Prevalence of alkane monooxygenase genes in Arctic and Antarctic hydrocarbon-contaminated and pristine soils

Abstract

The prevalence of four alkane monooxygenase genotypes (Pseudomonas putida GPo1, Pp alkB; Rhodococcus sp. strain Q15, Rh alkB1 and Rh alkB2; and Acinetobacter sp. strain ADP-1, Ac alkM) in hydrocarbon-contaminated and pristine soils from the Arctic and Antarctica were determined by both culture-independent (PCR hybridization analyses) and culture-dependent (colony hybridization analyses) molecular methods, using oligonucleotide primers and DNA probes specific for each of the alk genotypes. PCR hybridization of total soil community DNA detected the rhodococcal alkB genotypes in most of the contaminated (Rh alkB1, 18/20 soils; Rh alkB2, 13/20) and many pristine soils (Rh alkB1, 9/10 soils; Rh alkB2, 7/10), while Pp alkB was generally detected in the contaminated soils (15/20) but less often in pristine soils (5/10). Ac alkM was rarely detected in the soils (1/30). The colony hybridization technique was used to determine the prevalence of each of the alk genes and determine their relative abundance in culturable cold-adapted (5 ‡C) and mesophilic populations (37 ‡C) from eight of the polar soils. The cold-adapted populations, in general, possessed relatively higher percentages of the Rh alkB genotypes (Rh alkB1, 1.9% (0.55); Rh alkB2, 2.47% (0.89)), followed by the Pp alkB (1.13% (0.50)), and then the Ac alkM (0.53% (0.36)). The Rh alkB1 genotype was clearly more prevalent in culturable cold-adapted bacteria (1.9% (0.55)) than in culturable mesophiles (0.41 (0.55)), suggesting that cold-adapted bacteria are the predominant organisms possessing this genotype. Overall, these results indicated that (i) Acinetobacter spp. are not predominant members of polar alkane degradative microbial communities, (ii) Pseudomonas spp. may become enriched in polar soils following contamination events, and (iii) Rhodococcus spp. may be the predominant alkane-degradative bacteria in both pristine and contaminated polar soils. ß

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

“…A study on a similar creosote-contaminated site in Sweden, however, reported a decline in actinobacterial populations (assessed by phospholipid fatty acid analysis) from the hot spots of pollution (Tö rneman et al, 2008). Several investigations on hydrocarbon-contaminated cold sites have also demonstrated the dominance of Proteobacteria over Actinobacteria (Whyte et al, 2002;Margesin et al, 2003;Labbe et al, 2007;Ringelberg et al, 2008). Our findings suggest that among both groups of robust degraders, Actinobacteria were outcompeted by Proteobacteria in this aged creosote-polluted site.…”

Microbiology of Eutrophic (Ornithogenic and Hydrocarbon-Contaminated) Soil

“…Shifts in bacterial communities in response to hydrocarbon contamination have been reported in several Antarctic soils (Aislabie et al 1998;Whyte et al 2002;Saul et al 2005). Soils in the Ross Sea region contaminated with alkanes and polyaromatic hydrocarbons were found to have higher counts of cultureable heterotrophic bacteria and lower bacterial diversity than uncontaminated control soils (Saul et al 2005).…”

Diversity of Alkane Hydroxylase Systems in the Environment

“…Alaskan sediments Colony hybridization with alkB 39% of viable heterotrophs from uncontaminated soil contain alkB gene probe 67% of viable heterotrophs from contaminated soil contain alkB [97] Contaminated soil PCR followed by Southern blot Detection and quantification of alkB (and other genes) in soil: 1-10 with alkB gene probe gene copies per gram of soil can be detected [98 Variety of cold ecosystems PCR, and Southern blots None of the psychrophilic alkane degraders possess genes with alkB gene probe with high homology to P. putida alkB [99] Fuel oil-contaminated site Dot-blots DNA extracted from soil shows no significant hybridization with an alkB-gene probe [100] Shallow aquifer Southern blots 10-20% of the total bacterial community hybridizes with alkB gene probe with an alkB gene probe [101] Various sources PCR with highly degenerate Most alkane-degrading strains contain distantly related alkB homologs (54 bacterial strains) primers for alkB homologs (homology not sufficient for Southern or dot-blots) [50] Shallow aquifer Dot-blots with DNA extracted alkB genotypes start at 11% of total community, and peak at (natural attenuation site) from aquifer samples 52% after injection of synthetic jet fuel in the aquifer [102] Various sources Southern, colony and dot-blots, alkB genes (close homologs) are widespread only in short-chain n-alkane (54 bacterial strains) PCR followed by Southern degrading pseudomonads [76] Rhizosphere vs. bulk soil Multiplex PCR At a contaminated site alkB was 10 times more prevalent in the endophytic community compared to the bulk soil community [103] Propane and butaneDot-blots 8 of 15 strains (including pseudomonads and rhodococci) utilizing bacteria gave a strong signal, and 7 a weak signal with the IMT37 gene [37] Land treatment unit (LTU) PCR, terminal restriction alkB increased in abundance during the first 3 weeks of LTU operation, fragment length polymorphism and comprised > 80% of the total PCR products [104] Arctic and Antarctic soil PCR-hybridization Rhodococcal alkB genes occur in contaminated and pristine soils, and colony hybridization P. putida alkB occurs more frequently in contaminated soils [105] similar genes in other butane degraders (pseudomonads, rhodococci and unidentified bacteria). In a dot-blot experiment, 8 out of 15 propane or butane-degrading bacteria gave a strong signal with the gene-probe, while the remaining 7 gave a weak but detectable signal [37].…”