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Assessing the selective bioweathering of minerals by fungi in soil ecosystems

EMSL Project ID


Rock weathering replenishes nutrients in soil, shapes geochemical carbon sequestration, and drives physical, chemical, and biological processes at a multitude of scales. Globally, lithology type and distribution, climate, and ecosystem activity are predictors of mineral weathering rates and long-term carbon cycling. There is a serious knowledge deficit in understanding how fungi drive incipient mineral transformation in natural environments and how fungal-mineral interactions influence mineral weathering-- a critical yet underrepresented component of climate science and nutrient cycling models. Here, this proposal will develop an approach to address this overarching question: within the highly complex biological system that is natural soil, how do fungi selectively interact with minerals to induce the incipient stages of weathering under field conditions? Specifically, this work will focus on the role of soil fungi in regulating biogeochemical nutrient cycling by preferentially transforming mineral grains based on the elemental composition of mineral materials. The proposal will utilize samples retrieved from a pre-existing field experiment established by PI-Lybrand that builds on prior work with EMSL that established a coupled microscopy approach to assess biological weathering in soil ecosystems. The overarching goal of the proposal is to assess the relative pull of mineral matrix on fungal activity by developing a high resolution microscopy method to automate the identification of mineral grains by elemental composition that will then be combined with a survey of secondary electron images to confirm the presence or absence of fungal-mineral interactions on the identified grains. Three granular substrates were selected for the development of the proposed method given that granite, basalt, and quartz sand vary in rock-derived nutrient content and degree of weatherability based on grain size and elemental composition of the mineral materials. The mineral samples were deployed for six years in highly weathered granitic surface soils in a humid, hardwood forest (Calhoun Experimental Forest, S. Carolina). The proposed project will be accomplished in collaboration with EMSL using a suite of advanced analytical techniques including high resolution microscopy and mass spectrometry. Expected outcomes of this work will be the development of a high resolution microscopy method to automate mineral grain identification (100s to 1000s of grains per sample) and produce accompanying SEM imagery that will be subsequently surveyed to confirm the presence or absence of fungi on identified mineral grains. The method will provide a means to assess fungal-mineral interactions as a function of mineral type, which will advance our understanding of how fungi selectively weather minerals in natural soil conditions. The resulting approach will advance our predictive capabilities for estimating ecosystem level nutrient status- where biological contributions (e.g., fungi) represent a serious knowledge gap in nutrient cycling models and assessments of rock-derived on a global scale.

Project Details

Project type
Large-Scale EMSL Research
Start Date
End Date


Principal Investigator

Rebecca Lybrand
University of California, Davis


Eric Slessarev
Yale University

Dragos Zaharescu
University of California, Davis

Nikolla Qafoku
Pacific Northwest National Laboratory

Team Members

Solveig Sanchez
University of California, Davis

Madison Morris
University of California, Davis

Cassandra Collins
University of California, Davis