First released more than ten years ago (Geochemical Transactions, 2008), the free CHNOSZ R package for thermodynamic calculations and diagrams for geochemistry has seen continued growth and maintenance (Frontiers in Earth Science, 2019). Recent updates include functions for making diagrams with multiple metals (Applied Computing and Geosciences, 2021).

The OBIGT database in CHNOSZ has thermodynamic data from many published papers. My own contributions include estimates of thermodynamic properties relevant to aromatic maturity parameters in organic geochemistry (Geochimica et Cosmochimica Acta, 2013) and group contribution parameters for proteins that account for temperature and pH effects (Biogeosciences, 2006). When deployed at the genome scale, thermodynamic calculations indicate that overall protein synthesis from inorganic precursors is exergonic (releases energy) in the mixing zone of seawater and vent fluid at hydrothermal systems hosted in ultramafic rocks (Journal of Geophysical Research: Biogeosciences, 2021 ).

How are microbial communities shaped by gradients of temperature, redox, and water availability?

Proteins in various functional classes and phyla exhibit parallel trends of carbon oxidation state in a hot-spring metagenome (PLOS One, 2011 and 2013). But it's not just about redox; two chemical metrics (Z_C and n_H2O) of proteins vary along environmental redox gradients and salinity gradients (Frontiers in Microbiology, 2019; Biogeosciences, 2020).

Oxygen and water, bugs and us. The healthy human microbiome is shaped by the chemical characteristics of different body sites. Dysbiosis in COVID-19 is associated with more reduced microbial proteins, informing about how the body's internal chemical environment changes in disease (preprint: Dick, 2023).

Local and global chemical shaping of genomes. By combining taxonomic classifications with genome sequences, we can quantify genomic adaptation at the community level. Locally, carbon oxidation state (Z_C) of community reference proteomes tracks oxygen concentration in hydrothermal systems, shale gas wells, and redox-stratified water bodies (Microbial Ecology, 2023 ). Globally, protein Z_C is positively correlated with redox potential in aquatic, terrestrial, hydrothermal, and hyperalkaline environments, suggesting new ways in which genomic adaptation reflects physicochemical conditions (mSystems, 2023).

How can we get geochemical information from genomes? Distinct redox boundaries characterize evolutionary transitions in lineages of methanogens and ammonia-oxidizing Archaea. These boundaries are comparable to ranges of hydrogen activity found in modern ecosystems and could serve as proxies for past environments (Geobiology, 2023 ).

Stoichiometric hydration state (n_H2O) is the amount of water in balanced chemical reactions that represent changes in protein expression levels. In an analysis of hundreds of proteomic datasets (available in the canprot package), cancer tissue generally exhibits higher proteomic n_H2O than healthy tissue. In contrast, cells grown in high-glucose media or in 3D cell culture instead of monolayers are most often associated with relatively low proteomic n_H2O (Computational and Systems Oncology, 2021). These are the first results to suggest a physicochemical link between protein expression patterns and cellular water content, which is elevated in tumors and proliferating cells.