Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition

Abstract

Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions. Benzene was degraded at a rate of 0.15 μmol/mg protein/day and a first-order rate constant of 3.04/day which was fourfold higher than rates reported previously. Bacteria belonging to the Peptococcaceae were found to play an important role in this anaerobic benzene-degrading biofilm culture, but also members of the Anaerolineaceae were predicted to be involved in benzene degradation or benzene metabolite degradation based on Illumina MiSeq analysis of 16S ribosomal RNA genes. Biomass retention in the reactor using a filtration finger resulted in reduction of benzene degradation capacity. Detection of the benzene carboxylase encoding gene, abcA, and benzoic acid in the culture vessel indicated that benzene degradation proceeds through an initial carboxylation step.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-017-8214-8) contains supplementary material, which is available to authorized users.

Biodiversity and niche partitioning in an anaerobic benzene degrading culture

“…It was shown previously that a member of the Peptococcaceae was an important member of the anaerobic benzene degrading community [8,13,12,27,38]. Our data confirm that hypothesis and we postulate that a member of the Peptococcaceae is one of the primary benzene consumers with benzoate/hydroxybenzene, benzoyl-CoA and hydroxypimelyl-CoA as intermediates.…”

“…Some members of the Burkholderiales (MAGs 19, 25, 47 and 68) were also classified as benzene consumers. We noticed that they have the potential to make enzymes for degradation of benzoate and hydroxybenzene, two intermediates of benzene degradation, which may diffuse out of the primary consumers and become available to other members [13]. Burkholderiales were described as important species in enrichment cultures of anaerobic benzene-degrading microcosms and were suggested to use the methylation pathway for anaerobic benzene activation [8,39,40].…”

“…We used in total five out of six metatranscriptomes previously obtained from bioreactor samples and described by our collaborators [12,13] (Section S1.11 for details). All five samples were gathered by scraping off a confined area of thick parts of the biofilm or thin ones, originally referred to as brown and white biofilm, respectively.…”

“…This microbial community was inoculated from soil samples of a benzene-contaminated industrial site and has been maintained already for 15 years [8], which is enough time to purge a putative initial diversity by mechanisms like competitive exclusion and random fluctuations [9,10,11]. Nevertheless, the culture is currently remarkably rich in species [12,13]. Spatial and temporal heterogeneity as well as the variety of interactions between organisms are then created and maintained by the community itself, aided by mechanisms like wall adherence and patch formation.…”

“…Over the years, a biofilm developed on the interior glass wall of the bioreactor, hosting more than 100 different types of species based on 16S rRNA sequencing [13]. It has been hypothesized that these types of microbial community may hold many types of interaction between key players in benzene degradation and other members of the community [14].…”