux performed on moist soils. In practice a numerical iterative method must be implemented to find the value of k that minimises the discrepancy between the observed and modelled fluxes (Ogée et al, 2016;Sauze et al, 2017a).…”

“…Using a custom-made multiplexed system (Sauze et al, 2017a), six jars with six different soils and one empty jar (blank) were measured sequentially over ca. 18h to investigate simultaneously 6 different soils under identical conditions (Supplement Fig.…”

Soil COS Exchange: A Comparison of Three European Ecosystems

“…The increase in CO 2 emissions in SAV therefore indicates an increase in biological activity in the soil with increasing temperature, a common but very variable response of soils observed in many different ecosystems (Conant et al, ; Davidson et al, ; Davidson & Janssens, ; Jensen et al, ; Lloyd & Taylor, ). Since there are more accounts for biotic COS consumption (Kato et al, ; Kato et al, ; Kesselmeier et al, ; Masaki et al, ; Ogawa et al, ; Ogawa et al, ; Sauze et al, ) than biotic COS production (Conrad, ; Masaki et al, ) under ambient COS concentrations, it is tempting to link biological activity in oxic soils primarily to COS uptake. The co‐occurring increase in COS and CO 2 emissions in SAV could therefore mean that abiotic production of COS is increasing more strongly with temperature outweighing increased COS uptake due to higher biological activity or the underlying assumption of biotic COS contribution being primarily characterized by COS uptake in oxic soils is not universally true, and emissions associated to the soil biological activity could also occur.…”

“…In the few experiments where COS emission were detected (Bunk et al, ; Whelan et al, ), the corresponding soil samples were very dry, as with the SAV samples (Figure ). Other soil parameters, found to influence the soil COS exchange in the literature, are soil pH (Sauze et al, ) and soil nitrogen content (Kaisermann, Jones, et al, ; Meredith et al, ). Soil pH differed between our samples (Figure ) with COS uptake in the more acidic samples and COS production in the less acidic samples, while no apparent pattern emerged from the C/N ratio of our samples with regard to soil COS fluxes (supporting information Figure S3).…”

Microbial community responses determine how soil–atmosphere exchange of carbonyl sulfide, carbon monoxide, and nitric oxide responds to soil moisture

“…Before sequence analysis was performed with a standard QIIME pipeline, paired-end reads of 300 bp were merged with PEAR (Zhang et al, 2014), with maximum lengths of 500 or 550 bp for 16S rRNA and ITS, respectively, and cleaned with PrinSeq (Schmieder and Edwards, 2011). Specific criteria were used to proceed with the analysis only with high-quality reads in terms of sequence confidence: mean phred over 25 (probability that the base assigned by the sequencer is at least 99 %); trim quality window of 50 (space of nucleotides scanned for quality at each time); minimum length of 200 bp; removal of artificial duplicates obtained during sequencing; and only 1 % of bases, which were not recognized as ATGC, were allowed (Schmieder and Edwards, 2011). Pre-cleaned sequences were analyzed with QIIME version 1.9.1 (Caporaso et al, 2010), following usearch61 chimera (sequences that can be artificially created during amplification of DNA molecules for the sequencing) screening, and the operational (Abarenkov et al, 2010).…”