Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture

Author(s):  
Nidal Abu Laban ◽  
Draženka Selesi ◽  
Thomas Rattei ◽  
Patrick Tischler ◽  
Rainer U. Meckenstock
2008 ◽  
Vol 10 (7) ◽  
pp. 1703-1712 ◽  
Author(s):  
Umakanth Kunapuli ◽  
Christian Griebler ◽  
Harry R. Beller ◽  
Rainer U. Meckenstock

1998 ◽  
Vol 2 (3-4) ◽  
pp. 159-173 ◽  
Author(s):  
Jonathan M. Weiner ◽  
Terry S. Lauck ◽  
Derek R. Lovley

2012 ◽  
Vol 14 (5) ◽  
pp. 1171-1181 ◽  
Author(s):  
Bas M. van der Zaan ◽  
Flávia Talarico Saia ◽  
Alfons J. M. Stams ◽  
Caroline M. Plugge ◽  
Willem M. de Vos ◽  
...  

2019 ◽  
Author(s):  
Sophie I Holland ◽  
Richard J Edwards ◽  
Haluk Ertan ◽  
Yie Kuan Wong ◽  
Tonia L Russell ◽  
...  

Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, "DCMF", was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria and includes 96 predicted methylamine methyltransferases, which may provide clues to the basis of its DCM metabolism. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, available at http://www.slimsuite.unsw.edu.au/research/dcmf/.


2008 ◽  
Vol 74 (20) ◽  
pp. 6476-6480 ◽  
Author(s):  
A. R. Oka ◽  
C. D. Phelps ◽  
L. M. McGuinness ◽  
A. Mumford ◽  
L. Y. Young ◽  
...  

ABSTRACT Stable isotope probing (SIP) was used to identify the active members in a benzene-degrading sulfidogenic consortium. SIP-terminal restriction fragment length polymorphism analysis indicated that a 270-bp peak incorporated the majority of the 13C label and is a sequence closely related to that of clone SB-21 (GenBank accession no. AF029045). This target may be an important biomarker for anaerobic benzene degradation in the field.


2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Heiko Nacke ◽  
Laura L. Kirck ◽  
Sophia Schwarz ◽  
Dominik Schneider ◽  
Anja Poehlein ◽  
...  

ABSTRACT We sequenced the metagenome of a microbial community enriched under strictly anaerobic conditions from wastewater treatment plant-derived digester sludge. The metagenomic analysis of the enrichment revealed that Acetobacterium and methanogenic archaea belonged to the dominant prokaryotes, and genes encoding components of the Wood-Ljungdahl pathway were identified.


2019 ◽  
Vol 8 (11) ◽  
Author(s):  
Allan Devanadera ◽  
Felipe Vejarano ◽  
Yu Zhai ◽  
Chiho Suzuki-Minakuchi ◽  
Yoshiyuki Ohtsubo ◽  
...  

Here, we present the complete genome sequence of Azoarcus sp. strain DN11, a denitrifying bacterium capable of anaerobic benzene degradation.


2014 ◽  
Vol 65 (3) ◽  
pp. 1201-1213 ◽  
Author(s):  
Arturo Aburto-Medina ◽  
Andrew S. Ball

2005 ◽  
Vol 71 (9) ◽  
pp. 5427-5432 ◽  
Author(s):  
Romy Chakraborty ◽  
John D. Coates

ABSTRACT Benzene is a highly toxic industrial compound that is essential to the production of various chemicals, drugs, and fuel oils. Due to its toxicity and carcinogenicity, much recent attention has been focused on benzene biodegradation, especially in the absence of molecular oxygen. However, the mechanism by which anaerobic benzene biodegradation occurs is still unclear. This is because until the recent isolation of Dechloromonas strains JJ and RCB no organism that anaerobically degraded benzene was available with which to elucidate the pathway. Although many microorganisms use an initial fumarate addition reaction for hydrocarbon biodegradation, the large activation energy required argues against this mechanism for benzene. Other possible mechanisms include hydroxylation, carboxylation, biomethylation, or reduction of the benzene ring, but previous studies performed with undefined benzene-degrading cultures were unable to clearly distinguish which, if any, of these alternatives is used. Here we demonstrate that anaerobic nitrate-dependent benzene degradation by Dechloromonas strain RCB involves an initial hydroxylation, subsequent carboxylation, and loss of the hydroxyl group to form benzoate. These studies provide the first pure-culture evidence of the pathway of anaerobic benzene degradation. The outcome of these studies also suggests that all anaerobic benzene-degrading microorganisms, regardless of their terminal electron acceptor, may use this pathway.


1999 ◽  
Vol 65 (7) ◽  
pp. 3056-3063 ◽  
Author(s):  
Juliette N. Rooney-Varga ◽  
Robert T. Anderson ◽  
Jocelyn L. Fraga ◽  
David Ringelberg ◽  
Derek R. Lovley

ABSTRACT Microbial community composition associated with benzene oxidation under in situ Fe(III)-reducing conditions in a petroleum-contaminated aquifer located in Bemidji, Minn., was investigated. Community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent Fe(III)-reducing sites and from methanogenic and uncontaminated zones. Denaturing gradient gel electrophoresis of 16S rDNA sequences amplified with bacterial orGeobacteraceae-specific primers indicated significant differences in the composition of the microbial communities at the different sites. Most notable was a selective enrichment of microorganisms in the Geobacter cluster seen in the benzene-degrading sediments. This finding was in accordance with phospholipid fatty acid analysis and most-probable-number–PCR enumeration, which indicated that members of the familyGeobacteraceae were more numerous in these sediments. A benzene-oxidizing Fe(III)-reducing enrichment culture was established from benzene-degrading sediments and contained an organism closely related to the uncultivated Geobacter spp. This genus contains the only known organisms that can oxidize aromatic compounds with the reduction of Fe(III). Sequences closely related to the Fe(III) reducer Geothrix fermentans and the aerobe Variovorax paradoxus were also amplified from the benzene-degrading enrichment and were present in the benzene-degrading sediments. However, neither G. fermentans nor V. paradoxusis known to oxidize aromatic compounds with the reduction of Fe(III), and there was no apparent enrichment of these organisms in the benzene-degrading sediments. These results suggest thatGeobacter spp. play an important role in the anaerobic oxidation of benzene in the Bemidji aquifer and that molecular community analysis may be a powerful tool for predicting a site’s capacity for anaerobic benzene degradation.


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