Browsing by Author "Akob, Denise M."

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    Acetylenotrophy: a hidden but ubiquitous microbial metabolism?
    (Oxford University Press, 2018) Akob, Denise M.; Sutton, John M.; Fierst, Janna L.; Haase, Karl B.; Baesman, Shaun; Luther, George W., III; Miller, Laurence G.; Oremland, Ronald S.; United States Department of the Interior; United States Geological Survey; University of Alabama Tuscaloosa; University of Delaware
    Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.
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    Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil
    (American Society of Microbiology, 2022) Sutton, John M.; Bushman, Timothy J.; Akob, Denise M.; Fierst, Janna L.; University of Alabama Tuscaloosa; United States Department of the Interior; United States Geological Survey
    We report the genome of Rhodococcus opacus strain MoAcy1 (DSM 44186), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of similar to 8 Mbp and two closed plasmids, with a G+C content of 67.3%.
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    Detection of Diazotrophy in the Acetylene-Fermenting Anaerobe Pelobacter sp Strain SFB93
    (American Society of Microbiology, 2017) Akob, Denise M.; Baesman, Shaun M.; Sutton, John M.; Fierst, Janna L.; Mumford, Adam C.; Shrestha, Yesha; Poret-Peterson, Amisha T.; Bennett, Stacy; Dunlap, Darren S.; Haase, Karl B.; Oremland, Ronald S.; United States Department of the Interior; United States Geological Survey; University of Alabama Tuscaloosa; United States Department of Agriculture (USDA); Boeing
    Acetylene (C2H2) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C2H2 block assays of N2O reductase, and Pelobacter acetylenicus was shown to grow on C2H2 via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N(2)ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N(2)ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N(2)ase. Diazotrophic growth was observed under N-2 but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N(2)ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days. IMPORTANCE Here we show that a single Pelobacter strain can grow via acetylene fermentation and carry out nitrogen fixation, using the only two enzymes known to transform acetylene. These findings provide new insights into acetylene transformations and adaptations for nutrient (C and N) and energy acquisition by microorganisms. Enhanced understanding of acetylene transformations (i.e., extent, occurrence, and rates) in modern environments is important for the use of acetylene as a potential biomarker for extraterrestrial life and for degradation of anthropogenic contaminants.
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    Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments
    (Microbiology Society, 2021) Baesman, Shaun M.; Sutton, John M.; Fierst, Janna L.; Akob, Denise M.; Oremland, Ronald S.; United States Department of the Interior; United States Geological Survey; University of Alabama Tuscaloosa
    A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93(T), was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93(T) was capable of acetylenotrophic and diazotrophic growth, grew at 22-37 degrees C, pH 6.3-8.5 and in the presence of 10-45 g l(-1) NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93(T) represented a member of the genus Syntrophotalea with highest 16S rRNA gene sequence similarities to Syntrophotalea acetylenica DSM 3246(T) (96.6 %), Syntrophotalea carbinolica DSM 2380(T) (96.5 %), and Syntrophotalea venetiana DSM 2394(T) (96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93(T) had low genome-wide average nucleotide identity (81?87.5 %) and <70 % digital DNA-DNA hybridization value with other members of the genus Syntrophotalea. The phylogenetic position of SFB93(T) within the family Syntrophotaleaceae and as a novel member of the genus Syntrophotalea was confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species, Syntrophotalea acetylenivorans sp. nov., is proposed, with SFB93(T) (=DSM 106009(T)=JCM 33327(T)=ATCC TSD-118(T)) as the type strain.