Evolution of quinol oxidation within the heme‑copper oxidoreductase superfamily

Murali, Ranjani; Hemp, James; Gennis, Robert B.

doi:10.1016/j.bbabio.2022.148907

Cited by 20 publications

(25 citation statements)

References 74 publications

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“…7 ; Supplementary Data 9 ). Both lineages were recently shown to have a nod 63 . The nod affiliating with Sediminibacterium was sequenced at a depth of 700× corroborating the very high abundance of Sediminibacterium in the community (12%).…”

Section: Resultsmentioning

confidence: 99%

Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

et al. 2023

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Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 107 mL−1) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L−1 [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.

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Section: Resultsmentioning

confidence: 99%

Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

et al. 2023

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“…Nitrosopumilus and other ammonia-oxidizing archaea are widely distributed in the global ocean, and their habitats include seawaters and sediments having O 2 concentration below the detection limit of current technologies (Karner et al 2001; Könneke et al 2005; Molina et al 2010; Walker et al 2010; Beman et al 2012; Stewart et al 2012; Sollai et al 2019). This, in conjunction with the discovery of an NO dismutation phenotype in Pseudomonas aeruginosa that releases up to 20_µM O 2 to the extracellular milieu (Lichtenberg et al 2021), and the identification of nitric oxide dismutase genes in taxonomically diverse bacteria (Murali et al 2022; Ruff et al 2023), suggests that the molecular attributes of O 2 generation could be widespread across the taxonomic as well as ecological spectrum. So far as NO dismutation by N .…”

Section: Discussionmentioning

confidence: 98%

Extremely oligotrophic and complex carbon degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments

Sarkar,

Mondal,

Bhattacharya

et al. 2023

Preprint

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Sediments underlying marine hypoxias are huge sinks of unreacted complex organic matter, where despite acute O2-limitation aerobic bacterial communities thrive, and near-complete depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about how aerobic chemoorganotrophs survive in these sulfidic ecosystems, and what may be their potentials for degrading complex carbon compounds. To elucidate these questions, we isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a ∼3-m sediment horizon underlying the perennial hypoxia of the eastern Arabian Sea. High levels of sequence correspondence between the isolates’ genomes and the habitat’s metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment cores explored. The isolates could catabolize several complex organic compounds of marine and terrestrial origins, via aerobic respiration at high as well as low O2concentrations. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth in any of the strains, but enabled all of them to maintain a fraction of the cell population amidst prolonged anoxia. Under extreme oligotrophy, robust growth followed by protracted stationary phase was observed for all the isolates at low cell density, irrespective of whether O2was high or low. While metabolic deceleration was apparently central to the strains’ adaptation to dwindling organic carbon, O2-limitation could be potentially surmounted via supplies from known producers of biogenic O2, such asNitrosopumilusspecies, which had copious footprints in the habitat’s metagenomes.

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“…Interestingly, the majority of nir MAGs, particularly those with nirK , lack nor (Figure 4), despite the toxicity of the resultant NO. Diverse, non-canonical nor genes have recently been discovered [10, 11, 84] and comprise the majority of nor genes we identified. Few nir -possessing MAGs also carried the NO dismutase gene nod , indicating novel NO detoxification methods likely exist within environmental microbes beyond canonical nor and nod .…”

Section: Discussionmentioning

confidence: 99%

Section: Niche Differentiation Of Denitrifiers Carrying Each Genementioning

confidence: 92%

Genome-resolved metagenomics reveals abundant nitrate reducers and partitioning of nitrite usage within global oxygen deficient zones

Zhang

Sun

Jayakumar

et al. 2023

Preprint

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Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially-mediated pathway proceeding stepwise from NO3−to N2. This process may be performed entirely by complete denitrifiers capable of all four steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes are primarily carried by complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. From 56 metagenomes spanning all three major ODZs, we use genome-resolved metagenomics to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 metagenome-assembled genomes presents the largest collection of pelagic ODZ microbes and reveals a clearer picture of the nitrogen cycling community within this environment.

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Evolution of quinol oxidation within the heme‑copper oxidoreductase superfamily

Cited by 20 publications

References 74 publications

Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

Extremely oligotrophic and complex carbon degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments

Genome-resolved metagenomics reveals abundant nitrate reducers and partitioning of nitrite usage within global oxygen deficient zones

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