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Since the 2010 Deepwater Horizon oil well blowout in the Gulf of Mexico, there has been renewed interest in the biology of oil-degrading bacterial communities. One of the research focuses of our group is to use nucleic acid sequencing-based approaches to investigate the potential of indigenous bacteria to naturally metabolize hydrocarbons in the context of a spill event. Over the past several years, the throughput of modern sequencing technology platform instruments has dramatically increased with lower costs for sequencing and data generation but higher costs for data computation and downstream processing. This high throughput of data production has put massive pressure on existing computing and storage infrastructure and also significantly increased the complexity of sequence data analysis. Many research organizations are willing to incorporate nucleic acid sequencing technology into their R&D pipelines but can be discouraged and overwhelmed by the high costs of computing infrastructure and data analysis. This chapter will address good practices, methodology and key concepts in the analysis of shotgun metagenomic sequencing data obtained from laboratory experiments simulating conditions relevant to oil spills into natural ecosystems. Particular emphasis will be put on bioinformatics and data mining methodology to process sequencing data into meaningful biological information.

Terrestrial analogues for astrobiological investigations of Mars should include Earth's polar regions and as such, the Canadian high Arctic offers several unique cryoenvironments (sub zero saline springs, permafrost) that resemble the conditions that are known or are suspected to exist on Mars. This presentation will describe our recent research focused on detecting and examining microbial life in the unique cold saline/brine springs on Axel Heiberg Island with the overall goals of determining the low temperature limits of microbial life on Earth and if microbial communities inhabiting such cryoenvironments are active at ambient subzero temperatures. The presentation will focus on the microbiology and geochemistry of the Gypsum Hill (GH) and Lost Hammer Spring (LH) sites (Perreault et al, 2008; Niederberger et al. 2010). These unique subzero (0 to -5ºC) hypersaline springs (7.5 to 23% salinity) are characterized by thick extensive permafrost in an area with an average annual air temperature of -15°C and with air temperatures below -40°C common during the winter months. The presence of geomorphological features linked to water movement, such as fluvial valleys and flood channels on the surface of Mars signifies that water once flowed through the Martian landscape and thus, they could have been a potential abode for past or extant microbial life. These springs support viable microbial communities capable of activity at temperatures as low as -10ºC. The LH site also provides a model of how a methane seep can form in cryoenvironments and presents a mechanism that could possibly be contributing to reported methane plumes on Mars. The GH springs sulfide (25-100 ppm) and sulfate (2300-3700 mg/L) abundant system serving as an analogue for the abundant sulfate deposits and potential sulfate-rich brines on Mars that may have originated in the presence of sulfur-rich groundwater. Gas composition (C1-C4 hydrocarbons, He, H2, O2, N2, Ar, and CO2) and stable isotope (d13C and d2H values using compound specific isotope analysis) analyses of the saline spring gas samples has revealed the small amounts of hydrocarbons in gases exsolving from the Gypsum Hill springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy (Perreault et al. 2008) while the major gas emitted from LH spring is methane (~50 %) with carbon and hydrogen isotope signatures consistent with a thermogenic origin (Niederberger et al. 2010). However, the presence of anaerobic methane oxidizing archaea (ANME) in the LH source provide a model of methane-based metabolism in this extreme hypersaline, subzero environment., Analogue Sites for Mars Missions: MSL and Beyond, March 5-6, 2011, The Woodlands, TX, USA

217th ACS National Meeting, Anaheim, CA, USA, March 21-25, 1999, Series: American Chemical Society. Division of Fuel Chemistry. Preprints of symposia

The 8th International Symposium on Microbial Ecology, Halifax, Nova Scotia, August 09-14, 1998

The 2nd Phytoremediation Technical Seminar, June 12-13, 2000, Vancouver, B.C.

The 3rd International Conference Remediation of Chlorinated and Recalcitrant Compounds, Monterey, CA, USA, May 20-23, 2002

ARCSACC Conference - Assessment and Remediation of Contaminated Sites in Arctic and Cold Climates, Edmonton, May 07-08, 2001

The 90th Air & Waste Management Association Meeting, Paper # 97-A1464

Forum for Applied Biotechnology, September 24-25, 1998, Brugge, Belgium

The 48th Canadian Chemical Engineering Conference, London, Ontario, October 04-07, 1998

The 8th International Symposium on Microbial Ecology, Halifax, Nova Scotia, August 9-14, 1998

The 14th AEHS Annual West Coast Conference on Soils, Sediments, and Water, March 15-18, 2004 San Diego, CA, USA

The 48th Annual Meeting of the Canadian Society of Microbiologists, Guelph, Ontario, June 14-17, 1998

The 23rd Annual TTCP Meeting on Environmental Aspects of Energetic Materials, Quebec, Quebec, May 26-27, 1998

The 8th International Symposium on Microbial Ecology, Halifax, Nova Scotia, August 09-14, 1998

TTCP WPN/TP-4, May 26-27, 1998, Valcartier, Quebec

The 24th Annual Aquatic Toxicity Workshop, 1997

Fourth International Conference on Remediation of Chlorinated and Recalcitrant Compounds, May 24-27, 2004, Monterey, California, USA

The effect of contamination with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on an indigenous soil bacterial community was examined in two uncontaminated loam soil columns possessing native grasses. One column was spiked twice with RDX crystals for a total RDX load of 1000 mg (kg soil)-1. The reduced metabolite of RDX degradation, hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine, was observed in the column leachate, suggesting anaerobic degradation of RDX. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA from both contaminated and uncontaminated columns produced identical banding patterns which were stable over the course of the experimental period. The bacterial diversity remained high in the contaminated column, as determined by restriction fragment length polymorphism and rarefaction analyses of random 16S rDNA clones. These combined results suggested that long-term exposure to 1000 mg RDX (kg soil)-1 did not produce an observable effect on bacterial diversity or the numerically dominant members of the indigenous soil bacterial community. (c) Biosciences Information Services.

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 (5degreeC) and mesophilic populations (37degreeC) 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.on. (c) Biosciences Information Services.

Salon des technologies environnementales du Québec

TTCP WPN/TP-4, 26-27 May, Valcartier, Québec

Fourth International In Situ and On-Site Bioremediation Symposium, April 28-May 1, 1997, New Orleans, Louisiana

27th International Annual Conference of ICT, Karlsruhe, Germany, June 25-28, 1996

27th International Annual Conference of ICT, June 25-June 28, 1996, Karlsruhe, Federal Republic of Germany