Irene Davidova | University of Oklahoma (original) (raw)

Papers by Irene Davidova

International Biodeterioration & Biodegradation, Jul 1, 2023

The ISME Journal, Jun 28, 2007

Information on the susceptibility of higher molecular weight polynuclear aromatic hydrocarbons to... more Information on the susceptibility of higher molecular weight polynuclear aromatic hydrocarbons to anaerobic biodegradation is relatively rare. We obtained a sulfate-reducing bacterial enrichment capable of phenanthrene metabolism from a hydrocarbon-contaminated marine sediment. Phenanthrene degradation was in stoichiometric agreement with the theoretically expected amount of sulfate reduction and inhibited by molybdate. Mineralization of 14 C-phenanthrene by the enrichment was confirmed by the recovery of the expected amount of 14 CO 2 . Stable isotope studies with protonated or deuterated phenanthrene resulted in the detection of the correspondingly labeled phenanthrene carboxylic acid by gas chromatography-mass spectrometry. Comparison of the metabolite profile with a synthesized standard confirmed that the parent molecule was carboxylated at the C-2 position. Incorporation of 13 C-bicarbonate into the carboxyl group implicated a direct carboxylation of phenanthrene as a likely key initial reaction. Denaturing gradient gel electrophoresis analysis of the enrichment showed only two major bands and 16S rRNA sequences obtained by cloning clustered with known hydrocarbon-degrading sulfate-reducing d-proteobacteria, indicating their possible involvement in the anaerobic oxidation of phenanthrene via carboxylation as the initial activation reaction.

Corrosion and materials degradation, Jul 3, 2023

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Microbiology resource announcements, Apr 23, 2020

Anaerobic alkane metabolism is critical in multiple environmental and industrial sectors, includi... more Anaerobic alkane metabolism is critical in multiple environmental and industrial sectors, including environmental remediation, energy production, refined fuel stability, and biocorrosion. Here, we report the complete gap-closed genome sequence for a model n-alkane-degrading anaerobe, Desulfoglaeba alkanexedens ALDC.

Proceedings of the Oklahoma Academy of Science, Jul 11, 2016

Soils are frequently contaminated with hydrocarbons such as polyaromatic hydrocarbons (PAH). This... more Soils are frequently contaminated with hydrocarbons such as polyaromatic hydrocarbons (PAH). This contamination inhibits the growth of some microorganisms in the contaminated soils. However, the contamination may select for microorganisms capable of hydrocarbon degradation under aerobic or anaerobic conditions. Forty five strains of bacteria isolated from tallgrass prairie soil samples were screened for the ability to grow with naphthalene as sole carbon source under aerobic conditions by culturing on minimal medium containing naphthalene as the sole carbon source. Our results showed that none of the 45 strains were able to grow on naphthalene under these conditions. Three out of the 45 strains, e.g. one strain each classified as Ensifer, Stenotrophomonas, or Serratia, were tested for the ability to degrade naphthalene under nitrate reducing conditions. All three strains were facultative anaerobes and showed the physiology of nitrate or nitrate/nitrite reduction when grown under nitrate-reducing conditions in medium containing yeast extract. Two strains (e.g. Stenotrophomonas and Serratia) were tested for the ability to grow on naphthalene, gasoline, or benzene under nitrate-reducing conditions. The Serratia grew poorly on the hydrocarbons, but Stenotrophomonas reached its highest O.D. values on naphthalene. However, upon re-testing a wellwashed cell suspension of the Stenotrophomonas, no loss of naphthalene was found when grown under nitrate-reducing conditions. Although it might be expected that crude-oil contamination would select for PAH degraders, we did not find the nitrate reducing/nitrite reducing isolates to be capable of naphthalene-degradation under aerobic or nitrate-reducing conditions.

The public reporting burden for this collection of information is estimated to average 1 hour per... more The public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing the burden, to the Department of Defense, Executive Services and Communications Directorate (0704-0188). Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number.

Biofouling, May 1, 2012

Experiments were designed to evaluate the corrosion-related consequences of storing/transporting ... more Experiments were designed to evaluate the corrosion-related consequences of storing/transporting fatty acid methyl ester (FAME) alternative diesel fuel in contact with natural seawater. Coastal Key West, FL (KW), and Persian Gulf (PG) seawaters, representing an oligotrophic and a more organic-and inorganic mineral-rich environment, respectively, were used in 60 day incubations with unprotected carbon steel. The original microflora of the two seawaters were similar with respect to major taxonomic groups but with markedly different species. After exposure to FAME diesel, the microflora of the waters changed substantially, with Clostridiales (Firmicutes) becoming dominant in both. Despite low numbers of sulphate-reducing bacteria in the original waters and after FAME diesel exposure, sulphide levels and corrosion increased markedly due to microbial sulphide production. Corrosion morphology was in the form of isolated pits surrounded by an intact, passive surface with the deepest pits associated with the fuel/seawater interface in the Kw exposure. In the presence of FAME diesel, the highest corrosion rates measured by linear polarization occurred in the KW exposure correlating with significantly higher concentrations of sulphur and chlorine (presumed sulphide and chloride, respectively) in the corrosion products.

Methods in Enzymology, 2005

Recent progress in microbiology resulted in the enrichment and isolation of anaerobic bacteria ca... more Recent progress in microbiology resulted in the enrichment and isolation of anaerobic bacteria capable of the biodegradation of various hydrocarbons under a variety of electron-accepting conditions. Problems challenging the enrichment and isolation of anaerobic hydrocarbonclastic organisms required new approaches and modifications of conventional microbiological techniques. This chapter summarizes the collective experience accumulated in this area starting from anaerobic sampling precautions and includes all stages of cultivation from the construction of initial incubations to final isolation steps and the evaluation of culture purity.

Environmental Microbiology, Jun 27, 2016

This study elucidates the role of "Smithella" spp. in methanogenic paraffin biodegradation and us... more This study elucidates the role of "Smithella" spp. in methanogenic paraffin biodegradation and uses comparative genome analysis to illuminate energy conservation strategies in microbial syntrophic interactions.

Applied and Environmental Microbiology, Dec 1, 2005

Gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy were used to stu... more Gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy were used to study the metabolism of deuterated n-alkanes (C 6 to C 12) and 1-13 C-labeled n-hexane by a highly enriched sulfatereducing bacterial culture. All substrates were activated via fumarate addition to form the corresponding alkylsuccinic acid derivatives as transient metabolites. Formation of d 14-hexylsuccinic acid in cell extracts from exogenously added, fully deuterated n-hexane confirmed that this reaction was the initial step in anaerobic alkane metabolism. Analysis of resting cell suspensions amended with 1-13 C-labeled n-hexane confirmed that addition of the fumarate occurred at the C-2 carbon of the parent substrate. Subsequent metabolism of hexylsuccinic acid resulted in the formation of 4-methyloctanoic acid, and 3-hydroxy-4-methyloctanoic acid was tentatively identified. We also found that 13 C nuclei from 1-13 C-labeled n-hexane became incorporated into the succinyl portion of the initial metabolite in a manner that indicated that 13 C-labeled fumarate was formed and recycled during alkane metabolism. Collectively, the findings obtained with a sulfate-reducing culture using isotopically labeled alkanes augment and support the previously proposed pathway (H. Wilkes, R. Rabus, T. Fischer, A. Armstroff, A. Behrends, and F. Widdel, Arch. Microbiol. 177:235-243, 2002) for metabolism of deuterated n-hexane by a denitrifying bacterium.

International Journal of Systematic and Evolutionary Microbiology, Aug 12, 2022

A mesophilic sulphate-reducing micro-organism, able to grow chemolithoautotrophically with H2/CO2... more A mesophilic sulphate-reducing micro-organism, able to grow chemolithoautotrophically with H2/CO2 (20 : 80) and with elemental iron as a sole electron donor, was isolated from a consortium capable of degrading long-chain paraffins and designated strain DRH4T. Cells were oval shaped often with bright refractile cores and occurred singly or in pairs. The cells formed pili. Strain DRH4T could grow chemolithoautotrophically with H2/CO2 or elemental iron and chemoorganotrophically utilizing a number of organic substrates, such as fatty acids from formate to octanoate (C1–C8). Sulphate and thiosulphate served as terminal electron acceptors, but sulphite and nitrate did not. Optimal growth was observed from 37 to 40 °C and pH from 6.5 to 7.2. Strain DRH4T did not require NaCl for growth and could proliferate under a broad range of salinities from freshwater (1 g l−1 NaCl) to seawater (27 g l−1 NaCl) conditions. The genomic DNA G+C content was 54.46 mol %. Based on 16S rRNA gene sequence analysis. strain DRH4T was distinct from previously described Deltaproteobacteria species exhibiting the closest affiliation to Desulforhabdus amnigena ASRB1T, Syntrophobacterium sulfatireducens TB8106T and Desulfovirga adipica 12016T with 93.35, 93.42 and 92.85 % similarity, respectively. Strain DRH4T showed significant physiological differences with the aforementioned organisms. Based on physiological differences and phylogenetic comparisons, we propose to classify DRH4T as the type strain (=DSM 113 455T=JCM 39 248T) of a novel species of a new genus with the name Desulfoferrobacter suflitae gen. nov., sp. nov.

Studies in Surface Science and Catalysis, 2004

ABSTRACT There is a biotechnological link between oil and natural gas that is the product of the ... more ABSTRACT There is a biotechnological link between oil and natural gas that is the product of the relatively recent recognition that many hydrocarbons are susceptible to anaerobic biodegradation and can be converted into methane and carbon dioxide. Unlike the well-documented patterns of aerobic oil biodegradation, anaerobic hydrocarbon metabolism was dismissed as ecologically insignificant. This chapter reviews evidence for anaerobic hydrocarbon biodegradation and provide an overview of some of the more generalizing metabolic features. It explores whether these reactions can be predicted, identifies some of the implications for the ability of anaerobes to convert hydrocarbons into methane, and thereby, generates useful energy. There is ample evidence that anaerobic microbial processes occur under reservoir conditions. There is even evidence, albeit indirect, that such processes occur in situ. The most widely used indicator for biological methanogenesis comes from the carbon isotopic abundance signature of the methane in natural gas deposits. The chapter ends with a discussion on microbial enhanced energy recovery and carbon dioxide.

Journal of Biotechnology, Aug 1, 2017

Highlights  The chemistry and microbial community of shipboard oily wastewater chronically expos... more Highlights  The chemistry and microbial community of shipboard oily wastewater chronically exposed to petroleum hydrocarbons was characterized;  The composition and role of the indigenous microflora in the biodegradation and biocorrosion of both petroleum and hydroprocessed biodiesel fuel was determined;  The planktonic and sessile microbial communities involved in fuel biodegradation and steel biocorrosion were contrasted.  Ecological successional processes in chronically hydrocarbon-exposed marine microbial communities were substantially different from newly oil-polluted communities

International Journal of Systematic and Evolutionary Microbiology, Mar 1, 2016

A mesophilic deltaproteobacterium, designated strain SPR T , was isolated from a methanogenic con... more A mesophilic deltaproteobacterium, designated strain SPR T , was isolated from a methanogenic consortium capable of degrading long-chain paraffins. Cells were motile, vibrio-shaped, and occurred singly, in pairs or in clusters. Strain SPR T did not metabolize hydrocarbons but grew fermentatively on pyruvate and oxaloacetate and autotrophically with H 2 and CO 2. Thiosulfate served as a terminal electron acceptor, but sulfate or sulfite did not. The organism required at least 10 g NaCl l 21 and a small amount of yeast extract (0.001%) for growth. Optimal growth was observed between 30 and 37 8C and a pH range from 6.0 to 7.2.The DNA G+C content of SPR T 's genome was 52.02 mol%. Based on 16S rRNA gene sequence analysis, strain SPR T was distinct from previously described Deltaproteobacteria, exhibiting the closest affiliation to Desulfarculus baarsii DSM 2075 T and Desulfocarbo indianensis SCBM T , with only 91% similarity between their respective 16S gene sequences. In silico genome comparison supported the distinctiveness between strain SPR T and both Desulfocarbo indianensis SCBM T and Desulfarculus baarsii DSM 2075 T. Based on physiological differences, as well as phylogenetic and genomic comparisons, we propose to classify SPR T as the type strain (5DSM 100305 T 5JCM 30857 T) of a novel species of a new genus with the name Dethiosulfatarculus sandiegensis gen. nov., sp. nov. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Dethiosulfatarculus sandiegensis SPR T is KP868755. The draft genome assembly is available under GenBank accession number AZAC00000000. One supplementary figure and two supplementary tables are available with the online Supplementary Material.

International Journal of Systematic and Evolutionary Microbiology, Dec 1, 2006

Two novel sulfate-reducing bacteria, strains ALDC T and Lake, which were able to oxidize n-alkane... more Two novel sulfate-reducing bacteria, strains ALDC T and Lake, which were able to oxidize n-alkanes, were isolated from a naval oily wastewater-storage facility (VA, USA) and from oilfield production water (OK, USA), respectively. The type strain (ALDC T) had a narrow substrate specificity and could grow only with n-alkanes (from C 6 to C 12), pyruvate, butyrate, hexanoic acid and 4-methyloctanoic acid. Cells of strain ALDC T stained Gram-negative and were slightly curved, short rods with oval ends (2?5-3?061?0-1?4 mm), often occurring in pairs. Cells tended to form aggregates or large clusters and were non-motile and did not form endospores. Optimum growth occurred between 31 and 37 6C and at pH 6?5-7?2. NaCl was not required for growth, but salt concentrations up to 55 g l "1 could be tolerated. The DNA G+C content was 53?6 mol%. Phylogenetic analysis of the 16S rRNA genes revealed that strains ALDC T and Lake were closely related, but not identical (99?9 % similarity). The two strains were not closely related to other known alkane-degrading, sulfate-reducing bacteria or to other genera of the Deltaproteobacteria. Therefore, it is proposed that strain ALDC T (=JCM 13588 T =ATCC BAA-1302 T) represents the type strain of a novel species and genus, with the name Desulfoglaeba alkanexedens gen. nov., sp. nov. METHODS Source of organisms. Strain ALDC T was isolated from sludge collected from a naval, oily wastewater-storage facility at the US Navy Abbreviation: DGGE, denaturing gradient gel electrophoresis. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains ALDC T and Lake are DQ303457 and DQ303458, respectively.

Applied and Environmental Microbiology, Dec 1, 2000

We identified trace metabolites produced during the anaerobic biodegradation of H 26-and D 26-n-d... more We identified trace metabolites produced during the anaerobic biodegradation of H 26-and D 26-n-dodecane by an enrichment culture that mineralizes these compounds in a sulfate-dependent fashion. The metabolites are dodecylsuccinic acids that, in the case of the perdeuterated substrate, retain all of the deuterium atoms. The deuterium retention and the gas chromatography-mass spectrometry fragmentation patterns of the derivatized metabolites suggest that they are formed by COH or COD addition across the double bond of fumarate. As trimethylsilyl esters, two nearly coeluting metabolites of equal abundance with nearly identical mass spectra were detected from each of H 26-and D 26-dodecane, but as methyl esters, only a single metabolite peak was detected for each parent substrate. An authentic standard of protonated n-dodecylsuccinic acid that was synthesized and derivatized by the two methods had the same fragmentation patterns as the metabolites of H 26-dodecane. However, the standard gave only a single peak for each ester type and gas chromatographic retention times different from those of the derivatized metabolites. This suggests that the succinyl moiety in the dodecylsuccinic acid metabolites is attached not at the terminal methyl group of the alkane but at a subterminal position. The detection of two equally abundant trimethylsilyl-esterified metabolites in culture extracts suggests that the analysis is resolving diastereomers which have the succinyl moiety located at the same subterminal carbon in two different absolute configurations. Alternatively, there may be more than one methylene group in the alkane that undergoes the proposed fumarate addition reaction, giving at least two structural isomers in equal amounts.

Energy & Fuels, May 5, 2010

Biodiesels have gained widespread acceptance because they are domestically produced carbon-neutra... more Biodiesels have gained widespread acceptance because they are domestically produced carbon-neutral fuels that ultimately decrease greenhouse gas emissions and reduce dependence on fossil imports. While they are chemically and physically stable fuels, their susceptibility to biological degradation in the absence of oxygen is underexplored. We incubated five anaerobic inocula with biodiesel. The microorganisms originated from fresh and marine environments with differing histories of exposure to hydrocarbons, biodiesel, and oxygen. All inocula were able to biodegrade biodiesel within 1 month. Biodiesel metabolism accelerated the rate of both sulfate reduction and methanogenesis above biodiesel-unamended controls. Metabolite profiling indicated that the methyl esters of biodiesel were readily hydrolyzed to the corresponding suite of fatty acids, and the latter were also metabolized. Electrochemical/corrosion experiments showed that the anaerobic microbial metabolism of biodiesel in coastal seawater samples accelerated the rate of pitting corrosion in carbon steel. The susceptibility of biodiesel to anaerobic biodegradation and its propensity to stimulate biocorrosion suggest caution when integrating this alternate fuel with the existing infrastructure.

Microorganisms, Sep 21, 2021

FEMS Microbiology Ecology, Jul 8, 2019

An electron acceptor changed the structure of a paraffin-degrading methanogenic consortium such t... more An electron acceptor changed the structure of a paraffin-degrading methanogenic consortium such that hydrocarbon decay could be coupled to sulfate reduction and multiple mechanisms of iron corrosion were revealed.