April 5, 2024
Journal Article

Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry


Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. The soil microbial community composition was impacted more by irrigation and plant cover treatments than by soil depth. By contrast, metabolomes, lipidomes, and proteomes differed more with soil depth than treatments. Deep soil (>50 cm) had higher a soil pH and calcium concentrations, and higher levels of organic acids, bicarbonate, and triacylglycerides. By contrast, surface soil (0-5 cm) had higher concentrations of soil organic matter and organic carbon, oxidizable carbon, and total nitrogen. Surface soils also had higher amounts of sugars, sugar alcohols, phosphocholines, and proteins that reflect osmotic and oxidative stress responses. The lipidome was more responsive to perennial tall wheatgrass treatments compared to the metabolome or proteome, with a striking change in diacylglyceride composition. Permanganate oxidizable carbon was more consistently correlated to metabolites and proteins than soil organic and inorganic carbon, and soil organic matter. This study reveals specific compounds that reflect differences in organic, inorganic, and oxidizable soil C fractions that are impacted by interactions between irrigation-supplied moisture and plant cover in calcareous soil profiles. Importance Carbon is cycled through the air, plants, and belowground environment. Understanding soil carbon cycling in deep soil profiles will be important to mitigate climate change. Soil carbon cycling is impacted by water, plants, and soil microorganisms, in addition to soil mineralogy. Measuring biotic and abiotic soil properties provides a perspective of how soil microorganisms interact with the surrounding chemical environment. This study emphasizes the importance of considering biotic interactions with inorganic and oxidizable soil carbon in addition to total organic carbon in carbonate-containing soils for better informing soil carbon management decisions.

Published: April 5, 2024


Naasko K.I., D.T. Naylor, E.B. Graham, S.P. Couvillion, R.E. Danczak, N. Tolic, and C.D. Nicora, et al. 2023. Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry. mBio 14, no. 5:Art. No. e01758-23. PNNL-SA-187582. doi:10.1128/mbio.01758-23

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