Joseph M. Suflita

Desulfomonile tiedjei gen. nov. and sp. nov., a novel anaerobic, dehalogenating, sulfate-reducing bacterium

An anaerobic, dehalogenating, sulfate-reducing bacterium, strain DCB-1, is described and nutritionally characterized. The bacterium is a Gram-negative, nonmotile, non-sporeforming large rod with an unusual morphological feature which resembles a collar. The microorganism reductively dehalogenates meta substituted halobenzoates and also reduces sulfate, sulfite and thiosulfate as electron acceptors. The bacterium requires nicotinamide, 1,4-naphthoquinone and thiamine for optimal growth in a defined medium. The microorganism can grow autotrophically on H2:CO2 with sulfate or thiosulfate as terminal electron acceptors. It can also grow heterotrophically with pyruvate, several methoxybenzoates, formate plus sulfate or benzoate plus sulfate. It ferments pyruvate to acetate and lactate in the absence of other electron acceptors. The bacterium is inhibited by MoOinf4sup2-or SeOinf4sup2-as well as tetracycline, chloramphenicol, kanamycin or streptomycin. Cytochrome c3 and desulfoviridin have been purified from cells grown in defined medium. 16S rRNA sequence analysis indicates the organism is a new genus of sulfate-reducing bacteria in the delta subdivision of the class Proteobacteria. We propose that the strain be named Desulfomonile tiedjei.

Influence of surfactants on microbial degradation of organic compounds

Abstract Surfactants have the ability to increase aqueous concentrations of poorly soluble compounds and interfacial areas between immiscible fluids, thus potentially improving the accessibility of these substrates to microorganisms. However, both enhancements and inhibitions of biodegradation of organic compounds in the presence of surfactants have been reported. The mechanisms behind these phenomena are not well understood. To better understand the factors involved and the current state of knowledge in this field, a search of the literature concerning the influence of commercial surfactants and biosurfactants on microbial metabolism has been conducted. Factors pertaining to surfactant‐substrate interactions such as emulsification, solubilization, and partitioning of hydrocarbons between phases, all of which can influence accessibility of substrates to microorganisms, are of concern. Also, due to the direct interaction of surfactants with microorganisms, it appears that steric or conformational compatibi...

Pore‐size constraints on the activity and survival of subsurface bacteria in a late cretaceous shale‐sandstone sequence, northwestern New Mexico

To investigate the distribution of microbial biomass and activities to gain insights into the physical controls on microbial activity and potential long‐term survival in the subsurface, 24 shale and sandstone cores were collected from a site in northwestern New Mexico. Bacterial biomass in the core samples ranged from below detection to 31.9 pmol total phospholipid fatty acid (PLFA) g‐1 of rock with no apparent relationship between lithology and PLFA abundance. No metabolic activities, as determined by anaerobic mineralization of [14C]acetate and [14C]glucose and 35SO4 2‐ reduction, were detected in core samples with pore throats <0.2 fan in diameter, smaller than the size of known bacteria. However, enrichments revealed the presence of sulfate‐re‐ducing bacteria, and 35SO4 2‐ reduction was detected upon extended (14 days) incubation in some small‐pore‐throat samples. In contrast, relatively rapid rates of metabolic activity were more common in core samples containing a significant fraction of pore throat...

Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas

ABSTRACT World requirements for fossil energy are expected to grow by more than 50% within the next 25 years, despite advances in alternative technologies. Since conventional production methods retrieve only about one-third of the oil in place, either large new fields or innovative strategies for recovering energy resources from existing fields are needed to meet the burgeoning demand. The anaerobic biodegradation of n-alkanes to methane gas has now been documented in a few studies, and it was speculated that this process might be useful for recovering energy from existing petroleum reservoirs. We found that residual oil entrained in a marginal sandstone reservoir core could be converted to methane, a key component of natural gas, by an oil-degrading methanogenic consortium. Methane production required inoculation, and rates ranged from 0.15 to 0.40 μmol/day/g core (or 11 to 31 μmol/day/g oil), with yields of up to 3 mmol CH4/g residual oil. Concomitant alterations in the hydrocarbon profile of the oil-bearing core revealed that alkanes were preferentially metabolized. The consortium was found to produce comparable amounts of methane in the absence or presence of sulfate as an alternate electron acceptor. Cloning and sequencing exercises revealed that the inoculum comprised sulfate-reducing, syntrophic, and fermentative bacteria acting in concert with aceticlastic and hydrogenotrophic methanogens. Collectively, the cells generated methane from a variety of petroliferous rocks. Such microbe-based methane production holds promise for producing a clean-burning and efficient form of energy from underutilized hydrocarbon-bearing resources.

Anaerobic Biodegradation of Gasoline Oxygenates: Extrapolation of Information to Multiple Sites and Redox Conditions

A series of alcohol, ketone, ester, and ether oxygenates were tested for their susceptibility to anaerobic decay in samples from four chronically contaminated sedimentary environments. The effect of various electron acceptors on oxygenate biodegradation was also evaluated with a single inoculum source. In addition, two acetogenic bacteria were tested for their ability to metabolize selected oxygenate compounds. The susceptibility of the test oxygenates to anaerobic decay could be related to their chemical structure. That is, compounds other than the ethers that possessed primary or secondary substituted carbon atoms were readily degraded under all conditions tested while compounds that had tertiary substituted carbon atoms resisted biodegradation. The ether oxygenates were generally not degraded when incubated with various inocula, regardless of the electron acceptor status. The exceptions included methyl butyl ether, which was depleted in both sulfate-reducing and methanogenic incubations, and the partial transformation of methyl tert-butyl ether to tert-butanol after a 152-day acclimation period in a single replicate from a river sediment chronically contaminated with fuel. Heat-inactivated control incubations suggested that the latter transformation was biologically catalyzed. 47 refs., 1 fig., 3 tabs.

Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

Marine subsurface environments such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH) oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10) could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the Gulf of Mexico.

Anaerobic Oxidation of n-Dodecane by an Addition Reaction in a Sulfate-Reducing Bacterial Enrichment Culture

ABSTRACT We identified trace metabolites produced during the anaerobic biodegradation of H26- and D26-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 C—H or C—D 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 H26- and D26-dodecane, but as methyl esters, only a single metabolite peak was detected for each parent substrate. An authentic standard of protonatedn-dodecylsuccinic acid that was synthesized and derivatized by the two methods had the same fragmentation patterns as the metabolites of H26-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.

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfate-reducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptide- and amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria, and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely reinjected into reservoirs for oil recovery purposes, are biodegraded and can provide biocorrosive microbial communities with an important source of nutrients.

Ecology and evolution of microbial populations for bioremediation

Bioremediation exploits the genetic diversity and metabolic versatility of microorganisms for the transformation of contaminants into less-harmful end-products, which are then integrated into natural biogeochemical cycles. Understanding the ecology, physiology and evolution of degradative microorganisms is critical for the successful consideration and implementation of bioremediation. This article focuses on the common ecological and evolutionary constraints that influence bioremediation processes.

The Roles of Photooxidation and Biodegradation in Long-term Weathering of Crude and Heavy Fuel Oils

Abstract Although spilled oil is subject to a range of natural processes, only combustion, photooxidation and biodegradation destroy hydrocarbons and remove them from the biosphere. We present laboratory data that demonstrate the molecular preferences of these processes, and then examine some oil residues collected from previously documented releases to confirm the important roles that these processes play in removing spilled oil from both marine and terrestrial environments.