Author ORCID Identifier

https:/orcid.org/0000-0002-3990-2365

Date Available

4-30-2025

Year of Publication

2025

Document Type

Doctoral Dissertation

Degree Name

Doctor of Philosophy (PhD)

College

Agriculture, Food and Environment

Department/School/Program

Plant and Soil Sciences

Faculty

Hanna Poffenbarger

Faculty

Dave McNear

Faculty

Ole Wendroth

Abstract

Climate change is disrupting (agro)ecosystems, with the potential for significant losses in crop productivity and ecosystem resilience due to changes in water and biogeochemical cycling. These disruptions can also release more carbon dioxide into the atmosphere through the degradation of soil organic matter. Plant roots have emerged as a potential tool for mitigating these effects, given their roles in plant function and in driving soil biogeochemistry. While this interest is growing, our ability to implement root trait selection is limited due to constraints on characterizing roots and limited clarity on the effects of traits on plant and ecosystem function. My research has targeted both areas, through 1) developing a phenotyping platform for large crops and using it to characterize a panel of maize varieties, and 2) incubating different roots in multiple environments to evaluate how tissue chemistry influences soil organic matter dynamics during root decomposition.

Chapter one covers the development of a plant phenotyping platform and analysis method suitable for characterizing large, intact root systems. With the use of a purpose‐built imaging table and automated photo capture system, machine learning‐based image segmentation, and off‐the‐shelf trait analysis software, the method yielded results of comparable accuracy to commercial platforms without requiring prohibitively expensive equipment. This enables root studies to move beyond the limitations of scanner‐based methods, integrate whole‐system traits like root depth distribution, and save time on image capture.

In chapter two, we used this platform to assess breeding-driven changes in root traits relevant to resource acquisition and soil carbon (C) sequestration. We grew twelve maize (Zea mays L.) hybrids from the Corteva/Pioneer ERA panel, spanning from 1936 to 2014, in 1.5 m deep mesocosms. Intact root systems were imaged and analyzed, and roots and shoots were subjected to carbon and nitrogen analysis and infrared spectroscopic analysis to assess tissue composition. The newest hybrids produced 40% less root biomass and 36% less root length than the oldest hybrids with no changes in maximum rooting depth, and no clear shifts in chemical composition. Our results suggest that selection for yield has indirectly decreased root system size.

Chapter three covers a carbon-13 natural abundance study, in which roots of seven plant species with diverse tissue composition were incubated in the lab in contrasting soils for six months to track the movement of root C into organic matter. Soil respiration was measured throughout the incubation, and mesocosms were sampled over the course of the incubation to measure root-derived C. In both soils, respiration was greater and the amount of root C found in particulate organic matter (POM) was lower for treatments with low of suberin and phenols. More root C was found in mineral-associated organic matter (MAOM) for treatments with low levels of phenols. We also found chemical changes to MAOM, with the ratios of lignin subunits in MAOM, shifting towards those in the roots. Our results suggest that roots with high phenol and suberin contents contribute more to POM while roots with low phenol content contribute more to MAOM. and that regardless of degradability litter chemistry directly influences MAOM composition.

Chapter four covers a second carbon-13 study on the effects of root chemistry and soil environment under more realistic conditions. The roots of four species were packed into nylon-wrapped tubes with soil and incubated in the field at depths of 0-10 cm and 40-50 cm for one year. Roots with high G lignin and suberin had more of their C retained in particulate organic matter, while those with high H lignin and nitrogen had more C transferred into mineral-associated organic matter. The amount of root C in MAOM plateaued after six months for the more rapidly degrading litters, while it continued increasing for more slowly degrading litters, suggesting differences in the persistence of new MAOM. We also found that sugarcane, a relatively slowly degrading litter, formed similar amounts of MAOM as the rapidly degrading litters while retaining more C in POM. Thus, our results suggest there may be a middle ground in terms of litter degradability that allows for management of both fractions.

Digital Object Identifier (DOI)

https://doi.org/10.13023/etd.2025.90

Funding Information

This study was supported by the United States Department of Agriculture National Institute of Food and Agriculture (no.: 2019-67019-29401) from 2019 to 2025 and by the Salk Institute for Biological Studies from 2021 to 2024.

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