Occurrence and diversity of naphthalene dioxygenase genes in soil microbial communities from the Maritime Antarctic

Abstract

SummaryThe diversity of naphthalene dioxygenase genes (ndo) in soil environments from the Maritime Antarctic was assessed, dissecting as well the influence of the two vascular plants that grow in the Antarctic: Deschampsia antarctica and Colobanthus quitensis. Total community DNA was extracted from bulk and rhizosphere soil samples from Jubany station and Potter Peninsula, South Shetland Islands. ndo genes were amplified by a nested PCR and analysed by denaturant gradient gel electrophoresis approach (PCR-DGGE) and cloning and sequencing. The ndo-DGGE fingerprints of oil-contaminated soil samples showed even and reproducible patterns, composed of four dominant bands. The presence of vascular plants did not change the relative abundance of ndo genotypes compared with bulk soil. For non-contaminated sites, amplicons were not obtained for all replicates and the variability among the fingerprints was comparatively higher, likely reflecting a lower abundance of ndo genes. The phylogenetic analyses showed that all sequences were affiliated to the nahAc genes closely related to those described for Pseudomonas species and related mobile genetic elements. This study revealed that a microdiversity of nahAc-like genes exists in microbial communities of Antarctic soils and quantitative PCR indicated that their relative abundance was increased in response to anthropogenic sources of pollution.

Bacterial Targets as Potential Indicators of Diesel Fuel Toxicity in Subantarctic Soils

“…Pseudomonas, the most stimulated genus found here, has wellknown hydrocarbon-degrading capabilities, and its presence has been widely reported in petroleum hydrocarbon-contaminated sites in Antarctica and Macquarie Island (13,14,59). The other genus most stimulated in response to high diesel fuel concentrations was Parvibaculum, which has also been reported to have the genetic potential for hydrocarbon degradation (60). While the rapid stimulation of potential hydrocarbon degraders that we observed has been well documented, the full extent of species inhibited with diesel fuel (contributing up to 80% of the total abundance in control communities) has not previously been highlighted (Table 4, Fig.…”

Culturable heterotrophic bacteria from Potter Cove, Antarctica, and their hydrolytic enzymes production

“…With a unique climate and Antarctic location, Potter Cove and Potter Peninsula have frequently been the focus of interest for scientists looking for a site for long-term ecological research and monitoring programmes. In recent years, several studies have been conducted to evaluate the effect of UV radiation on bacteria isolated from the water column of Potter autochthonous bacterial consortia for on-site bioremediation of hydrocarbon-contaminated soils Vá zquez et al 2009;Ruberto et al 2010), to detect the presence and diversity of naphthalene dioxygenase genes in soils (Flocco et al 2009) and to screen for bacterial extracellular proteases for their use in the cleaning and food industries (Vá zquez et al 2004;Vá zquez et al 2005;Vá zquez et al 2008). A bacterial strain isolated from surface marine water of Potter Cove was described as a new species, Bizionia argentinensis (Bercovich et al 2008), and its complete genome has been sequenced and is being thoroughly studied (Lanzarotti et al 2011).…”

Soil Type-Dependent Responses to Phenanthrene as Revealed by Determining the Diversity and Abundance of Polycyclic Aromatic Hydrocarbon Ring-Hydroxylating Dioxygenase Genes by Using a Novel PCR Detection System

“…For more than a decade, cultivation-independent approaches have also been employed to unravel the responses of microbial communities in soils and sediments to PAH pollution. In all these studies, PCR amplification of PAH-degrading gene fragments from nucleic acids directly extracted from environmental samples was used to explore the abundance and diversity of PAH ring-hydroxylating dioxygenase (PAH-RHD ␣ ) genes (4,8,9,13,14,22,34,37). Despite the known biases of PCR amplification from mixed templates, these techniques allow highly sensitive and specific detection even from minute amounts of nucleic acids.…”