November 7, 2023
Research Highlight

Irrigation And Perennial Crops Impact Soil Biogeochemistry Down to a Depth of Three Feet

Molecular analysis unveils depth and irrigation-dependent variations in plant-microbe interactions

An image of a soil core

Deep soil cores provide novel insights into soil ecology 3 feet underground.

(Photo by Kirsten Hofmockel | Pacific Northwest National Laboratory)

The Science                                

Soil is a massive reservoir of carbon, holding three times the amount of carbon than in the atmosphere. This reservoir is under threat from increased drought due to climate change. Plant-microbe interactions, especially in poor or marginal soils, may help to mitigate these carbon losses. Soil carbon cycling and storage is mediated by microorganisms that are responding to the chemical, biological, and physical characteristics of the surrounding environment, including soil moisture and plant cover. This study investigated how irrigation and perennial plant cover impact soil carbon cycling in the top 3 feet of a marginal soil. Researchers at Pacific Northwest National Laboratory (PNNL) found that although the microbial community composition was most sensitive to irrigation and plants, their metabolites, lipids, and proteins differed even more among soil depths. Calcium, a common element in marginal soils, has a strong influence on the collection of lipids and proteins in the soil profiles. Calcium can form complexes with inorganic carbon fractions (i.e., carbonates). Soils planted with deep-rooted perennial grasses had higher levels of bicarbonate, a form of inorganic carbon, than unplanted soils. The PNNL study shows the potential for carbon accumulation as inorganic carbon in carbonate-containing soils.

The Impact

The team at PNNL is the first to investigate the small molecule profiles of soil microbial communities in calcareous or carbonate-containing, soil profiles. These fine-resolution measures provided evidence of how specific soil carbon compounds are distributed in the soil under drought-stressed conditions. This study fuels future investigations of deep soil microbial metabolism related to soil carbon cycling using advanced molecular approaches. The results of this study are relevant to the fields of soil and crop science, microbiology, agriculture, and sustainability.


This research investigates how irrigation and perennial plants impact the soil microbial community and soil carbon metabolism in surface, subsurface, and deep soil layers. Measuring biotic and abiotic soil properties revealed how water, plants, microorganisms, and soil chemistry interact to regulate soil carbon cycling. Irrigation and plant cover treatments had a stronger influence on soil microbial community composition than soil depth. This work emphasizes the importance of considering diverse forms of carbon stabilization that can occur in marginal soils and contributes to researchers’ understanding of how certain agricultural practices may mitigate the effects of climate change on soil carbon dynamics.

PNNL Contacts

Katherine Naasko, Pacific Northwest National Laboratory,

Kirsten Hofmockel, Pacific Northwest National Laboratory,


This program is supported by the Department of Energy (DOE) Office of Science, through the Genomic Science program, Biological Environmental Research program. A portion of this work was performed in EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility at PNNL. EMSL is sponsored by the Biological and Environmental Research program. PNNL is a multiprogram national laboratory operated by Battelle for DOE.

Published: November 7, 2023

Naasko, K., D. Naylor, K. S. Hofmockel, J. Jansson, M. Parsek. 2023. “Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry.” mBIO. DOI: