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

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.

How drought modulates carbon-use efficiency and soil carbon formation in rhizosphere, detritusphere, and bulk soils

<p>Carbon use efficiency (CUE) is theorized to be positively associated with the formation of microbially-derived, mineral-associated soil carbon.  Yet few empirical studies have directly tested this relationship. Moreover, it is unclear: (1) how differences between distinct soil microbial communities (for example, differences in competitive interactions and/or growth rate among rhizosphere, detritusphere, and bulk soil communities) may yield different relationships between carbon-use efficiency and soil carbon formation, and (2) how microbial ecophysiology – such as physiological changes induced by drought – may modulate the strength and/or direction of the CUE-soil carbon relationship.</p><p>To investigate these questions, we conducted a 12-week <sup>13</sup>C tracer study to track the movement of two dominant sources of plant carbon – rhizodeposition and root detritus – into soil microbial communities and carbon pools under normal moisture vs drought conditions. Using a continuous <sup>13</sup>CO<sub>2</sub>-labeling system, we grew the Mediterranean annual grass <em>Avena barbata</em> in controlled growth chambers and measured the formation of organic matter from <sup>13</sup>C-enriched rhizodeposition. As the plants grew, we harvested rhizosphere and bulk soil at three time points (4, 8, and 12 weeks) to capture changes in soil carbon pools and microbial community dynamics. In parallel microcosms, we tracked the formation of soil carbon derived from <sup>13</sup>C-enriched <em>A. barbata</em> root detritus during 12 weeks of decomposition; harvesting detritusphere and bulk soil at 4,8, and 12 weeks. In all microcosms, we manipulated soil moisture to generate drought (7.8 ± 2.1 % soil moisture) and ‘normal moisture’ (15.1 ± 4.2 % soil moisture) treatments.</p><p>In all samples (over 150 observations), we measured CUE via the <sup>18</sup>O-H<sub>2</sub>O method, and quantified the formation of different <sup>13</sup>C-soil organic carbon pools via density fractionation. Here we will present data on how soil moisture influences CUE in rhizosphere, detritusphere, and bulk soil communities, and whether differences in CUE are correlated with the formation of mineral-associated soil organic carbon. These results will help to illustrate whether CUE acts as a lynchpin variable with predictive power for stable soil carbon formation, or whether other microbial traits may require consideration.</p><p> </p><p> </p>