Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments

Abstract

SummaryMicrobial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction‐based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next‐generation sequencing, provide unsurpassed detection ability, which has enabled large‐scale comparative genomic and whole‐genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic‐acid‐based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions.

Short-term enhancement effect of nitrogen addition on microbial degradation and plant uptake of polybrominated diphenyl ethers (PBDEs) in contaminated mangrove soil

“…This result indicated that anaerobic reductive debromination was the main process to remove PBDEs in mangrove soil, as reported by previous studies [8,9]. Some anaerobes could effectively use halogenated organic compounds as terminal electron acceptors and replace chlorine/bromine with hydrogen through a process termed dehalorespiration [34]. Dehalobacter spp.…”

“…and Dehalococcoides spp. were reported to couple their growth to the dechlorination of PCBs and pentachlorophenol (PCP) [33,34]. In this study, consistent patterns of variation were found between the abundances of these two dehalogenating bacteria and PBDE removal rate in mangrove soil could adjust the soil C/N ratio to a more suitable level for the activity of dehalogenating bacteria [33,36].…”

“…Microbial reductive dehalogenation has been considered as an important mechanism for the transformation and degradation of halogenated organic pollutants, such as chlorophenol, PCBs and PBDEs, in anaerobic environments [33,34]. In this study, all soils were anaerobic, with Eh values ranging from −93 ± 17 to −156 ± 35 mV, and three lower PBDE congeners, namely BDE-7, -17 and -28, were detected in the soil (Fig.…”

In situ detection of alkB2 gene involved in Alcanivorax borkumensis SK2T hydrocarbon biodegradation

“…Nevertheless, Hassanshahian and colleagues recognized some limitations of the method after thoroughly testing its specificity and reproducibility. Limitations in the utilization of PCR-based methods for the specific biomonitoring of environmental samples emerged in several studies, mainly due to the biases related to DNA extraction, especially when complex environmental matrices, such as contaminated marine water, are treated (Moraru et al, 2010;Matturro et al, 2012;Ding and He, 2012).…”

Ecophysiology and environmental distribution of organohalide-respiring bacteria

“…Degenerate primers are widely used to amplify rdhA genes, especially when the aim is to amplify genes from uncultivated OHRB for which genomic information is not available. Degenerate primers are usually designed based on conserved regions of RDase catalytic subunit encoding genes by aligning amino acids sequences found in sequence databases like GenBank [270], and using specific approaches including ConsensusDegenerate Hybrid Oligonucleotide Primer (CDHOP) [271]. The first set of degenerate primers (primer pair 1, based on twin-arginine signal peptides, iron-sulfur clusters, and five additional highly conserved sequence motifs (Figure 3.3), which were used to target rdhA genes from different ortho-chlorophenol-and chloroethene-dechlorinating OHRB.…”