Anaerobic Degradation of Ethylbenzene by a New Type of Marine Sulfate-Reducing Bacterium

ABSTRACT Anaerobic degradation of the aromatic hydrocarbon ethylbenzene was studied with sulfate as the electron acceptor. Enrichment cultures prepared with marine sediment samples from different locations showed ethylbenzene-dependent reduction of sulfate to sulfide and always contained a characteristic cell type that formed gas vesicles towards the end of growth. A pure culture of this cell type, strain EbS7, was isolated from sediment from Guaymas Basin (Gulf of California). Complete mineralization of ethylbenzene coupled to sulfate reduction was demonstrated in growth experiments with strain EbS7. Sequence analysis of the 16S rRNA gene revealed a close relationship between strain EbS7 and the previously described marine sulfate-reducing strains NaphS2 and mXyS1 (similarity values, 97.6 and 96.2%, respectively), which grow anaerobically with naphthalene and m-xylene, respectively. However, strain EbS7 did not oxidize naphthalene, m-xylene, or toluene. Other compounds utilized by strain EbS7 were phenylacetate, 3-phenylpropionate, formate, n-hexanoate, lactate, and pyruvate. 1-Phenylethanol and acetophenone, the characteristic intermediates in anaerobic ethylbenzene degradation by denitrifying bacteria, neither served as growth substrates nor were detectable as metabolites by gas chromatography-mass spectrometry in ethylbenzene-grown cultures of strain EbS7. Rather, (1-phenylethyl)succinate and 4-phenylpentanoate were detected as specific metabolites in such cultures. Formation of these intermediates can be explained by a reaction sequence involving addition of the benzyl carbon atom of ethylbenzene to fumarate, carbon skeleton rearrangement of the succinate moiety (as a thioester), and loss of one carboxyl group. Such reactions are analogous to those suggested for anaerobic n-alkane degradation and thus differ from the initial reactions in anaerobic ethylbenzene degradation by denitrifying bacteria which employ dehydrogenations.

Download Full-text

Comparison of Mechanisms of Alkane Metabolism under Sulfate-Reducing Conditions among Two Bacterial Isolates and a Bacterial Consortium

Applied and Environmental Microbiology ◽

10.1128/aem.02896-05 ◽

2006 ◽

Vol 72 (6) ◽

pp. 4274-4282 ◽

Cited By ~ 82

Author(s):

Amy V. Callaghan ◽

Lisa M. Gieg ◽

Kevin G. Kropp ◽

Joseph M. Suflita ◽

Lily Y. Young

Keyword(s):

Bacterial Consortium ◽

Gas Chromatography Mass Spectrometry ◽

Degradation Mechanisms ◽

Bacterial Isolates ◽

Alkane Degradation ◽

Tetradecanoic Acid ◽

Mass Spectral ◽

Sulfate Reducing ◽

Reducing Conditions ◽

Fumarate Addition

ABSTRACT Recent studies have demonstrated that fumarate addition and carboxylation are two possible mechanisms of anaerobic alkane degradation. In the present study, we surveyed metabolites formed during growth on hexadecane by the sulfate-reducing isolates AK-01 and Hxd3 and by a mixed sulfate-reducing consortium. The cultures were incubated with either protonated or fully deuterated hexadecane; the sulfate-reducing consortium was also incubated with [1,2-13C2]hexadecane. All cultures were extracted, silylated, and analyzed by gas chromatography-mass spectrometry. We detected a suite of metabolites that support a fumarate addition mechanism for hexadecane degradation by AK-01, including methylpentadecylsuccinic acid, 4-methyloctadecanoic acid, 4-methyloctadec-2,3-enoic acid, 2-methylhexadecanoic acid, and tetradecanoic acid. By using d 34-hexadecane, mass spectral evidence strongly supporting a carbon skeleton rearrangement of the first intermediate, methylpentadecylsuccinic acid, was demonstrated for AK-01. Evidence indicating hexadecane carboxylation was not found in AK-01 extracts but was observed in Hxd3 extracts. In the mixed sulfate-reducing culture, however, metabolites consistent with both fumarate addition and carboxylation mechanisms of hexadecane degradation were detected, which demonstrates that multiple alkane degradation pathways can occur simultaneously within distinct anaerobic communities. Collectively, these findings underscore that fumarate addition and carboxylation are important alkane degradation mechanisms that may be widespread among phylogenetically and/or physiologically distinct microorganisms.

Download Full-text

Biodegradation of an Alicyclic Hydrocarbon by a Sulfate-Reducing Enrichment from a Gas Condensate-Contaminated Aquifer

Applied and Environmental Microbiology ◽

10.1128/aem.69.1.434-443.2003 ◽

2003 ◽

Vol 69 (1) ◽

pp. 434-443 ◽

Cited By ~ 76

Author(s):

Luis A. Rios-Hernandez ◽

Lisa M. Gieg ◽

Joseph M. Suflita

Keyword(s):

Mass Spectrometry ◽

Denaturing Gradient Gel Electrophoresis ◽

Community Analysis ◽

Gas Condensate ◽

Microbial Community Analysis ◽

Gas Chromatography Mass Spectrometry ◽

Rrna Gene ◽

Contaminated Aquifer ◽

Sulfate Reducing ◽

Gradient Gel Electrophoresis

ABSTRACT We used ethylcyclopentane (ECP) as a model alicyclic hydrocarbon and investigated its metabolism by a sulfate-reducing bacterial enrichment obtained from a gas condensate-contaminated aquifer. The enrichment coupled the consumption of ECP with the stoichiometrically expected amount of sulfate reduced. During ECP biodegradation, we observed the transient accumulation of metabolite peaks by gas chromatography-mass spectrometry, three of which had identical mass spectrometry profiles. Mass-spectral similarities to analogous authentic standards allowed us to identify these metabolites as ethylcyclopentylsuccinic acids, ethylcyclopentylpropionic acid, ethylcyclopentylcarboxylic acid, and ethylsuccinic acid. Based on these findings, we propose a pathway for the degradation of this alicyclic hydrocarbon. Furthermore, a putative metabolite similar to ethylcyclopentylsuccinic acid was also found in samples of contaminated groundwater from the aquifer. However, no such finding was evident for samples collected from wells located upgradient of the gas condensate spill. Microbial community analysis of the ECP-degrading enrichment by denaturing gradient gel electrophoresis revealed the presence of at least three different organisms using universal eubacterial primers targeting 550 bp of the 16S rRNA gene. Based on sequence analysis, these organisms are phylogenetically related to the genera Syntrophobacter and Desulfotomaculum as well as a member of the Cytophaga-Flexibacter-Bacteroides group. The evidence suggests that alicyclic hydrocarbons such as ECP can be anaerobically activated by the addition to the double bond of fumarate to form alkylsuccinate derivatives under sulfate-reducing conditions and that the reaction occurs in the laboratory and in hydrocarbon-impacted environments.

Download Full-text

Degradation of Phenol via Phenylphosphate and Carboxylation to 4-Hydroxybenzoate by a Newly Isolated Strain of the Sulfate-Reducing Bacterium Desulfobacterium anilini

Applied and Environmental Microbiology ◽

10.1128/aem.00203-09 ◽

2009 ◽

Vol 75 (13) ◽

pp. 4248-4253 ◽

Cited By ~ 34

Author(s):

Young-Beom Ahn ◽

Jong-Chan Chae ◽

Gerben J. Zylstra ◽

Max M. Häggblom

Keyword(s):

Anaerobic Degradation ◽

Enrichment Culture ◽

Phenol Degradation ◽

Reaction Pathways ◽

Rrna Gene ◽

Dna Homology ◽

Sulfate Reducing ◽

Degrading Bacterium ◽

Bacterium Strain ◽

The 16S Rrna Gene

ABSTRACT A sulfate-reducing phenol-degrading bacterium, strain AK1, was isolated from a 2-bromophenol-utilizing sulfidogenic estuarine sediment enrichment culture. On the basis of phylogenetic analysis of the 16S rRNA gene and DNA homology, strain AK1 is most closely related to Desulfobacterium anilini strain Ani1 (= DSM 4660T). In addition to phenol, this organism degrades a variety of other aromatic compounds, including benzoate, 2-hydroxybenzoate, 4-hydroxybenzoate, 4-hydroxyphenylacetate, 2-aminobenzoate, 2-fluorophenol, and 2-fluorobenzoate, but it does not degrade aniline, 3-hydroxybenzoate, 4-cyanophenol, 2,4-dihydroxybenzoate, monohalogenated phenols, or monohalogenated benzoates. Growth with sulfate as an electron acceptor occurred with acetate and pyruvate but not with citrate, propionate, butyrate, lactate, glucose, or succinate. Strain AK1 is able to use sulfate, sulfite, and thiosulfate as electron acceptors. A putative phenylphosphate synthase gene responsible for anaerobic phenol degradation was identified in strain AK1. In phenol-grown cultures inducible expression of the ppsA gene was verified by reverse transcriptase PCR, and 4-hydroxybenzoate was detected as an intermediate. These results suggest that the pathway for anaerobic degradation of phenol in D. anilini strain AK1 proceeds via phosphorylation of phenol to phenylphosphate, followed by carboxylation to 4-hydroxybenzoate. The details concerning such reaction pathways in sulfidogenic bacteria have not been characterized previously.

Download Full-text

Isolation and Characterization of a Sulfate-Reducing Bacterium That Anaerobically Degrades Alkanes

Applied and Environmental Microbiology ◽

10.1128/aem.65.7.2969-2976.1999 ◽

1999 ◽

Vol 65 (7) ◽

pp. 2969-2976 ◽

Cited By ~ 158

Author(s):

Chi Ming So ◽

L. Y. Young

Keyword(s):

Phenotypic Characterization ◽

Rrna Gene ◽

Stoichiometric Ratio ◽

Alkane Degradation ◽

Sulfate Reducing ◽

Isolation And Characterization ◽

Nacl Concentration ◽

History Of ◽

Widespread Phenomenon ◽

Chain Lengths

ABSTRACT An alkane-degrading, sulfate-reducing bacterial strain, AK-01, was isolated from an estuarine sediment with a history of chronic petroleum contamination. The bacterium is a short, nonmotile, non-spore-forming, gram-negative rod. It is mesophilic and grows optimally at pH 6.9 to 7.0 and at an NaCl concentration of 1%. Formate, fatty acids (C4 to C16) and hydrogen were readily utilized as electron donors. Sulfate, sulfite, and thiosulfate were used as electron acceptors, but sulfur, nitrite, and nitrate were not. Phenotypic characterization and phylogenetic analysis based on 16S rRNA gene sequence indicate that AK-01 is most closely related to the generaDesulfosarcina, Desulfonema, andDesulfococcus in the delta subdivision of the classProteobacteria. It is phenotypically and phylogenetically different from strains Hxd3 and TD3, two previously reported isolates of alkane-degrading, sulfate-reducing bacteria. The alkanes tested to support growth of AK-01 had chain lengths of C13 to C18. 1-Alkenes (C15 and C16) and 1-alkanols (C15 and C16) also supported growth. The doubling time for growth on hexadecane was 3 days, about four times longer than that for growth on hexadecanoate. Mineralization of hexadecane was indicated by the recovery of14CO2 from cultures grown on [1-14C]hexadecane. Degradation of hexadecane was dependent on sulfate reduction. The stoichiometric ratio (as moles of sulfate reduced per mole of hexadecane degraded) was 10.6, which is very close to the theoretical ratio of 12.25, assuming a complete oxidation to CO2. Anaerobic alkane degradation by sulfate reducers may be a more widespread phenomenon than was previously thought.

Download Full-text

Anaerobic 1-Alkene Metabolism by the Alkane- and Alkene-Degrading Sulfate Reducer Desulfatibacillum aliphaticivorans Strain CV2803T

Applied and Environmental Microbiology ◽

10.1128/aem.01097-07 ◽

2007 ◽

Vol 73 (24) ◽

pp. 7882-7890 ◽

Cited By ~ 25

Author(s):

Vincent Grossi ◽

Cristiana Cravo-Laureau ◽

Alain Méou ◽

Danielle Raphel ◽

Frédéric Garzino ◽

...

Keyword(s):

Fatty Acids ◽

Inorganic Carbon ◽

Direct Evidence ◽

Gas Chromatography Mass Spectrometry ◽

Sulfate Reducing ◽

Branched Fatty Acids ◽

Initial Activation ◽

Fumarate Addition ◽

Chain Lengths ◽

Methyl Branched Fatty Acids

ABSTRACT The alkane- and alkene-degrading, marine sulfate-reducing bacterium Desulfatibacillum aliphaticivorans strain CV2803T, known to oxidize n-alkanes anaerobically by fumarate addition at C-2, was investigated for its 1-alkene metabolism. The total cellular fatty acids of this strain were predominantly C-(even number) (C-even) when it was grown on C-even 1-alkenes and predominantly C-(odd number) (C-odd) when it was grown on C-odd 1-alkenes. Detailed analyses of those fatty acids by gas chromatography-mass spectrometry after 6- to 10-week incubations allowed the identification of saturated 2- and 4-ethyl-, 2- and 4-methyl-, and monounsaturated 4-methyl-branched fatty acids with chain lengths that correlated with those of the 1-alkene. The growth of D. aliphaticivorans on (per)deuterated 1-alkenes provided direct evidence of the anaerobic transformation of these alkenes into the corresponding 1-alcohols and into linear as well as 10- and 4-methyl-branched fatty acids. Experiments performed with [13C]bicarbonate indicated that the initial activation of 1-alkene by the addition of inorganic carbon does not occur. These results demonstrate that D. aliphaticivorans metabolizes 1-alkene by the oxidation of the double bond at C-1 and by the subterminal addition of organic carbon at both ends of the molecule [C-2 and C-(ω-1)]. The detection of ethyl-branched fatty acids from unlabeled 1-alkenes further suggests that carbon addition also occurs at C-3. Alkylsuccinates were not observed as potential initial intermediates in alkene metabolism. Based on our observations, the first pathways for anaerobic 1-alkene metabolism in an anaerobic bacterium are proposed. Those pathways indicate that diverse initial reactions of 1-alkene activation can occur simultaneously in the same strain of sulfate-reducing bacterium.

Download Full-text

Microbial Diversity Dynamics in a Methanogenic-Sulfidogenic UASB Reactor

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18031305 ◽

2021 ◽

Vol 18 (3) ◽

pp. 1305

Author(s):

E. Fernández-Palacios ◽

Xudong Zhou ◽

Mabel Mora ◽

David Gabriel

Keyword(s):

Paper Industry ◽

Chemical Species ◽

Methanogenic Archaea ◽

Granular Sludge ◽

Upflow Anaerobic Sludge Blanket ◽

Uasb Reactor ◽

Anaerobic Sludge ◽

Rrna Gene ◽

Sulfate Reducing ◽

Long Run

In this study, the long-term performance and microbial dynamics of an Upflow Anaerobic Sludge Blanket (UASB) reactor targeting sulfate reduction in a SOx emissions treatment system were assessed using crude glycerol as organic carbon source and electron donor under constant S and C loading rates. The reactor was inoculated with granular sludge obtained from a pulp and paper industry and fed at a constant inlet sulfate concentration of 250 mg S-SO42−L−1 and a constant C/S ratio of 1.5 ± 0.3 g Cg−1 S for over 500 days. Apart from the regular analysis of chemical species, Illumina analyses of the 16S rRNA gene were used to study the dynamics of the bacterial community along with the whole operation. The reactor was sampled along the operation to monitor its diversity and the changes in targeted species to gain insight into the performance of the sulfidogenic UASB. Moreover, studies on the stratification of the sludge bed were performed by sampling at different reactor heights. Shifts in the UASB performance correlated well with the main shifts in microbial communities of interest. A progressive loss of the methanogenic capacity towards a fully sulfidogenic UASB was explained by a progressive wash-out of methanogenic Archaea, which were outcompeted by sulfate-reducing bacteria. Desulfovibrio was found as the main sulfate-reducing genus in the reactor along time. A progressive reduction in the sulfidogenic capacity of the UASB was found in the long run due to the accumulation of a slime-like substance in the UASB.

Download Full-text

Ecological Response in the Integrated Process of Biostimulation and Bioaugmentation of Diesel-Contaminated Soil

Applied Sciences ◽

10.3390/app11146305 ◽

2021 ◽

Vol 11 (14) ◽

pp. 6305

Author(s):

Xiaosen Li ◽

Yakui Chen ◽

Xianyuan Du ◽

Jin Zheng ◽

Diannan Lu ◽

...

Keyword(s):

Nitrogen Cycle ◽

Contaminated Soil ◽

Quantitative Polymerase Chain Reaction ◽

Chemical Properties ◽

Gas Chromatography Mass Spectrometry ◽

Functional Genes ◽

Alkane Degradation ◽

Degrading Bacteria ◽

Polycyclic Aromatic ◽

Amine Compounds

The study applied microbial molecular biological techniques to show that 2.5% to 3.0% (w/w) of diesel in the soil reduced the types and number of bacteria in the soil and destroyed the microbial communities responsible for the nitrogen cycle. In the meantime, the alkane degradation gene alkB and polycyclic aromatic hydrocarbons (PAHs) degradation gene nah evolved in the contaminated soil. We evaluated four different remediation procedures, in which the biostimulation-bioaugmentation joint process reached the highest degradation rate of diesel, 59.6 ± 0.25% in 27 days. Miseq sequencing and quantitative polymerase chain reaction (qPCR) showed that compared with uncontaminated soil, repaired soil provides abundant functional genes related to soil nitrogen cycle, and the most significant lifting effect on diesel degrading bacteria γ-proteobacteria. Quantitative analysis of degrading functional genes shows that degrading bacteria can be colonized in the soil. Gas chromatography-mass spectrometry (GC-MS) results show that the components remaining in the soil after diesel degradation are alcohol, lipids and a small amount of fatty amine compounds, which have very low toxicity to plants. In an on-site remediation experiment, the diesel content decreased from 2.7% ± 0.3 to 1.12% ± 0.1 after one month of treatment. The soil physical and chemical properties returned to normal levels, confirming the practicability of the biosimulation-bioaugmentation jointed remediation process.

Download Full-text

Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽

10.3390/metabo11080482 ◽

2021 ◽

Vol 11 (8) ◽

pp. 482

Author(s):

Jae-Kwon Jo ◽

Seung-Ho Seo ◽

Seong-Eun Park ◽

Hyun-Woo Kim ◽

Eun-Ju Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

High Fat Diet ◽

Amplicon Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Underlying Mechanisms ◽

Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

Download Full-text

Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription

Genes ◽

10.3390/genes12070961 ◽

2021 ◽

Vol 12 (7) ◽

pp. 961

Author(s):

Kanwal Tariq ◽

Ann-Kristin Östlund Farrants

Keyword(s):

Stress Responses ◽

Ribosomal Gene ◽

Chromatin Remodelling ◽

Chromatin State ◽

Rrna Gene ◽

Open Chromatin ◽

Histone Chaperones ◽

Embryonic Cells ◽

Cell Type ◽

Chromatin States

Ribosomal transcription constitutes the major energy consuming process in cells and is regulated in response to proliferation, differentiation and metabolic conditions by several signalling pathways. These act on the transcription machinery but also on chromatin factors and ncRNA. The many ribosomal gene repeats are organised in a number of different chromatin states; active, poised, pseudosilent and repressed gene repeats. Some of these chromatin states are unique to the 47rRNA gene repeat and do not occur at other locations in the genome, such as the active state organised with the HMG protein UBF whereas other chromatin state are nucleosomal, harbouring both active and inactive histone marks. The number of repeats in a certain state varies on developmental stage and cell type; embryonic cells have more rRNA gene repeats organised in an open chromatin state, which is replaced by heterochromatin during differentiation, establishing different states depending on cell type. The 47S rRNA gene transcription is regulated in different ways depending on stimulus and chromatin state of individual gene repeats. This review will discuss the present knowledge about factors involved, such as chromatin remodelling factors NuRD, NoRC, CSB, B-WICH, histone modifying enzymes and histone chaperones, in altering gene expression and switching chromatin states in proliferation, differentiation, metabolic changes and stress responses.

Download Full-text