Biology subjects

LaBonte, S.

Publications and source records attributed to LaBonte, S..

3 recordsLinked to original sources

bioRxiv2026

Saprotrophic soil fungus dissolves lithium lepidolite through inositol rescue metabolism

Microbial weathering of minerals represents a key biogeochemical process through which microorganisms access essential nutrients locked within rock and ore substrates. In this study, we investigated the metabolic response of a model fungus during growth on lithium (Li) ore to elucidate the mechanisms underpinning biologically mediated mineral weathering and subsequent metal mobilization. Our results revealed a distinct metabolic shift in the fungus when cultivated on Li ore, characterized by altered patterns of organic acid production and energy metabolism. This shift coincided with measurable weathering of the Li ore matrix and the consequent release of soluble Li into the surrounding environment, demonstrating a direct link between fungal metabolic reprogramming and mineral breakdown. Importantly, these observations are consistent with metabolic shifts documented in previous studies of mineral weathering by this fungus, suggesting that such responses constitute a conserved and reproducible strategy employed during the colonization of mineral substrates. Although the present work was conducted using a single model microorganism under controlled conditions, the findings carry broader ecological implications. Natural microbial communities inhabiting mineral-rich environments may undergo analogous metabolic shifts when weathering minerals to acquire limiting nutrients, thereby contributing to large-scale elemental cycling and metal release. Understanding these processes not only advances fundamental knowledge of microbe-mineral interactions but also informs emerging applications in biomining and bio-based recovery of critical metals such as lithium. Collectively, this study highlights the central role of microbial metabolism in driving mineral weathering and offers a framework for predicting and harnessing similar processes within complex microbial communities. IMPORTANCEThe model fungus exhibits a distinct, reproducible shift in metabolism--particularly in organic acid production and energy pathways--when grown on Li ore, directly linking cellular metabolism to mineral breakdown. This metabolic shift promotes weathering of the ore matrix and the release of soluble lithium, demonstrating a biological route for liberating a critical metal from its mineral host. Because similar shifts occur across different minerals, natural microbial communities likely employ comparable strategies to weather minerals and acquire limiting nutrients, contributing to global elemental cycling. These findings provide a foundation for sustainable biomining and bio-based recovery of lithium and other critical metals, offering a lower-impact alternative to conventional extraction methods.

microbiology↗

bioRxiv2021

Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills. Significance StatementThe primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.

bioinformatics↗

bioRxiv2019

Cariogenic Streptococcus mutans produces strain-specific antibiotics that impair commensal colonization

Streptococcus mutans is a common constituent of dental plaque and an etiologic agent of dental caries (tooth decay). Here we elucidate a biosynthetic pathway, encoded by globally distributed strains of S. mutans, which produces a series of bioactive small molecules including reutericyclin and two N-acyl tetramic acid analogues active against oral commensal bacteria. This pathway may provide S. mutans with a competitive advantage, promoting dysbiosis and caries pathogenesis.

microbiology↗