Stable Isotope Probing Identifies Novel m-Xylene Degraders in Soil Microcosms from Contaminated and Uncontaminated Sites

Abstract

The remediation of groundwater contaminated with benzene, toluene, ethylbenzene, and the xylenes (BTEX) typically involves in situ biodegradation. Although the mechanisms of aerobic BTEX biodegradation in laboratory cultures have been well studied, less is known about the microorganisms responsible in mixed culture samples or at contaminated sites. In this study, the microorganisms responsible for in situ degradation within mixed culture samples were investigated using the molecular method stable isotope probing (SIP). For this, m-xylene was utilized as a model BTEX contaminant. Specifically, DNA-based SIP was utilized to identify active m-xylene degraders in microcosms constructed with soil from three sources (a gasoline-contaminated site and two agricultural sites). Replicate microcosms were amended with either labeled ( 13 C) or unlabeled m-xylene, and the extracted DNA samples were ultracentrifuged, fractioned, and subjected to terminal restriction fragment length polymorphism (TRFLP). The dominant m-xylene degraders (responsible for 13 C uptake) were determined by comparing relative abundance of TRFLP phylotypes in heavy fractions of labeled m-xylene ( 13 C) amended samples to the controls (from unlabeled m-xylene amended samples). Four phylotypes were identified as the dominant m-xylene degrading species, falling within either the β Proteobacteria or the Bacilli. Of these, two 16S rRNA gene sequences were highly novel, displaying very limited similarity (94% and 90%) to any previously reported 16S rRNA gene sequence. Further, three of these phylotypes fell within genera with limited or no previous links to BTEX degradation, suggesting much information is still to be gained concerning the identity of microorganisms responsible for degradation within mixed culture samples.

Microbial community changes in contaminated soils in response to phenanthrene amendment

“…300 ng PCR products were purified with QIA quick PCR purification kit (Qiagen Inc., German), following the manufacturer's instructions and digested with HaeIII (Saibaisheng Gene Tech, China) with a 6 hour incubation period. Additional digests (HhaI and MspI) for TRFLP analyses were included to correlate the TRFLP fragment lengths to the in silico cut sites of the cloned 16S rRNA gene sequences and thus determine the identity of the significantly enriched fragments (Cupples and Sims, 2007;Xie et al, 2010). The fragment pattern was detected using an ABI 3730 DNA Analyzer (Applied Biosystems) set at the Genescan mode.…”

Review of Environmental and Human Exposure to Persistent Organic Pollutants

“…POPs have a very long life and they persist in the environment for a long time including soils, as sediments in air or biota (Kallenborn, 2006;Porta et al, 2008). There is no consensus among the academic professionals (Xie et al, 2010;Wang et al, 2012) on the exact meaning of the term persistent and how long a product should exist in the environment to be labelled as persistent compound. However, in practice, POPs are classified as compounds which can have half-life period running into many years (Xie et al, 2010).…”

A Review of the Accumulation and Distribution of Persistent Organic Pollutants in the Environment

“…There is no consensus among the academic professionals on the exact meaning of the term persistent and how long should a product exist in the environment before they can be labelled as persistent compounds. However, in practice, POPs are classified as compounds which can have half-life period running into many years [1].…”

“…There is no consensus among the academic professionals on the exact meaning of the term persistent and how long should a product exist in the environment before they can be labelled as persistent compounds. However, in practice, POPs are classified as compounds which can have half-life period running into many years [1].Toxicity, high persistence and bioaccumulation ability are factors being focused on in the latest environment based studies. According to the study [2] POPs are among the most important subset of Persistent, Bioaccumulative and Toxic (PBT) chemicals including pesticides like γ-hexachlorocyclohexane or 1,1,1-trichloro-2,2-diethane, polychlorinated biphenyls, polycyclic aromatic hydrocarbons (PAHs), polychlorinated naphthalenes, polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans, as well as groups of brominated flame retardants (BFRs) such as polybrominated biphenyls, hexabromocyclododecane, chlorine-containing molecules like polybrominated diphenyl ethers and tetrabromobisphenol.…”