ABSTRACT Fungal mineral weathering regulates the bioavailability of inorganic nutrients from mineral surfaces to organic matter and increase the bioavailable fraction of nutrients. Such weathering strategies are classified as biomechanical or biochemical. In the case of fungal uptake of mineral...
Introduction: Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community...
Abstract Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry–rewet events occurs...
Primary publication pre-print. Cite as: arXiv:2410.09346 [q-bio.MN]
Citation: Mejia-Rodriguez D, Kim H, Sadler N, Li X, Bohutskyi P, Valiev M, Qian WJ, Cheung MS. PTM-Psi: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions. Protein Sci. 2023 Dec;32(12)...
Citation : Reichart NJ, Steiger AK, Van Fossen EM, McClure R, Overkleeft HS, Wright AT. Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing. ISME Commun. 2023 Sep 30;3(1):106. doi: 10.1038/s43705-023...
The research goal of this project is to establish model synthetic microbial communities to understand the rules regulating their biological function in order to utilize them as next generation bioproduction platforms capable of reducing carbon and nitrogen footprints in biomanufacturing processes.
The soil microbiome performs many functions that are key to ecology, agriculture, and nutrient cycling. However, because of the complexity of this ecosystem we do not know the molecular details of the interactions between microbial species that lead to these important functions. Here, we use a...
"Moisture modulates soil reservoirs of active DNA and RNA viruses" Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect...
Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil...
The research goal of this project is to construct and streamline an approach to identify phenotype-relevant signatures by integrating various proteomics data. Leveraging protein structures and interaction networks, we will map structural changes and post-translational modifications to identify...
The research goal of this project is to build and understand model communities that show carbon storage phenotypes
The research goal of this project is to develop a biologically informed machine learning (ML) model that integrates datasets from different studies, and leverages current biological knowledge in an automated manner, to improve predictions in biological data analysis.
By developing explainable, predictive metabolic models of individual microbes, we aim to design consortia that convert light and abundant atmospheric gases into high-value molecules through microbial division of labor.
