Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

Abstract

Aims: In order to develop effective bioremediation strategies for polyaromatic hydrocarbons (PAHs) degradation, the composition and metabolic potential of microbial communities need to be better understood, especially in highly PAH contaminated sites in which little information on the cultivation‐independent communities is available. Methods and Results: Coal‐tar‐contaminated soil was collected, which consisted of 122·5 mg g−1 total extractable PAH compounds. Biodegradation studies with this soil indicated the presence of microbial community that is capable of degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene at 50 ppm each. PCR clone libraries were established from the DNA of the coal‐tar‐contaminated soil, targeting the 16S rRNA to characterize (i) the microbial communities, (ii) partial gene fragment encoding the Rieske iron sulfur center (α‐subunit) common to all PAH dioxygenase enzymes and (iii) β‐subunit of dioxygenase. Phylotypes related to Proteobacteria (Alpha‐, Epsilon‐ and Gammaproteobacteria), Acidobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA derived clone libraries. Many of the gene fragment sequences of α‐subunit and β‐subunit of dioxygenase obtained from the respective clone libraries fell into clades that are distinct from the reference dioxygenase gene sequences. Presence of consensus sequence of the Rieske type [2Fe‐2S] cluster binding site suggested that these gene fragments encode for α‐subunit of dioxygenase gene. Conclusions: Sequencing of the cloned libraries representing α‐subunit gene fragments (Rf1) and β‐subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal‐tar‐contaminated soil. Significance and Impact of the Study: The combination of the Rieske primers and bacterial community profiling represents a powerful tool for both assessing bioremediation potential and the exploration of novel dioxygenase genes in a contaminated environment.

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

“…Group 12 also contained abundant OTUs affiliated with acetogenic Acetobacterium, while associated production waters harbored methanogenic archaea affiliated with acetoclastic Methanosarcina. Indeed, the high abundance of potential acetogenic and methanogenic microbes agrees with previous reports implicating these taxa in syntrophic coal-to-methane transformations (41), where uncultured Rhodobacteraceae members identified here may play important roles in initial aromatic hydrocarbon degradation, as previously reported for representative isolates (42,43). Metagenome sequencing and binning.…”

Monitoring of microbial hydrocarbon remediation in the soil

“…However, the microbial community structure changes and diversity decreases due to environmental stresses or disturbances (Macnaughton et al 1999; Atlas and Philp 2005). The reports about the relationship between environmental pollution and the shifts in soil microbial communities are well established together with the phenomenon that changes in community structure usually result in the emergence of dominant populations within the disturbed communities that can survive toxic contamination and have enhanced physiological and substrate utilization capabilities (Miller et al 2002; Margesin et al 2003; Zucchi et al 2003; Evans et al 2004; Alquati et al 2005; Vinas et al 2005; Hamamura et al 2006; Maila et al 2006; Popp et al 2006; Smalla et al 2007; Ge et al 2008; Rodrigues et al 2009; Wolicka et al 2009; Kumar and Khanna 2010). …”

“…Bioremediation, especially when it can be carried out in situ, offers a cost-effective means of pollutant cleanup. It is an enhancement of the natural fate of biodegradable pollutants and therefore a green solution to the problem of environmental pollution with little or no ecological impact (Cappello et al 2007; Kumar and Khanna 2010). The end products of ultimate biodegradation (also known as mineralization) such as water and carbon dioxide are innocuous to man and the environment.…”

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

“…Additionally, organisms affiliated to the family Holophagaceae (203-bp TRF), Acidobacteria Gp2 (77-bp TRF) in phylum Acidobacteria, and family Xanthomonadaceae (69-bp TRF) in phylum Gammaproteobacteria were also observed in the 16S rRNA clone library. The phylum Acidobacteria has been linked to the degradation of PAHs [31] and polychlorinated biphenyls (PCBs) [32] from contaminated soil and sediment. Microorganisms in the family Xanthomonadaceae have also been linked to the degradation of PAHs in soils using SIP and other methods [13,33].…”