aerobic respiration Archives - Astrobiology

Phylogenetic tree of bacteria showing the occurrence of respiratory quinones.

Biochemistry & Organic Chemistry, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

A Novel Quinone Biosynthetic Pathway Illuminates The Evolution Of Aerobic Metabolism

by Keith CowingJanuary 24, 2025January 24, 2025

The dominant organisms in modern oxic ecosystems rely on respiratory quinones with high redox potential (HPQs) for electron transport in aerobic respiration and photosynthesis. The diversification of quinones, from low […]

Spores of the parasite H. salminicola swim under a microscope. Those alien "eyes" are actually stinger cells, one of the few features this organism hasn't evolved away. (Image credit: Stephen Douglas Atkinson)

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Habitable Zones, Microbiology & Virology, Status Report

Henneguya salminicola Lacks A Mitochondrial Genome And Does Not Require Oxygen

by Keith CowingJanuary 12, 2025January 11, 2025

Mitochondrial respiration is an ancient characteristic of eukaryotes. However, it was lost independently in multiple eukaryotic lineages as part of adaptations to an anaerobic lifestyle.

Phylogenetic tree of bacteria showing the occurrence of respiratory quinones. Quinones with high redox potential (UQ, PQ, mPQ) occur only in aerobic Nitrospirota, Pseudomonadota, and Cyanobacteriota. Low potential quinones occur in anaerobic Nitrospirota (MK), some Pseudomonadota (MK), and all Cyanobacteriota (PhQ). Asterisks indicate strains in which presence of mPQ has been verified experimentally. See Fig. S11-13 for detailed trees. The maximum-likelihood phylogenetic tree was constructed from 120 concatenated single copy marker proteins (58) of 547 isolate genomes and metagenome-assembled genomes, covering all bacterial phyla, and rooted using the DST group to approximate the bacterial root (59). Quinone occurrences were derived from instrumental analysis of isolates or inferred from the presence of key biosynthesis genes (SI results; Supplementary Datafile S3; including literature data). Phenotype oxytolerance was curated from strain descriptions. Selected classes/orders denoted inside of rings. Selected phyla denoted outside of rings: ACD, Aquificota-Campylobacterota-Deferribacterota; Desulfob., Desulfobacterota; DST, Deinococcota-Synergistota227 Thermotogota; FA, Firmicutes-Actinobacteriota; FCB, Fibrobacterota-Chlorobacteria-Bacteroidota; Marg., “Candidatus Margulisbacteria”; Myxoc., Myxococcota; Nitrospin., Nitrospinota; PVC, Planctomycetota229 Verrucomicrobiota-Chlamydiota; Seri., “Candidatus Sericytochromatia”; Vamp., Vampirovibrionophyceae -- biorxiv.org

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Status Report

A Novel Quinone Biosynthetic Pathway Illuminates The Evolution Of Aerobic Metabolism

by Keith CowingAugust 12, 2024August 10, 2024

The dominant organisms in modern oxic ecosystems rely on respiratory quinones with high redox potential (HPQs) for electron transport in aerobic respiration and photosynthesis.

Bacterial evolution through geological time. (a) The early evolution of bacterial genetic diversity in the Archaean (David and Alm 2010) is reflected by rapid increase in gene content disparity (see Supplementary Material). (b) A persistent higher diversification rate of aerobes since the GOE. The line charts the relative diversification rate (the ratio of the inverse of the waiting time to the next speciation event) for aerobic and anaerobic lineages, revealing a persistent higher diversification rate of aerobes for most of the Earth’s history since the GOE. Rates equilibrated prior to the NOE, before a return to higher diversification rates for aerobes since the GOE. The dotted line denotes a ratio of 1, where the diversification rate of aerobic and anaerobic lineages is equal. Terminal branches were omitted and ratios since 100 Mya were not calculated do to a low number of nodes. (c) Spread of aerobic metabolism by HGT. Transitions from anaerobic to aerobic lifestyles have outnumbered transitions in the reverse direction/back transitions/returns to anaerobicity for most of Earth history since the GOE. The plots show the ratio of aerobic to anaerobic transition rates on the dated species tree during each time period. The dotted line denotes a ratio of 1, where transitions occur in both directions at the same rate. The small number of nodes since ~200 Ma greatly increases uncertainty for both analyses, as reflected in the wide confidence intervals of posterior node age estimates. Ratios since 100 Mya were not calculated due to a low number of nodes. (d) shows the number of aerobic lineages according to Figure 2, e) qualitative sketch of atmospheric oxygen levels through time based on (Lyons, Reinhard, and Planavsky 2014; Poulton et al. 2021; Krause et al. 2022). The grey line shows the Moon-forming impact at ~4.52 Ga; the green line at ~3.23 Ga reflects the presence of fossil and isotopic evidence for oxygenic photosynthesis; the red line at ~2.33 Ga reflects the end of the GOE (see calibrations in Supplementary Material). --- biorxiv.org

Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Microbiology & Virology, Origin & Evolution of Life, Status Report

An Evolutionary Timescale For Bacteria Calibrated Using The Great Oxidation Event

by Keith CowingAugust 16, 2023August 16, 2023

Most of life’s diversity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time.

Two proposed mechanisms for H2O2 generation at quartz–water interfaces. (A) Stress-induced cleavage of Si–O bonds. Applied force is represented by a linear falling potential (dashed line), which is added to the Morse potential of the unstretched Si–O bond (dotted line), thus resulting in a force-deformed Morse potential (solid line). The new dissociation energy D′ is smaller than D in the case of a stretching force. Modified after Kauzmann et al. (42). The probability of generation of surface-bound radicals in quartz therefore increases during mechanical processes. (B) Contact of water on freshly fractured surface of abraded quartz. Modified after Schoonen et al. (32). (C) Generation of H2O2 and O2 in the reaction between H2O and oxygen radical (≡SiO•). (D) Generation of rocky H2O2 and O2 in the reaction between H2O and peroxy radical (≡SiOO•). Surface-bound radicals are formed through homolysis of Si–O bonds, including ≡SiO•, ≡SiOO•, and E′ center (≡Si•), while surface charges (≡Si+ and ≡SiO–) for heterolysis. Silanol groups (≡SiOH) are end products on quartz surface after hydroxylation. -- Guangzhou Institute

Astrogeology, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Habitable Zones, Origin & Evolution of Life, Press Release

A Novel Origin Of Abiotic Oxidants On Early Earth: Minerals

by Keith CowingMarch 23, 2023March 23, 2023

Molecular oxygen (O2) is essential for respiration on today’s Earth, but the early atmosphere was almost devoid of oxygen until the Great Oxidation Event. How then did Earth’s atmosphere become […]