High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Abstract

Genes encoding key enzymes of catabolic pathways can be targeted by DNA fingerprinting to explore genetic degradation potential in pristine and polluted soils. We performed a greenhouse microcosm experiment to elucidate structural and functional bacterial diversity in polyaromatic hydrocarbon (PAH)-polluted soil and to test the suitability of birch (Betula pendula) for remediation. Degradation of PAHs was analysed by high-performance liquid chromatography, DNA isolated from soil amplified and fingerprinted by restriction fragment length polymorphism (RFLP) and terminal restriction fragment length polymorphism (T-RFLP). Bacterial 16S rRNA T-RFLP fingerprinting revealed a high structural bacterial diversity in soil where PAH amendment altered the general community structure as well as the rhizosphere community. Birch augmented extradiol dioxygenase diversity in rhizosphere showing a rhizosphere effect, and further pyrene was more efficiently degraded in planted pots. Degraders of aromatic compounds upon PAH amendment were shown by the changed extradiol ring-cleavage community structure in soil. The RFLP analysis grouped extradiol dioxygenase marker genes into 17 distinct operational taxonomic units displaying novel phylogenetic clusters of ring-cleavage dioxygenases representing putative catabolic pathways, and the peptide sequences contained conserved amino-acid signatures of extradiol dioxygenases. A branch of major environmental TS cluster was identified as being related to Parvibaculum lavantivorans ring-cleavage dioxygenase. The described structural and functional diversity demonstrated a complex interplay of bacteria in PAH pollution. The findings improve our understanding of rhizoremediation and unveil the extent of uncharacterized enzymes and may benefit bioremediation research by facilitating the development of molecular tools to detect and monitor populations involved in degradative processes.

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

“…For instance, bacteria appeared to be generally stimulated in contaminated soils along with many functions, whereas fungi were more clearly stimulated in non-contaminated soils. Similarly, the rhizosphere effect of birch on soil microbial communities was reported to depend on PAH concentration (Sipilä et al, 2008). One possible explanation for this result is that plants recruit the rhizosphere microbial communities from the adjacent bulk soil (de Ridder-Duine et al, 2005;Dennis et al, 2010;Lundberg et al, 2012), and that contaminated and non-contaminated soils harbored different starting microbial communities (Figure 4).…”

Freshwater sediment pesticide biodegradation potential as an ecological indicator of microbial recovery following a decrease in chronic pesticide exposure: A case study with the herbicide diuron

“…Specific information on the potential of biodegradation can be obtained by examining functional genes encoding enzymes involved in degradation pathways (Smith andOsborn, 2008 andBombach et al, 2010). For example, in the case of diuron, Pesce et al (2013) recently demonstrated that diuron mineralization kinetics obtained with soil samples were correlated to diuron-degrading genetic potentials estimated from the quantification of the abundance of the phenlylurea hydrolase gene puhB, confirming that degradation genes could be potential biomarkers for the detection of organic xenobiotics (Sipilä et al, 2008). In addition, Monard et al (2013) recently showed that atrazine mineralizing ability of different soils was correlated to the expression level of atzD gene, coding for an enzyme responsible for s-triazine ring opening.…”

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

“…These wholecommunity fingerprinting approaches have been used recently successfully to study complex bacterial communities, to estimate the diversity and relative abundance of individual bacterial species within detectable bacterial communities (Hewson and Fuhrman 2004;Fedi et al 2005;Sipilä et al 2008;Iannelli et al 2012;Vajna et al 2012). In addition, using traditional selective cultivation dependent microbiological methods we are able to isolate site specific hydrocarbonoclastic bacterial strains which could form the basis of a new bacterial inoculant for bioremediation purposes.…”