Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2404.07137

Microbial iron reduction under oxic conditions: implications for subsurface biogeochemistry

Giulia Ceriotti·Alice Bosco-Santos·Sergey M. Borisov·Jasmine S. Berg
View original source ↗Read source document ↗Export metadata ↓

Abstract

Iron (Fe) reduction is one of Earth's most ancient microbial metabolisms, but after atmosphere-ocean oxygenation, this anaerobic process was relegated to niche anoxic environments below the water and soil surface. However, new technologies to monitor redox processes at the microscale relevant to microbial cells have recently revealed that the oxygen (O2) concentrations controlling the distribution of aerobic and anaerobic metabolisms are more heterogeneous than previously believed. To explore how O2 levels regulate microbial Fe reduction, we cultivated a facultative Fe-reducing bacterium using a cutting-edge microfluidic reactor integrated with transparent planar O2 sensors. Contrary to expectations, microbial growth induced Fe(III)-oxide (ferrihydrite) reduction under fully oxygenated conditions without forming O2-depleted microsites. Batch incubations highlighted the importance of the process at a larger scale, fundamentally changing our understanding of Fe cycling from the conceptualization of metal and nutrient mobility in the subsurface to our interpretation of Fe mineralogy in the rock record.

Explore related subjects

physics.bio-phphysics.geo-ph

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Giulia Ceriotti, Alice Bosco-Santos, Sergey M. Borisov, Jasmine S. Berg. 2024-04-10. Microbial iron reduction under oxic conditions: implications for subsurface biogeochemistry. https://arxiv.org/abs/2404.07137

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Signature of mechanically induced cell extrusions in cell size distribution

How a growing tissue organizes its own homeostatic state is a central question in the physics of living matter. We show that when a growing epithelial sheet counteracts increasing cell density by mechanically squeezing cells out of its plane, a homeostatic in-plane pressure emerges as a generalization of a yield stress. We find that in the quasistatic growth limit the homeostatic state is marginally stable, with a pseudogap in the distribution of local distances to the extrusion threshold pressure. Because such mechanically induced extrusions arise from an instability of individual cells, the pseudogap is imprinted in the distribution of cell areas. This provides an image-based way to test for presence of mechanically induced extrusions and we identify this signature in the developing wing epithelium of \textit{D.~melanogaster}. We expect the same principles to apply to confined three-dimensional tissues.

physics.bio-ph↗
arXiv2026

Towards Accurate Prediction of Mutation-Induced Changes in Protein Structure

Proteins can possess numerous mutations relative to their wild-type amino acid sequences with minimal impact to their structure and function. However, in other cases, even a single amino acid mutation relative to the wild-type sequence can lead to a large change in structure or even a disease phenotype. While the accuracy of wild-type protein structure prediction has improved significantly in recent years, it remains difficult to accurately predict the structure of mutant proteins. Here, we characterize the local mutation-induced structural changes in proteins for a dataset of wildtype and the corresponding single-amino acid mutant x-ray crystal structures from the Protein Data Bank (PDB). We find that mutation-induced structural changes in these proteins are localized at the site of the mutation, decaying rapidly with increasing spatial distance from the mutation site. In addition, we evaluate how well AlphaFold3 can recapitulate the observed mutation-induced structural deformations in the x-ray crystal structures. We find that the accuracy of the AlphaFold3 predictions decreases strongly with increasing mutation-induced deformation. In contrast to the results for AlphaFold3, the Pearson correlation between a single physical feature, i.e. the change in solvent accessibility, and the mutation-induced deformation does not depend on the magnitude of the deformation. Our results and analyses provide a framework for further studies aimed at predicting the structural changes in proteins caused by single amino acid mutations.

physics.bio-ph↗
arXiv2026

Biology and Physics

This article frames the relation between biology and physics by characterizing the former as a subdiscipline rather than a special case of the latter. To do this, we posit biological physics as the science of living matter in contrast to classic biophysics, the study of organismal properties by physical techniques. At the scale of the individual cell, living matter is nonunitary, i.e., not composed of aggregated subunits, and has features (e.g., intracellular organizational arrangements and biomolecular condensates) that are unlike any materials of the nonliving world. In transiently or constitutively multicellular forms (social microorganisms, animals, plants), living matter sustains physical processes that are generic (shared with nonliving matter, e.g., subunit communication by molecular diffusion in cellular slime molds), biogeneric (analogous to nonliving matter but realized through cellular activities, e.g., subunit demixing in animal embryos) or nongeneric (pertaining to sui generis materials, e.g., budding of active solids in plants). This "forms of matter" perspective is philosophically situated in the dialectical materialism of Engels and Hessen and the multilevel physicalism of Neurath and the logical empiricists. We counterpose this view to informationism and to genetic and other hierarchically reductionist physical theories of biological systems and highlight open questions regarding incompletely characterized and enigmatic forms of living matter.

physics.bio-ph↗