Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing

Bozinovski, D.M.; Herrmann, Steffi; Richnow, Hans H.; Bergen, Martin von; Seifert, Jana; Vogt, Carsten

doi:10.1111/j.1574-6941.2012.01334.x

Cited by 24 publications

(14 citation statements)

References 52 publications

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“…For example, Spirochaetes have been regularly observed in sulfate-reducing naphthalene-degrading enrichment cultures [Kümmel et al, 2015;Selesi et al, 2010], and phylotypes affiliated to the Epsilonproteobacteria were detected in several BTEX-degrading sulfatereducing enrichment cultures [Bozinovski et al, 2012[Bozinovski et al, , 2014Herrmann et al, 2010;Pilloni et al, 2011]. It is currently unclear whether these relationships also exist under in situ conditions or whether they are supported by special conditions in the microcosms ('cultivation artefacts').…”

Section: Syntrophic and Commensalistic Relationshipsmentioning

confidence: 98%

“…In the cultures tested so far, xylene is also activated via fumarate addition by BSS. The key players and enzymatic disposition of an m -xylene-degrading sulfate-reducing culture enriched from BTEX-contaminated groundwater have been elucidated by DNA-SIP and protein-SIP using partially 13 C-labeled m -xylene [Bozinovski et al, 2012;Herrmann et al, 2009]. These studies showed that a phylotype affiliated to the Desulfobacteraceae was the main m -xylene-assimilating organism due to the dominance of its 16S rRNA gene in heavy DNA, and the high percentage of identified 13 C-labeled proteins affiliated to this family.…”

Section: Xylene Isomersmentioning

confidence: 99%

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Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

et al. 2016

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Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using ¹³C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.

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Section: Syntrophic and Commensalistic Relationshipsmentioning

confidence: 98%

Section: Xylene Isomersmentioning

confidence: 99%

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

et al. 2016

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“…Protein-SIP has also been used to probe the degradation of m-xylene in a sulphate-reducing enrichment from the Zeitz aquifer (Bozinovski et al. 2012). Peptides of proteins involved in sulphate reduction, xylene oxidation and C1 metabolism in members of the Desulfobacteraceae were identified as 13 C labelled.…”

Section: Anaerobic Degraders Of Btex Hydrocarbons In Situmentioning

confidence: 99%

The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers

Lueders¹

2016

FEMS Microbiology Ecology

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The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. 13C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation.

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“…Several sulphate-reducing Deltaproteobacteria enriched from the terrestrial subsurface have been described to mineralize BTEX compounds [Abu Laban et al, 2015;Beller et al, 1996;Bombach et al, 2010;Bozinovski et al, 2012;Sun and Cupples, 2012;Weelink et al, 2010] or PAHs [Meckenstock and Mouttaki, 2011]. Members of the Geobacteriaceae ( Geobacter spp.…”

Section: Anaerobic Degradersmentioning

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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Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing

Cited by 24 publications

References 52 publications

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers

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

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