Real Roy

University of Victoria, Biology, Faculty Member

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Être et êtres chez deux philosophes du XIIe-XIIIe siècles : Zhu Xi et Thomas d’Aquin

Laval théologique et philosophique, 1988

ont chacun développé une synthèse philosophique présentant d'étonnantes similarités lorsqu 'elles... more ont chacun développé une synthèse philosophique présentant d'étonnantes similarités lorsqu 'elles sont comparées. Nous analysons, ici, l'ontologie telle que formulée par chaque auteur, en faisant bien ressortir les correspondances s'établissant entre li et existence, qi et essence, Taiji et Dieu. I.

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Links between methane oxidation rates and methanotroph community composition in a pine forest soil

The main gap in our knowledge about what determines the rate of CH4 oxidation in forest soils is ... more The main gap in our knowledge about what determines the rate of CH4 oxidation in forest soils is the biology of the microorganisms involved, the identity of which remains unclear. In this study, we used stable-isotope probing (SIP) following 13CH4 incorporation into phospholipid fatty acids (PLFAs) and DNA/RNA, and sequencing of methane mono-oxygenase (pmoA) genes, to identify the influence of variation in community composition on CH4 oxidation rates. The rates of 13C incorporation into PLFAs differed between horizons, with low 13C incorporation in the organic soil and relatively high 13C incorporation into the two mineral horizons. The microbial community composition of the methanotrophs incorporating the 13C label also differed between horizons, and statistical analyses suggested that the methanotroph community composition was a major cause of variation in CH4 oxidation rates. Both PLFA and pmoA-based data indicated that CH4 oxidizers in this soil belong to the uncultivated ‘uplan...

Effect and fate of various nitrogen sources on hexadecane mineralization in a diesel-contaminated soil (8th Int'l Symp. on Microbial Ecology, Halifax, Nova Scotia, August 9-14)

Methane metabolism and nitrogen cycling in freshwater sediment of a polluted ecosystem : Hamilton Harbour (Canada)

ABSTRACT

Effect of water management on soil microbial communities and atmospheric trace gases (8th Int'l Symp. on Microbial Ecology, Halifax, Nova Scotia, August 9-14)

Addition of water to the soil (rain, irrigation, flooding) decreases the availability of O 2. For... more Addition of water to the soil (rain, irrigation, flooding) decreases the availability of O 2. For example, nitrifying and denitrifying bacteria respond strongly to changes in soil water and O 2 availability by producing more or less of the atmospheric trace gases NO and N 2 O. Consumption of NO also responds to O 2 availability, as it may proceed by reductive or oxidative pathways. Complete depletion of O 2 in the soil (e.g. flooding of rice fields) results in the sequential change of the redox processes until CH 4 is emitted into the atmosphere. Driving forces are the availability of electron donors (organic substrates) and electron acceptors (mainly the content of iron). It is interesting to note that CH 4 production starts almost instantaneously after flooding, then comes to a halt as soon as competing redox processes (iron and sulfate reduction) start, and finally resumes vigorously when ferric iron and sulfate are depleted. Drainage of submerged fields, even short-term, regenerates sulfate and ferric iron and results in long-lasting inhibition of CH 4 production.

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Effect of methane metabolism on nitrification and nitrous oxide production in polluted freshwater sediment

Applied and Environmental Microbiology

We report the effect of CH4 and of CH4 oxidation on nitrification in freshwater sediment from Ham... more We report the effect of CH4 and of CH4 oxidation on nitrification in freshwater sediment from Hamilton Harbour, Ontario, Canada, a highly polluted ecosystem. Aerobic slurry experiments showed a high potential for aerobic N20 production in some sites. It was suppressed by C2H2, correlated to N03production, and stimulated by NH4 concentration, supporting the hypothesis of a nitrification-dependent source for this N20 production. Diluted sediment slurries supplemented with CH4 (1 to 24 ,uM) showed earlier and enhanced nitrification and N20 production compared with unsupplemented slurries (.l IFM CH4). This suggests that nitrification by methanotrophs may be significant in freshwater sediment under certain conditions. Suppression of nitrification was observed at CH4 concentrations of 84 ,eM and greater, possibly through competition for 02 between methanotrophs and NH4+-oxidizing bacteria and/or competition for mineral N between these two groups of organisms. In Hamilton Harbour sediment, the very high CH4 concentrations (1.02 to 6.83 mM) which exist would probably suppress nitrification and favor NH4' accumulation in the pore water. Indeed, NH4+ concentrations in Hamilton Harbour sediment are higher than those found in other lakes. We conclude that the impact of CH4 metabolism on N cycling processes in freshwater ecosystems should be given more attention. Nitrification, which is the successive oxidation of NH4' to N02and NO3by NH4+and N02-oxidizing bacteria (3), plays a key role in the cycling of mineral N in aquatic ecosystems. It leads to loss of fixed N to the atmosphere when coupled to denitrification, the dissimilatory reduction of NO3to N2 (27). Nitrate availability often limits denitrification in freshwater sediment (26, 48), which often makes nitrification the rate-limiting step in the recycling of mineral N in eutrophic aquatic systems. Nitrification has wide implications for the environmental quality of aquatic systems. It may be an important process in relation to NH4' toxicity in sediments (17, 47).

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Effect of water management on soil microbial communities and atmospheric trace gases

Addition of water to the soil (rain, irrigation, flooding) decreases the availability of O 2 . Fo... more Addition of water to the soil (rain, irrigation, flooding) decreases the availability of O 2 . For example, nitrifying and denitrifying bacteria respond strongly to changes in soil water and O 2 availability by producing more or less of the atmospheric trace gases NO and N 2 O. Consumption of NO also responds to O 2 availability, as it may proceed by reductive or oxidative pathways. Complete depletion of O 2 in the soil (e.g. flooding of rice fields) results in the sequential change of the redox processes until CH 4 is emitted into the atmosphere. Driving forces are the availability of electron donors (organic substrates) and electron acceptors (mainly the content of iron). It is interesting to note that CH 4 production starts almost instantaneously after flooding, then comes to a halt as soon as competing redox processes (iron and sulfate reduction) start, and finally resumes vigorously when ferric iron and sulfate are depleted. Drainage of submerged fields, even short-term, regene...

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Response of an intertidal sediment microbial community to nutrients following a controlled oil spill

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Differential inhibition by allylsulfide of nitrification and methane oxidation in freshwater sediment

Applied and environmental microbiology, 1995

Addition of nitrapyrin, allylthiourea, C(inf2)H(inf2), and CH(inf3)F to freshwater sediment slurr... more Addition of nitrapyrin, allylthiourea, C(inf2)H(inf2), and CH(inf3)F to freshwater sediment slurries inhibited CH(inf4) oxidation and nitrification to similar extents. Dicyandiamide and allylsulfide were less inhibitory for CH(inf4) oxidation than for nitrification. Allylsulfide was the most potent inhibitor of nitrification, and the estimated 50% inhibitory concentrations for this process and CH(inf4) oxidation were 0.2 and 121 (mu)M, respectively. At a concentration of 2 (mu)M allylsulfide, growth and CH(inf4) oxidation activity of Methylosinus trichosporium OB3b were not inhibited. Allylsulfide at 200 (mu)M inhibited the growth of M. trichosporium by approximately 50% but did not inhibit CH(inf4) oxidation activity. Nitrite production by cells of M. trichosporium was not significantly affected by allylsulfide, except at a concentration of 2 mM, when growth and CH(inf4) oxidation were also inhibited by about 50%. Methane monooxygenase activity present in soluble fractions of M. tr...

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Effects of methane metabolism on nitrification and nitrous oxide production in polluted freshwater sediment

Applied and environmental microbiology, 1994

We report the effect of CH(4) and of CH(4) oxidation on nitrification in freshwater sediment from... more We report the effect of CH(4) and of CH(4) oxidation on nitrification in freshwater sediment from Hamilton Harbour, Ontario, Canada, a highly polluted ecosystem. Aerobic slurry experiments showed a high potential for aerobic N(2)O production in some sites. It was suppressed by C(2)H(2), correlated to NO(3) production, and stimulated by NH(4) concentration, supporting the hypothesis of a nitrification-dependent source for this N(2)O production. Diluted sediment slurries supplemented with CH(4) (1 to 24 muM) showed earlier and enhanced nitrification and N(2)O production compared with unsupplemented slurries (</=1 muM CH(4)). This suggests that nitrification by methanotrophs may be significant in freshwater sediment under certain conditions. Suppression of nitrification was observed at CH(4) concentrations of 84 muM and greater, possibly through competition for O(2) between methanotrophs and NH(4) -oxidizing bacteria and/or competition for mineral N between these two groups of organ...

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Denitrification in artic soils: Activities and PCR detection of denitrification genes (48th Annual Meeting of the Canadian Society of Microbiologists, Guelph, Ontario, June 14-17)

Greenhouse Gas Exchange and Biogeochemistry of Fertilized Canadian Plantation Forests

ABSTRACT Canada&#39;s ratification of the Kyoto Protocol in 2002 has raised questions of the ... more ABSTRACT Canada&#39;s ratification of the Kyoto Protocol in 2002 has raised questions of the role of ecosystem management as a tool to temporarily reduce the net greenhouse gas burden of the forestry industry and potentially generate emission offset credits. We examined growing season methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2) fluxes, soil nutrient chemistry, and microbial biomass and CH4-oxidizing bacterial communities in 20-year-old sub-boreal lodgepole pine and maritime hemlock plantations under control conditions and simulated operational fertilization with N (200kg urea-N per ha, applied twice) and N, P, K, and micronutrients. CH4 uptake was significantly greater in the lodgepole pine site than in the hemlock site (152-221 and 57-81 micrograms CH4 consumed per square meter per hour), and there were no significant differences among treatments at either site. Among sites, treatments, and sampling times, CH4 uptake correlated positively with NH4 concentrations and negatively with extractable organic N:P quotients, indicating that this process may potentially be limited by nutrient availability to the CH4-oxidizing bacteria. N2O efflux was measured sporadically at a few flux collars, but was not significantly different from zero at any site, treatment, or time. Soil respiration (CO2 efflux) rates were faster in the hemlock than lodgepole pine site (243-409 and 100-266 milligrams CO2 per square meter per hour), and significant treatment differences were observed at individual times, though with fertilized plots exhibiting both faster and slower rates than controls. Soil respiration correlated significantly with microbial biomass C and N and NO3. Within each site, soil respiration, but not CH4 uptake, was positively correlated with soil temperature. New experiments examining the short-term effects of fertilization on greenhouse gas exchanges are underway, and both short and long-term effects will be evaluated in relation to changes in C storage in plant biomass, litter, and soil organic matter under the same fertilized and control conditions.

Aerobic Methanotrophy and Nitrification: Processes and Connections

eLS, 2001

ABSTRACT Ammonia and methane are structurally similar molecules. Not surprisingly therefore, micr... more ABSTRACT Ammonia and methane are structurally similar molecules. Not surprisingly therefore, microorganisms that use methane as a sole energy source (methanotrophs) and microorganisms that use ammonia as a sole energy source (ammonia oxidisers or nitrifiers) share many similarities. They have several key enzymes in common, most especially the ammonia monooxygenase/particulate methane monooxygenase enzyme family. The two groups are proposed to have a common evolutionary history. They occupy similar ecological niches, and compete for nitrogen. Enzymatically, nitrifiers are capable of methane oxidation, and methanotrophs are capable of nitrification. Microbial ecologists have attempted to find specific inhibitors for either group in order to study their respective roles in the environment. The contribution of ammonia oxidisers to methanotrophy in natural systems appears to be very minor, however methanotrophs may sometimes have important roles in the nitrogen cycle. Key Concepts: Some bacteria and archaea are capable of using methane or ammonia as energy sources.Methanotrophs and ammonia oxidisers are each highly specialised to living on their particular substrate.Methanotrophs and ammonia oxidisers have several key enzymes in common, and may share a common evolutionary history.Both groups must cope with toxic by-products of ammonia oxidation.Methanotrophs may be important in the environmental nitrogen cycle, but ammonia oxidisers do not affect the methane cycle.Ammonia oxidising archaea appear to outcompete ammonia oxidising bacteria under ammonia-limiting and acidic conditions.Keywords:methane;ammonia;nitrification;methanotrophy;ammonia oxidation;nitrous oxide;denitrification;chemolithotrophy;biogeochemistry

Vaccine hesitancy

Human Vaccines & Immunotherapeutics, 2013

Despite being recognized as one of the most successful public health measures, vaccination is per... more Despite being recognized as one of the most successful public health measures, vaccination is perceived as unsafe and unnecessary by a growing number of individuals. Lack of confidence in vaccines is now considered a threat to the success of vaccination programs. vaccine hesitancy is believed to be responsible for decreasing vaccine coverage and an increasing risk of vaccine-preventable disease outbreaks and epidemics. This review provides an overview of the phenomenon of vaccine hesitancy. First, we will characterize vaccine hesitancy and suggest the possible causes of the apparent increase in vaccine hesitancy in the developed world. Then we will look at determinants of individual decision-making about vaccination.

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Production and Consumption of Methane in Soil, Peat, and Sediments from a Hydro-Electric Reservoir (Robert-Bourassa) and Lakes in the Canadian Taiga

Environmental Science, 2005

Functional and structural aspects of the indigenous methanogenic and methanotrophic microbial pop... more

Potential Activity and Diversity of Methanotrophic Bacteria in Forest Soil, Peat, and Sediments from a Hydroelectric Reservoir (Robert-Bourassa) and Lakes in the Canadian Taiga

Soil Science, 2006

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Denitrification and methane production in sediment of Hamilton Harbour (Canada)

Microbial Ecology, 1994

Systematic sampling of 21 sites covering Hamilton Harbour (Lake Ontario, Canada) was carried out ... more Systematic sampling of 21 sites covering Hamilton Harbour (Lake Ontario, Canada) was carried out during the summer in 1990 and 1991 in order to study how well environmental factors, such as 02, N037, and organic carbon, and the spatial structure can explain observed variation of potential denitrification, CH4 and CO2 production, as well as N2 fixation in sediment slurries. Using canonical redundancy analysis and an extension of this method to partial out the variance into spatial and environmental components, we found that most of the explained fraction of potential microbial activities (70-90%) was accounted for by the significant environmental variables (NH4+, particulate carbon, dissolved organic carbon, dissolved 02, depth, and temperature) and not much by the spatial polynomial trend surface. We found significant path coefficients (0.53 and 0.57 in 1990 and 1991) between CO2 production and potential denitrification, which suggests that denitrifiers are dependent upon a heterotrophic bacterial population for directly assimilable carbon sources. We also found significant path coefficients between particulate carbon and both CH4 production (0.67 and 0.33) and CO2 production (0.50 and 0.38), while significant path coefficients were also found between dissolved organic carbon and CO2 production (0.34 and 0.47). We conclude that beside well-known abiotic factors such as 02, N03-, and organic carbon, a biotic factor involved in carbon metabolism may be important in explaining the spatial variation of denitrification capacity in the sediment of Hamilton Harbour.

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Hydrological reconstruction from tree-ring multi-proxies over the last two centuries at the Caniapiscau Reservoir, northern Québec, Canada

Journal of Hydrology, 2014

The objective of this study was to reconstruct 200 years of spring (Q spr), summer (Q sum) and an... more The objective of this study was to reconstruct 200 years of spring (Q spr), summer (Q sum) and annual (Q ann) water supply variability at the Caniapiscau Reservoir in a remote area of northern Quebec. This region which is a key hydropower region of North America lacks long-term hydrological series, and tree-ring proxies are seen here as the best alternative for the extension of the climatic series beyond instrumental records. Thus, ring widths, ring densities and stable isotope ratios (d 13 C and d 18 O) were used to perform paleohydrological reconstructions. The following reconstruction techniques were evaluated for each variable reconstructed: partial least square (PLS) regression applied to all of the tree-ring series, PLS regression applied to selected tree-ring series, and the best analogue method (BAM) applied to selected tree-ring series. These three reconstructions were then combined in a composite reconstruction. Reconstruction verification shows that the annual and summer water supply reconstruction quality is good. Conversely, the verification tests disqualified our spring water supply reconstruction. The reconstructed long-term water supply variations over the last two centuries are dominated by decadal to sub-decadal fluctuations, including distinct long hydrological periods during which water supplies change in intensity and variability. Annual water supplies (Q ann) inversely correlate with both winter and summer indices. Annual water supplies (Q ann) inversely correlate with Arctic oscillation (AO) and North Atlantic Oscillation (NAO) winter and summer indices. Also, AO indices also influence Q ann to a greater degree than NAO indices. Finally, summer water supplies inversely correlate only with summer indices.

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N 2 O emissions and carbon sequestration in a nitrogen-fertilized Douglas fir stand

Journal of Geophysical Research, 2008

This study investigated how nitrogen (N) fertilization with 200 kg N ha À1 of a 58-yearold West C... more This study investigated how nitrogen (N) fertilization with 200 kg N ha À1 of a 58-yearold West Coast Douglas fir stand influenced its net greenhouse gas (GHG) global warming potential (GWP) in the first year after fertilization. Effects of fertilization on GHG GWP were calculated considering changes in soil N 2 O emissions, measured using the static chamber technique and the soil N 2 O gradient technique; eddy covariance (EC) measured net ecosystem productivity (NEP); and energy requirements of fertilizer production, transport, and its aerial spreading. We found significant N 2 O losses in fertilized plots compared to a small uptake in nonfertilized plots. Chamber-measured N loss in the fertilized plots was about 16 kg N 2 O ha À1 in the first year, which is equivalent to 10 kg N ha À1 or 5% of the applied fertilizer N. Soil N 2 O emissions measured using the gradient technique, however, exceeded the chamber measurements by about 50%. We also compared a polymer-coated slow-release urea with regular urea and found that the former delayed N 2 O emissions but the year-end total loss was about the same as that from regular urea. Change in NEP due to fertilization was determined by relating annual NEP for the nonfertilized stand to environmental controls using an empirical and a process-based model. Annual NEP increased by 64%, from 326 g C m À2 , calculated assuming that the stand was not fertilized, to the measured value of 535 g C m À2 with fertilization. At the end of the year, net change in GHG GWP was À2.28 t CO 2 ha À1 compared to what it would have been without fertilization, thereby indicating favorable effect of fertilization even in the first year after fertilization with significant emissions of N 2 O.

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In Vitro Methane Removal by Volcanic Pumice Soil Biofilter Columns over One Year

Journal of Environment Quality, 2012

Soil methane (CH(4)) biofilters, containing CH(4)-oxidizing bacteria (methanotrophs), are a promi... more Soil methane (CH(4)) biofilters, containing CH(4)-oxidizing bacteria (methanotrophs), are a promising technology for mitigating greenhouse gas emissions. However, little is known about long-term biofilter performance. In this study, volcanic pumice topsoils (0-10 cm) and subsoils (10-50 cm) were tested for their ability to oxidize a range of CH(4) fluxes over 1 yr. The soils were sampled from an 8-yr-old and a 2-yr-old grassed landfill cover and from a nearby undisturbed pasture away from the influence of CH(4) generated by the decomposing refuse. Methane was passed through the soils in laboratory chambers with fluxes ranging from 0.5 g to 24 g CH(4) m(-3) h(-1). All topsoils efficiently oxidized CH(4). The undisturbed pasture topsoil exhibited the highest removal efficiency (24 g CH(4) m(-3) h(-1)), indicating rapid activation of the methanotroph population to the high CH(4) fluxes. The subsoils were less efficient at oxidizing CH(4) than the topsoils, achieving a maximum rate oxidation rate of 7 g CH(4) m(-3) h(-1). The topsoils exhibited higher porosities; moisture contents; surface areas; and total C, N, and available-P concentrations than the subsoils, suggesting that these characteristics strongly influence growth and activity of the CH(4)-oxidizing bacteria. Soil pH values and available-P levels gradually declined during the trial, indicating a need to monitor chemical parameters closely so that adjustments can be made when necessary. However, other key soil physicochemical parameters (moisture, total C, total N) increased over the course of the trial. This study showed that the selected topsoils were capable of continually sustaining high CH(4) removal rates over 1 yr, which is encouraging for the development of biofilters as a low-maintenance greenhouse gas mitigation technology.

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