Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria

Bozinovski, D.M.; Taubert, Martin; Kleinsteuber, Sabine; Richnow, Hans H.; Bergen, Martin von; Vogt, Carsten; Seifert, Jana

doi:10.1016/j.syapm.2014.07.005

Cited by 30 publications

(17 citation statements)

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“…Epsilonproteobacteria , Deltaproteobacteria , Bacteroidetes and Treponema ) in this consortium. Thus, a metagenome of the culture was sequenced which significantly improved the identification of ( C-m -xylene [Bozinovski et al, 2014]. The upper pathway for m -xylene transformation to 3-methylbenzoyl-coenzyme A (CoA) was fully elucidated for the Desulfobacteraceae phylotype, including fumarate addition as initial enzymatic step.…”

Section: Xylene Isomersmentioning

confidence: 99%

“…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: 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: Xylene Isomersmentioning

confidence: 99%

Section: Syntrophic and Commensalistic Relationshipsmentioning

confidence: 99%

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

et al. 2016

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“…B). Because PRI is an anaerobic environment (Table ), the higher numbers of proteins from Epsilonproteobacteria most likely reflect their association with anoxic sites; notably, members of this class have also been found to be abundant in pollutant‐degrading microbial consortia operating under aerobic conditions . However, the proteins assigned to Gammaproteobacteria were detected at higher number in MES than in HAV (2.8‐fold) and PRI (2.6‐fold) (Fig.…”

Section: Resultsmentioning

confidence: 93%

Metaproteomics and metabolomics analyses of chronically petroleum‐polluted sites reveal the importance of general anaerobic processes uncoupled with degradation

et al. 2015

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Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi‐enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large‐scale chronic pollution is yet to be defined, particularly in anaerobic and micro‐aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen‐depleted petroleum‐polluted sediments.

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“…After formation of dihydroxylated compounds, there were two manners of ring cleavage, ortho (between the two hydroxylated carbons) or meta (between a hydroxylated and non-hydroxylated carbon) (Bozinovski et al, 2014;Prabhu and Phale, 2003;J. Q.…”

Section: Mineralization Of O-xylene By Strain Hj1mentioning

confidence: 99%

Degradation of o-xylene by a novel strain, Zoogloearesiniphila HJ1: Identification, kinetics and metabolic pathway

2017

Global NEST Journal

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Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria

Cited by 30 publications

References 38 publications

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Metaproteomics and metabolomics analyses of chronically petroleum‐polluted sites reveal the importance of general anaerobic processes uncoupled with degradation

Degradation of o-xylene by a novel strain, Zoogloearesiniphila HJ1: Identification, kinetics and metabolic pathway

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