Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation.

Carbon-fixing micro-organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro-organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.

Linkages between Sphagnum metabolites and peatland CO2 uptake are sensitive to seasonality in warming trends.

Plants produce a wide diversity of metabolites. Yet, our understanding of how shifts in plant metabolites as a response to climate change feedback on ecosystem processes remains scarce. Here, we test to what extent climate warming shifts the seasonality of metabolites produced by Sphagnum mosses, and what are the consequences of these shifts for peatland C uptake. We used a reciprocal transplant experiment along a climate gradient in Europe to simulate climate change. We evaluated the responses of primary and secondary metabolites in five Sphagnum species and related their responses to gross ecosystem productivity (GEP). When transplanted to a warmer climate, Sphagnum species showed consistent responses to warming, with an upregulation of either their primary or secondary metabolite according to seasons. Moreover, these shifts were correlated to changes in GEP, especially in spring and autumn. Our results indicate that the Sphagnum metabolome is very plastic and sensitive to warming. We also show that warming-induced changes in the seasonality of Sphagnum metabolites have consequences on peatland GEP. Our findings demonstrate the capacity for plant metabolic plasticity to impact ecosystem C processes and reveal a further mechanism through which Sphagnum could shape peatland responses to climate change.

Photosynthetic microorganisms effectively contribute to bryophyte CO2 fixation in boreal and tropical regions.

Photosynthetic microbes are omnipresent in land and water. While they critically influence primary productivity in aquatic systems, their importance in terrestrial ecosystems remains largely overlooked. In terrestrial systems, photoautotrophs occur in a variety of habitats, such as sub-surface soils, exposed rocks, and bryophytes. Here, we study photosynthetic microbial communities associated with bryophytes from a boreal peatland and a tropical rainforest. We interrogate their contribution to bryophyte C uptake and identify the main drivers of that contribution. We found that photosynthetic microbes take up twice more C in the boreal peatland (~4.4 mg CO2.h-1.m-2) than in the tropical rainforest (~2.4 mg CO2.h-1.m-2), which corresponded to an average contribution of 4% and 2% of the bryophyte C uptake, respectively. Our findings revealed that such patterns were driven by the proportion of photosynthetic protists in the moss microbiomes. Low moss water content and light conditions were not favourable to the development of photosynthetic protists in the tropical rainforest, which indirectly reduced the overall photosynthetic microbial C uptake. Our investigations clearly show that photosynthetic microbes associated with bryophyte effectively contribute to moss C uptake despite species turnover. Terrestrial photosynthetic microbes clearly have the capacity to take up atmospheric C in bryophytes living under various environmental conditions, and therefore potentially support rates of ecosystem-level net C exchanges with the atmosphere.

Peatland microhabitat heterogeneity drives phototrophic microbe distribution and photosynthetic activity.

Phototrophic microbes are widespread in soils, but their contribution to soil carbon (C) uptake remains underexplored in most terrestrial systems, including C-accreting systems such as peatlands. Here, by means of metabarcoding and ecophysiological measurements, we examined how microbial photosynthesis and its biotic (e.g., phototrophic community structure, biomass) and abiotic drivers (e.g., Sphagnum moisture, light intensity) vary across peatland microhabitats. Using a natural gradient of microhabitat conditions from pool to forest, we show that the structure of phototrophic microbial communities shifted from a dominance of eukaryotes in pools to prokaryotes in forests. We identified five groups of co-occurring phototrophic operational taxonomic units with specific environmental preferences across the gradient. Along with such structural changes, we found that microbial C uptake was the highest in the driest and shadiest microhabitats. This study renews and improves current views on phototrophic microbes in peatlands, as the contribution of microbial photosynthesis to peatland C uptake has essentially been studied in wet microhabitats.

Winter climate change increases physiological stress in calcareous fen bryophytes.

Calcareous spring fens are among the rarest and most endangered wetland types worldwide. The majority of these ecosystems can be found at high latitudes, where they are affected by above average rates of climate change. Particularly winter temperatures are increasing, which results in decreased snow cover. As snow provides an insulating layer that protects ecosystems from subzero temperatures, its decrease is likely to induce stress to plants. To investigate the sensitivity of the bryophyte community - key to the functioning of calcareous spring fens - to changing climatic conditions, we studied the annual variation in ecophysiology of two dominant bryophytes: Campylium stellatum and Scorpidium scorpioides. Further, a snow removal experiment was used to simulate the effect of changing winter conditions. In both species, we observed lowest efficiency of photosystem II (Fv/Fm) in spring, indicating physiological stress, and highest chlorophyll-a, -b and carotenoid concentrations in autumn. Snow removal exacerbated physiological stress in bryophytes. Consequently Fv/Fm, pigment concentrations and chlorophyll to carotenoids ratios declined, while chlorophyll-a to -b ratios increased. Moreover, these effects of winter climate change cascaded to the growing season. C. stellatum, a low hummock inhabitor, suffered more from snow removal (annual mean decline in Fv/Fm 7.7% and 30.0% in chlorophyll-a) than S. scorpioides, a hollow species (declines 5.4% and 14.5%, respectively). Taken together, our results indicate that spring fen bryophytes are negatively impacted by winter climate change, as a result of longer frost periods and increased numbers of freeze-thaw cycles in combination with higher light intensity and dehydration.