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

Naasko, Katherine I.; Naylor, Daniel; Graham, Emily B.; Couvillion, Sneha P.; Danczak, Robert; Tolic, Nikola; Nicora, Carrie; Fransen, Steven; Tao, Haiying; Hofmockel, Kirsten S.; Jansson, Janet K.; Parsek, ed., Matthew

doi:10.1128/mbio.01758-23

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

Journal Article · Tue Oct 31 00:00:00 EDT 2023 · mBio (Online)

DOI:https://doi.org/10.1128/mbio.01758-23· OSTI ID:2001137

^[1]; Naylor, Daniel ^[2]; Graham, Emily B. ^[2]; Couvillion, Sneha P. ^[2]; Danczak, Robert ^[2]; Tolic, Nikola ^[2]; Nicora, Carrie ^[2]; Fransen, Steven ^[3]; Tao, Haiying ^[4];

^[5];

^[2]; Parsek, ed., Matthew

Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory , Richland, Washington, USA, Department of Crop and Soil Sciences, Washington State University , Pullman, Washington, USA
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory , Richland, Washington, USA
Department of Crop and Soil Sciences, Washington State University , Prosser, Washington, USA
Department of Plant Science and Landscape Architecture, University of Connecticut , Storrs, Connecticut, USA
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory , Richland, Washington, USA, Department of Agronomy, Iowa State University , Ames, Iowa, USA

ABSTRACT 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 1 m in depth from irrigated and planted field treatments and was 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 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, 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 carbon 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.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC05-76RL1830; FWP 70880

OSTI ID:: 2001137

Alternate ID(s):: OSTI ID: 2007544

Report Number(s):: PNNL-SA-187582; e01758-23

Journal Information:: mBio (Online), Journal Name: mBio (Online) Vol. 14 Journal Issue: 5; ISSN 2150-7511

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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soil microbiome
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Title: Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry

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