Browsing by Author "Sutton, John M."

Now showing 1 - 7 of 7
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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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    Caenorhabditis elegansdauers vary recovery in response to bacteria from natural habitat
    (Wiley, 2020) Bubrig, Louis T.; Sutton, John M.; Fierst, Janna L.; University of Alabama Tuscaloosa
    Many species use dormant stages for habitat selection by tying recovery to informative external cues. Other species have an undiscerning strategy in which they recover randomly despite having advanced sensory systems. We investigated whether elements of a species' habitat structure and life history can bar it from developing a discerning recovery strategy. The nematodeCaenorhabditis eleganshas a dormant stage called the dauer larva that disperses between habitat patches. On one hand,C. eleganscolonization success is profoundly influenced by the bacteria found in its habitat patches, so we might expect this to select for a discerning strategy. On the other hand,C. elegans' habitat structure and life history suggest that there is no fitness benefit to varying recovery, which might select for an undiscerning strategy. We exposed dauers of three genotypes to a range of bacteria acquired from the worms' natural habitat. We found thatC. elegansdauers recover in all conditions but increase recovery on certain bacteria depending on the worm's genotype, suggesting a combination of undiscerning and discerning strategies. Additionally, the worms' responses did not match the bacteria's objective quality, suggesting that their decision is based on other characteristics.
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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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    Genome Size Changes by Duplication, Divergence, and Insertion in Caenorhabditis Worms
    (Oxford University Press, 2023) Adams, Paula E.; Eggers, Victoria K.; Millwood, Joshua D.; Sutton, John M.; Pienaar, Jason; Fierst, Janna L.; University of Alabama Tuscaloosa; Auburn University; Florida International University
    Genome size has been measurable since the 1940s but we still do not understand genome size variation. Caenorhabditis nematodes show strong conservation of chromosome number but vary in genome size between closely related species. Androdioecy, where populations are composed of males and self-fertile hermaphrodites, evolved from outcrossing, female-male dioecy, three times in this group. In Caenorhabditis, androdioecious genomes are 10-30% smaller than dioecious species, but in the nematode Pristionchus, androdioecy evolved six times and does not correlate with genome size. Previous hypotheses include genome size evolution through: 1) Deletions and "genome shrinkage" in androdioecious species; 2) Transposable element (TE) expansion and DNA loss through large deletions (the "accordion model"); and 3) Differing TE dynamics in androdioecious and dioecious species. We analyzed nematode genomes and found no evidence for these hypotheses. Instead, nematode genome sizes had strong phylogenetic inertia with increases in a few dioecious species, contradicting the "genome shrinkage" hypothesis. TEs did not explain genome size variation with the exception of the DNA transposon Mutator which was twice as abundant in dioecious genomes. Across short and long evolutionary distances Caenorhabditis genomes evolved through small structural mutations including gene-associated duplications and insertions. Seventy-one protein families had significant, parallel decreases across androdioecious Caenorhabditis including genes involved in the sensory system, regulatory proteins and membrane-associated immune responses. Our results suggest that within a dynamic landscape of frequent small rearrangements in Caenorhabditis, reproductive mode mediates genome evolution by altering the precise fates of individual genes, proteins, and the phenotypes they underlie.
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    De NovoGenome Assemblies for Three North American Bumble Bee Species:Bombus bifarius,Bombus vancouverensis, andBombus vosnesenskii
    (Oxford University Press, 2020) Heraghty, Sam D.; Sutton, John M.; Pimsler, Meaghan L.; Fierst, Janna L.; Strange, James P.; Lozier, Jeffrey D.; University of Alabama Tuscaloosa; Ohio State University
    Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America,Bombus bifarius,Bombus vancouverensis, andBombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We presentde novogenome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 - 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome,Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.
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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.