Soil organic carbon fractionation and metagenomics pipeline to link carbon content and stability with microbial composition – First results investigating fungal endophytes

Abstract

Society needs to capture gigatons of carbon dioxide from the atmosphere annually and then store it long-term to limit and ultimately reverse the effects of climate change. Bringing lost carbon back into agricultural soils should be a priority as it brings the added benefit of improving soil properties. Linking soil organic carbon (SOC) fractions of different stability with soil microbial composition can help understand and subsequently manage SOC storage. Here we develop a pipeline for evaluating the effects of microbial management on SOC content using rapid and low-cost SOC fractionation and metagenomics approaches. We tested the methods in a wheat pot trial inoculated with 17 individual endophytic fungal isolates. Two fungi increased total SOC in the area under the plant stem by ~15%. The fractionation assay showed that the medium stability soil aggregate carbon fraction (AggC) was increased by one of these fungi (+21%) and the chemically recalcitrant proportion (bleach oxidation) of AggC by the other (+35%). Both fungi increased mineral-associated organic carbon (MAOC), the long-term SOC storage, by ~10%. We used rapid, portable, low-cost, whole metagenome long read sequencing to detect a shift in the microbial composition for one of the fungi-inoculated treatments. This treatment showed a more diverse microbial community and a higher quantity of DNA in soil. The results emphasise the link between composition and abundance of soil microorganisms with soil carbon formation. Our dual carbon fractional and metagenomic analysis pipeline can be used to further test the effects of microbial management and ultimately to model the soil factors that influence SOC storage, such as nutrient and water availability, starting SOC content, soil texture and aggregation.

Stabilisation of soil organic matter with rock dust partially counteracted by plants

“…The data from this trial are openly available ([dataset] Buss et al., 2023a, 2023b). Statistical analyses were conducted in R (2022.12.0) and most visualisations in SigmaPlot ( systat Software Inc., San Jose CA, USA).…”

“…Full details about the soil carbon fractionation that distinguishes free POM, AggOM and MAOM are described previously (Buss, Sharma, et al., 2021). In short: 10 g of soil was shaken with a total volume of 50 mL of deionised water.…”

“…Full details about the method to determine microbial composition were described previously (Buss, Sharma, et al., 2021). In short: a commercial DNA extraction kit (DNeasy PowerSoil Pro Kit, Qiagen, Hilden, Germany) was used for extracting DNA from the dried soil and the samples were barcoded with the ‘Native Barcoding kit’ (Oxford Nanopore Technology, Oxford, UK) and run on a Flongle flow cell (Oxford Nanopore Technology, Oxford, UK).…”

“…Full details about the method to determine microbial composition were described previously (Buss, Sharma, et al, 2021). and operational taxonomic units (phylum, class or order) that were only detected once in a sample were excluded.…”

Distribution of soil bacteria involved in C cycling across extensive environmental and pedogenic gradients

“…The coarse unprotected particulate organic matter shows the highest influence on microbial community composition (Tian et al, 2017), while MAOC is more likely to associate with fungal groups and their necromass (Luo et al, 2021). As above, linking soil C fractions with soil microbial composition could provide a better understanding of soil C cycling (Buss et al, 2021).…”