Biology subjects

Shock, E.

Publications and source records attributed to Shock, E..

3 recordsLinked to original sources

bioRxiv2025

Metal speciation and bioavailability in microbial growth media

Microbial growth in both natural environments and artificial media is strongly influenced by metal speciation, which can be quantitatively modeled for a given chemical composition. Despite its importance, metal speciation is rarely incorporated into the design of microbial growth experiments, often leading to misinterpretations of metal bioavailability and toxicity. In this study, we revisit two historical microbial investigations: one that drew inaccurate conclusions due to the absence of speciation calculations, and another that relied on flawed assumptions about metal speciation. Through targeted recalculations, we demonstrate how these oversights impacted the interpretation of metal-microbe interactions including the applicability of the free ion activity model (FIAM). Additionally, we perform metal speciation analyses for a bacterial growth medium to illustrate how speciation can clarify distinctions between stimulatory and non-essential metals. Further simulations were conducted for six DSMZ-listed microbial media and six chemical variants of a representative medium, using estimated stability constants where experimental data were unavailable. Collectively, this work underscores the value of integrating metal speciation calculations into microbial research to improve the accuracy of conclusions regarding metal bioavailability and toxicity.

microbiology↗

bioRxiv2025

Metal speciation in blood plasma

Metal speciation in blood plasma is heavily influenced by proteins and peptides including transferrin, albumin, and glutathione. Despite this, few studies have incorporated these large molecules in speciation calculations, probably due to a lack of experimental measurements. Additionally, there is increasing evidence that metal complexes of small molecules are bioavailable. Due to the limitations posed by analytical techniques, thermodynamic models can serve as an excellent alternative to experimental measurements of metal speciation. In this work, we predict metal speciation for several biologically relevant metals incorporating complexes with proteins, peptides and small molecules. We supplemented experimental measurements from the literature with linear free energy estimates to fulfill the inventory of stability constants required to perform these calculations. In addition to evaluating the speciation of naturally present metals, we also predict the speciation of metals used for therapeutic applications like anticancer drugs, antidiabetics and antacids. Our results indicate that metal speciation is heavily dependent on pH and chelator concentration and can change drastically as metals move from blood plasma to inside cells. Additionally, metal speciation can be dominated by proteins like transferrin and is subject to change as metals cross the blood-brain barrier. Our results corroborate many experimental measurements and can help design future experiments investigating the biological impact of metal-based drugs and metal-toxicity.

biochemistry↗

bioRxiv2025

Methanotrophy Under Extreme Alkalinity in a Serpentinizing System

Serpentinization produces hyperalkaline, H2- and CH4-rich fluids that support microbial life in extreme conditions and serve as analogs for ocean worlds such as Enceladus. While methane production in these systems has been well studied, methane consumption--especially under high pH--remains poorly understood. Here, we present isotopic, geochemical, and genomic evidence for hyperalkaliphilic (pH > 11) methanotrophy in the Samail Ophiolite in Oman. Using models that account for fluid mixing and gas exsolution, we identify {delta}13CH4 enrichment that cannot be explained by abiotic processes alone. The enrichment of 13CH4 co-occurs with methanotroph 16S rRNA gene sequences, particularly in fluids formed by mixing CH4-rich, anoxic fluids with oxidant-rich surface waters. Shotgun metagenomics reveals a metagenome-assembled genome affiliated with Methylovulum, encoding a complete methane oxidation pathway, multiple carbon assimilation routes, and Na+/H+ antiporters--adaptations likely enabling growth above pH 11. Methanotroph diversity and abundance peak in mixed fluids but are suppressed at total ammonia nitrogen concentrations >20 M. Anaerobic methane-oxidizing archaea (ANME) may also contribute to CH4 oxidation in the deep subsurface. Our findings highlight the viability of methanotrophy under extreme alkaline conditions and provide a framework for interpreting {delta}13CH4 signals in serpentinizing environments on Earth and beyond.

microbiology↗