Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients

Frontiers in Microbiology
Jeffrey M DickAnhuai Lu

Abstract

There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be a...Continue Reading

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Citations

Mar 17, 2021·Marine Pollution Bulletin·Rongjun ShiQingzhi Zhu

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Methods Mentioned

BETA
PCR

Software Mentioned

R
. py
autoskewer
parallel
Skewer
CHNOSZ
sortme
Zenodo
FragGeneScan
GitHub

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