Anaerobic phenanthrene mineralization by a carboxylating sulfate-reducing bacterial enrichment

Davidova, Irene A.; Gieg, Lisa M.; Duncan, Kathleen E.; Suflita, Joseph M.

doi:10.1038/ismej.2007.48

Cited by 80 publications

(59 citation statements)

References 38 publications

(36 reference statements)

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“…The PAHs naphthalene methylnaphthalene, phenanthrene and biphenyl (not a real PAH sensu stricto) have been shown to be degraded as the sole source of carbon and energy under anoxic conditions [Annweiler et al, , 2002Davidova et al, 2007;Selesi and Meckenstock, 2009]. The anaerobic degradation of PAHs with four or more rings was also explored.…”

Section: Microcosm Studies Showing Anaerobic Degradation Of Pahmentioning

confidence: 99%

“…In addition to naphthalene and benzene, the nonsubstituted three-ring PAH phenanthrene was proposed to be activated via carboxylation which was based on the detection of phenanthrene-2-carboxylic acid as major metabolite in culture supernatants [Davidova et al, 2007;Zhang and Young, 1997]. To date, enzymes involved in anaerobic phenanthrene degradation are unknown, but the enzyme reaction has been successfully measured in dense cell suspension of a phenanthrene-degrading, sulfate-reducing enrichment culture [Cunha et al, unpubl.…”

Section: Anaerobic Activation Of Phenanthrene and Biphenylmentioning

confidence: 99%

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Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons

Meckenstock

Boll

Mouttaki³

et al. 2016

Microb Physiol

231

165

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Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.

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Section: Microcosm Studies Showing Anaerobic Degradation Of Pahmentioning

confidence: 99%

Section: Anaerobic Activation Of Phenanthrene and Biphenylmentioning

confidence: 99%

Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons

Meckenstock

Boll

Mouttaki³

et al. 2016

Microb Physiol

231

165

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“…Currently, three alternative strategies for the anaerobic activation of aromatic hydrocarbons are known [Heider, 2007;Widdel and Rabus, 2001]: (1) the addition of a methyl or methylene group of substituted aromatic compounds across the double bond of fumarate (socalled 'fumarate addition'), (2) hydroxylation independent of molecular oxygen in the degradation of substituted benzenes such as ethylbenzene [Johnson et al, 2001;Kniemeyer and Heider, 2001] and (3) carboxylation, described for the activation of non-substituted naphthalene and benzene [Abu Laban et al, 2010;Holmes et al, 2011;Meckenstock and Mouttaki, 2011] and phenanthrene [Davidova et al, 2007]. Fumarate addition was first described for the activation of toluene catalyzed by the enzyme benzylsuccinate synthase (BSS) of Thauera aromatica strain K172 [Biegert et al, 1996].…”

Section: Catabolic Pathwaysmentioning

confidence: 99%

Functional Gene Markers for Fumarate-Adding and Dearomatizing Key Enzymes in Anaerobic Aromatic Hydrocarbon Degradation in Terrestrial Environments

et al. 2016

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Anaerobic degradation is a key process in many environments either naturally or anthropogenically exposed to petroleum hydrocarbons. Considerable advances into the biochemistry and physiology of selected anaerobic degraders have been achieved over the last decades, especially for the degradation of aromatic hydrocarbons. However, researchers have only recently begun to explore the ecology of complex anaerobic hydrocarbon degrader communities directly in their natural habitats, as well as in complex laboratory systems using tools of molecular biology. These approaches have mainly been facilitated by the establishment of a suite of targeted marker gene assays, allowing for rapid and directed insights into the diversity as well as the identity of intrinsic degrader populations and degradation potentials established at hydrocarbon-impacted sites. These are based on genes encoding either peripheral or central key enzymes in aromatic compound breakdown, such as fumarate-adding benzylsuccinate synthases or dearomatizing aryl-coenzyme A reductases, or on aromatic ring-cleaving hydrolases. Here, we review recent advances in this field, explain the different detection methodologies applied, and discuss how the detection of site-specific catabolic gene markers has improved the understanding of processes at contaminated sites. Functional marker gene-based strategies may be vital for the development of a more elaborate population-based assessment and prediction of aromatic degradation potentials in hydrocarbon-impacted environments.

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“…et al, under review), and in recovering the complete genomes of key player bacteria in two anaerobic phenanthrene degrading enrichment cultures of medium complexity, i.e. harboring about 50 distinct genomes ([18] and Himmelberg A. et al, manuscript in preparation). Table 3 summarizes the results from one of these experiments, showing that the initial global metagenome assembly actually targeted only two (Bin IV and Bin V) out of the five abundance classes, while reads from the most abundant bin –whose estimated size is consistent with the occurrence within it of a single 6.5–6.8 Mbp genome- were discarded.…”

Section: Results and Discussionmentioning

confidence: 99%

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes

et al. 2016

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BackgroundMetagenomics holds great promises for deepening our knowledge of key bacterial driven processes, but metagenome assembly remains problematic, typically resulting in representation biases and discarding significant amounts of non-redundant sequence information. In order to alleviate constraints assembly can impose on downstream analyses, and/or to increase the fraction of raw reads assembled via targeted assemblies relying on pre-assembly binning steps, we developed a set of binning modules and evaluated their combination in a new “assembly-free” binning protocol.ResultsWe describe a scalable multi-tiered binning algorithm that combines frequency and compositional features to cluster unassembled reads, and demonstrate i) significant runtime performance gains of the developed modules against state of the art software, obtained through parallelization and the efficient use of large lock-free concurrent hash maps, ii) its relevance for clustering unassembled reads from high complexity (e.g., harboring 700 distinct genomes) samples, iii) its relevance to experimental setups involving multiple samples, through a use case consisting in the “de novo” identification of sequences from a target genome (e.g., a pathogenic strain) segregating at low levels in a cohort of 50 complex microbiomes (harboring 100 distinct genomes each), in the background of closely related strains and the absence of reference genomes, iv) its ability to correctly identify clusters of sequences from the E. coli O104:H4 genome as the most strongly correlated to the infection status in 53 microbiomes sampled from the 2011 STEC outbreak in Germany, and to accurately cluster contigs of this pathogenic strain from a cross-assembly of these 53 microbiomes.ConclusionsWe present a set of sequence clustering (“binning”) modules and their application to biomarker (e.g., genomes of pathogenic organisms) discovery from large synthetic and real metagenomics datasets. Initially designed for the “assembly-free” analysis of individual metagenomic samples, we demonstrate their extension to setups involving multiple samples via the usage of the “alignment-free” d2S statistic to relate clusters across samples, and illustrate how the clustering modules can otherwise be leveraged for de novo “pre-assembly” tasks by segregating sequences into biologically meaningful partitions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1186-3) contains supplementary material, which is available to authorized users.

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Anaerobic phenanthrene mineralization by a carboxylating sulfate-reducing bacterial enrichment

Cited by 80 publications

References 38 publications

Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons

Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons

Functional Gene Markers for Fumarate-Adding and Dearomatizing Key Enzymes in Anaerobic Aromatic Hydrocarbon Degradation in Terrestrial Environments

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes

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