A survey of indigenous microbial hydrocarbon degradation genes in soils from Antarctica and Brazil

Abstract

Total community DNA from 29 noncontaminated soils and soils impacted by petroleum hydrocarbons and chloro-organics from Antarctica and Brazil were screened for the presence of nine catabolic genes, encoding alkane monooxygenase or aromatic dioxygenases, from known bacterial biodegradation pathways. Specific primers and probes targeting alkane monooxygenase genes were derived from Pseudomonas putida ATCC 29347 (Pp alkB), Rhodococcus sp. strain Q15 (Rh alkB1, Rh alkB2), and Acinetobacter sp. ADP-1 (Ac alkM). In addition, primers and probes detecting aromatic dioxygenase genes were derived from P. putida ATCC 17484 (ndoB), P. putida F1 (todC1), P. putida ATCC 33015 (xylE and cat23), and P. pseudoalcaligenes KF707 (bphA). The primers and probes were used to analyze total community DNA extracts by using PCR and hybridization analysis. All the catabolic genes, except the Ac alkM, were detected in contaminated and control soils from both geographic regions, with a higher frequency in the Antarctic soils. The alkane monooxygenase genes, Rh alkB1 and Rh alkB2, were the most frequently detected alk genes in both regions, while Pp alkB was not detected in Brazil soils. Genes encoding the aromatic dioxygenases toluene dioxygenase (todC1) and biphenyl dioxygenase (bphA) were the most frequently detected in Antarctica, and todC1 and catechol-2,3-dioxygenase (cat23) were the most frequent in Brazil soils. Hybridization analysis confirmed the PCR results, indicating that the probes used had a high degree of homology to the genes detected in the soil extracts and were effective in detecting biodegradative potential in the indigenous microbial population.

Isolation of Surfactant-Resistant Pseudomonads from the Estuarine Surface Microlayer

“…Screening for genes encoding naphthalene dioxygenase (ndo), the enzyme involved in the first step of the aerobic degradation pathway of naphthalene, was unsuccessful for all isolates. However, the presence of ndo genes or the capacity for naphthalene degradation should not be excluded, because the primers employed do not cover the high diversity of known ndo genes [23] and especially not all the pathways involved in hydrocarbon degradation [44]. Moreover, catabolic genes, like ndo, are frequently found in mobile genetic elements, namely plasmids [62].…”

Identification of bacteria associated with a disease affecting the marine sponge Ianthella basta in New Britain, Papua New Guinea

“…This leads to rapid tissue necrosis at the site of the pathogen, as appears to be occurring with I. basta. The kin group to the above strain is comprised of P. alcaligenes, a very common marine bacterium (Lorenz & Sikorski 2000) including forms that are toxic to fish (Kobayashi et al 2004), shrimp, and scallops (Alavandi et al 2004); P. fulva, found in leaf litter on soils (Luz et al 2003) and used in fungicide sprays on rice and other crops (Xie et al 2003); and P. putida and other Pseudomonas spp., which are also used as anti-fungal sprays and have forms that cause tomato disease (Pedley et al 2004) and are used for biodegradation of DDT (Kamanavalli et al 2004). The third Pseudomonas isolate belonged to a more distantly related group.…”

Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils

“…Conversely, the selection pressure imparted by contamination with a particular complex mixture, such as crude oil, may result in the selection of similar microbial populations across widely different soil environments. Although research has been conducted in many ecologically and geographically diverse contaminated soil environments (12,17,20,23,46), there are no comprehensive studies that focus systematically on the identification of microbial populations associated with hydrocarbon degradation across different geographical locations where the various soil types exhibit distinctly different physical-chemical and biological properties. To understand the impacts of hydrocarbon mixture perturbation on soil microbial communities, it is important to determine whether microbial population responses to a constant complex mixture vary across soil types or if consistent patterns in the populations selected are observed across a wide range of soil environments.…”